Second Meeting on the Critical Assessment of Techniques for Protein Structure Prediction

Targets

The table below contains the summary on the proteins used as prediction targets in CASP2 process and current status of public release of their 3D structures.

Target identity

Structure availability at CASP2

Expected public release of structures
Reference
Prediction category

Target description

T0001 PDB code 1VDR Pieper, U; Kapadia, G; Mevarech, M; Herzberg, O. (1998) Structural features of halophilicity derived from the crystal structure of dihydrofolate reductase from the Dead Sea halophilic archaeon, Haloferax volcanii. Structure, 6:75-88. C Dihydrofolate reductase, Haloferax volcanii, 162a.a.

T0002 PDB code 1TDJ Gallagher, DT; Gilliland, GL; Xiao, G; Zondlo, J; Fisher, KE; Chinchilla, D; Eisenstein, E. (1998) Structure and control of pyridoxal phosphate dependent allosteric threonine deaminase. Structure, 6:465-475. C,F/A Threonine Deaminase, E. coli, 514a.a.

T0003 PDB code 2GPR Huang, K; Kapadia, G; Zhu, PP; Peterkofsky, A; Herzberg, O. (1998) A promiscuous binding surface: crystal structure of the IIA domain of the glucose-specific permease from Mycoplasma capricolum. Structure, 6:697-710. C Phosphotransferase enzyme IIA domain, Mycoplasma capricolum, 154a.a.

T0004 PDB code 1SRO Bycroft,M., Hubbard,T.J., Proctor,M., Freund,S.M., Murzin,A.G. (1997) The solution structure of the S1 RNA binding domain: a member of an ancient nucleic acid-binding fold. Cell 88: 235-242 F/A Polyribonucleotide Nucleotidyltransferase, S1 motif, E. coli, 84a.a.

T0005 PDB code 1FIB Yee, V.C., Pratt, K.P., Cote, H.C., Trong, I.L., Chung, D.W., Davie, E.W., Stenkamp, R.E. and Teller, D.C. (1997) Crystal structure of a 30 kDa C-terminal fragment from the gamma chain of human fibrinogen. Structure, 5:125-38. F/A Gamma Fibrinogen C terminus, Human, 268a.a.

T0006 - F/A Outer Membrane Phospholipase A, Escherichia coli, 269a.a

T0007 - C Neurocalcin-delta, Bovine, 193a.a.

T0008 PDB code 1COI Ogihara,N.L., Weiss,M.S., Degrado,W.F., Eisenberg, D. (1997) The crystal structure of the designed trimeric coiled coil coil-V(a)L(d): Implications for engineering crystals and supramolecular assemblies. PROTEIN SCIENCE, V6 N1:80-88. C,F/A De Novo designed peptide, 29a.a.

T0009
PDB code 1JER
Hart, P.J., Nersissian, A.M., Herrmann, R.G., Nalbandyan, R.M., Valentine, J.S. and Eisenberg, D. (1996). A missing link in cupredoxins: Crystal structure of cucumber stellacyanin at 1.6 A resolution. Protein Science 5, 2175 - 2183.

C Cucumber Stellacyanin, Cucumis sativus, 109a.a.

T0010 PDB code 1BP1 Beamer, L.J., Carroll, S.F. and Eisenberg, D. (1997) Crystal structure of human BPI and two bound phospholipids at 2.4 angstrom resolution. Science, 276:1861-4. F/A bactericial/permeablility-increasing protein, Human, 456a.a.

T0011 PDB code 1AH6 Prodromou, C; Roe, SM; Piper, PW; Pearl, LH. (1997) A molecular clamp in the crystal structure of the N-terminal domain of the yeast Hsp90 chaperone. Nat. Struct. Biol., 4:477-482. F/A Hsp-90 N-terminal domain, S.cerevisiae, 220a.a.

T0012 PDB code 1PCI Groves, M.R., Taylor, M.A., Scott, M., Cummings, N.J., Pickersgill, R.W. and Jenkins, J.A. (1996) The prosequence of procaricain forms an alpha-helical domain that prevents access to the substrate-binding cleft. Structure, 4:1193-203. C,F/A Proregion of Procaricain, Carica papaya, 107a.a.

T0013 [**] Individual request Please acknowledge pre-publication information from A.J. Kalb(Gilboa), F. Frolow and R. Ventura. D Complex of concanavalin A and methyl alpha-D-arabinofuranoside, 237a.a.

T0014 ??? Annette K. Shrive, Igor Polikarpov, Tino Krell, Andrew Coulson, John R. Coggins, Alastair R. Hawkins & Lindsay Sawyer (1997) Three-dimensional structure of type I dehydroquinase - an enzyme recruited for a role in eukaryotic transcription regulation. Nature Structural Biology, submitted.
An 'unpublished results' reference would be: Annette K. Shrive, Igor Polikarpov & Lindsay Sawyer
F/A 3-Dehydroquinase, Salmonella typhi, 252a.a.

T0015 PDB code 1CUM Tanner, J. J., Lei, B., Tu, S-C. and Krause, K. L. (1996) Flavin reductase P: Structure of an enzyme that reduces flavin. Biochemistry, 35, 13531-13539. C NADPH:FMN oxidoreductase, vibrio harveyi, 240a.a.

T0016 PDB code 1PPR Hofmann, E; Wrench, PM; Sharples, FP; Hiller, RG; Welte, W; Diederichs, K. (1996) Structural basis of light harvesting by carotenoids: peridinin-chlorophyll-protein from Amphidinium carterae. Science, 272:1788-1791. F/A Peridinin Chlorophyll Protein, Amphidinium carterae, 312a.a.

T0017 Early 1998 Gaoyi Xiao, Jihong Chen, Xinhua Ji, Gary L. Gilliland and Richard N. Armstrong C Glutathione transferase, rattus liver, 217a.a.

T0018 Released! Fleury D., Bizebard T., Skehel J.J. & Knossow M. D Hemagglutinin-fab complex, influenza virus, 950a.a.

T0019 - F/A RepA1, E. coli, 340a.a.

T0020 PDB code 1AK1 Al-Karadaghi, S., Hansson, M., Nikonov, S., Jonsson, B. & Hederstedt, L. (1997) Crystal structure of ferrochelatase: the terminal enzyme in heme biosynthesis. Structure, 5:1501-1510. F/A Ferrochelatase, B. subtilis, 320a.a.

T0021 - C,F/A KorB C-terminal domain, E. coli, 64a.a.

T0022 PDB code 1FUI Seemann, J.E. & Schulz, G.E. (1997) Structure and mechanism of L-fucose isomerase from Escherichia coli. J. Mol. Biol., 273:256-268. F/A L-Fucose-Isomerase, E. coli, 591a.a.

T0023 - F/A KDO8P Synthase, E. coli, 284a.a.

T0024 PDB code 1U9A Tong, H., Hateboer, G., Perrakis, A., Bernards, R. and Sixma, T.K. (1997) Crystal structure of murine/human Ubc9 provides insight into the variability of the ubiquitin-conjugating system. J. Biol. Chem. 272:21381-21387. C UBC9, mouse/human, 158a.a.

T0025 - C Adrenodoxin, mitochondria of bovine adrenal cortex, 128a.a.

T0026 - F/A ArgR N-term domain, E. coli, 79a.a.

T0027 PDB code 1IDK Mayans, O., Scott, M., Connerton, I., Gravesen, T., Benen, J., Visser, J., Pickersgill, R. & Jenkins, J. (1997) Two crystal structures of pectin lyase A from Aspergillus reveal a pH driven conformational change and striking divergence in the substrate-binding clefts of pectin and pectate lyases. Structure, 5:677-689. C Pectin lyase A, Aspergillus niger, 359a.a.

T0028 PDB code 1EG1 Kleywegt, GJ, Zou, J-Y, Divne, C, Davies, GJ, Sinning, I, Stahlberg, J, Reinikainen, T, Srisodsuk, M, Teeri, TT & Jones TA. (1997) The crystal structure of the catalytic core domain of endoglucanase I from Trichoderma reesei at 3.6 A resolution, and a comparison with related enzymes. J. Mol. Biol., 272:383-397.
C Endoglucanase I (catalytic domain), Trichoderma reesei, 371a.a.

T0029 - C Enolpyruvyltransferase, Enterobacter cloacae, 419a.a.

T0030 PDB code 1FGP Holliger, P. and Riechmann, L. (1997) A conserved infection pathway for filamentous bacteriophages is suggested by the structure of the membrane penetration domain of the minor coat protein g3p from phage fd. Structure, 5:265-75. F/A domain 1 of protein g3, filamentous phage fd, 66a.a.

T0031 PDB code 1AGJ Vath, G.M., Earhart, C.A., Rago, J.V., Kim, M.H., Bohach, G.A., Schlievert, P.M., and Ohlendorf, D.H. (1997) The Structure of the Superantigen Exfoliative Toxin A Suggests a Novel Regulation as a Serine Protease. Biochemistry 36, 1559-1566.

F/A Exfoliative toxin A, S. aureus, 242a.a.

T0032 PDB code 1BEO Boissy, G., de La Fortelle, E., Kahn, R., Huet, J.C., Bricogne, G., Pernollet, J.C., Brunie, S. (1996) Crystal structure of a fungal elicitor secreted by Phytophthora cryptogea, a member of a novel class of plant necrotic proteins. Structure, 4:1429-39. F/A beta-cryptogein, fungus phytophthora cryptogea, 98a.a.

T0033 ??? Kurinov Igor V. and Harrison Robert W. (1996) unpublished D trypsin/pentamidine complex, 231a.a.

T0034 ??? Kurinov Igor V. and Harrison Robert W. (1996) unpublished D trypsin/amiloride complex, 231a.a.

T0035 ??? D pancreatic elastase/SBA complex, 240a.a.

T0036 ??? D pancreatic elastase/SBB complex, 240a.a.

T0037 PDB code 1AA2 Carugo, K.D., Banuelos, S. & Saraste, M. (1997) Crystal structure of a calponin homology domain. Nature Struct. Biol., 4:175-179. F/A calponon homology domain of beta-spectrin, Homo sapiens, 109a.a.

T0038 PDB code 1ULO Philip E. Johnson, Manish D. Joshi, Peter Tomme, Douglas G. Kilburn, Lawrence P. McIntosh. "Structure of the N-Terminal Cellulose-Binding Domain of Cellulomonas fimi CenC Determined by Nuclear Magnetic Resonance Spectroscopy", Biochemistry 35, 14381-14394, (1996). F/A CBDN1, Cellulomonas fimi, 152a.a.

T0039 ??? D Fructose-1,6-Bisphosphatase, Human/Aica-Riboside Phosphate complex, 335a.a.

T0040 ??? D Pancreatic trypsin, Bovine/INH complex, 245a.a.

T0041 ??? D Pancreatic trypsin, Bovine/INI complex, 245a.a.

T0042 PDB code 1NKL Liepinsh,E., Andersson, M., Ruysschaert, J.-M. and Otting, G. (1997) Saposin fold revealed by the NMR structure of NK-lysin. Nature Struct. Biol., 4:793-795. F/A NK-lysin, pig, 78a.a.

Target identity	Structure availability at CASP2	Expected public release of structures	Reference	Prediction category	Target description
T0001		PDB code 1VDR	Pieper, U; Kapadia, G; Mevarech, M; Herzberg, O. (1998) Structural features of halophilicity derived from the crystal structure of dihydrofolate reductase from the Dead Sea halophilic archaeon, Haloferax volcanii. Structure, 6:75-88.	C	Dihydrofolate reductase, Haloferax volcanii, 162a.a.
T0002		PDB code 1TDJ	Gallagher, DT; Gilliland, GL; Xiao, G; Zondlo, J; Fisher, KE; Chinchilla, D; Eisenstein, E. (1998) Structure and control of pyridoxal phosphate dependent allosteric threonine deaminase. Structure, 6:465-475.	C,F/A	Threonine Deaminase, E. coli, 514a.a.
T0003		PDB code 2GPR	Huang, K; Kapadia, G; Zhu, PP; Peterkofsky, A; Herzberg, O. (1998) A promiscuous binding surface: crystal structure of the IIA domain of the glucose-specific permease from Mycoplasma capricolum. Structure, 6:697-710.	C	Phosphotransferase enzyme IIA domain, Mycoplasma capricolum, 154a.a.
T0004		PDB code 1SRO	Bycroft,M., Hubbard,T.J., Proctor,M., Freund,S.M., Murzin,A.G. (1997) The solution structure of the S1 RNA binding domain: a member of an ancient nucleic acid-binding fold. Cell 88: 235-242	F/A	Polyribonucleotide Nucleotidyltransferase, S1 motif, E. coli, 84a.a.
T0005		PDB code 1FIB	Yee, V.C., Pratt, K.P., Cote, H.C., Trong, I.L., Chung, D.W., Davie, E.W., Stenkamp, R.E. and Teller, D.C. (1997) Crystal structure of a 30 kDa C-terminal fragment from the gamma chain of human fibrinogen. Structure, 5:125-38.	F/A	Gamma Fibrinogen C terminus, Human, 268a.a.
T0006	-			F/A	Outer Membrane Phospholipase A, Escherichia coli, 269a.a
T0007	-			C	Neurocalcin-delta, Bovine, 193a.a.
T0008		PDB code 1COI	Ogihara,N.L., Weiss,M.S., Degrado,W.F., Eisenberg, D. (1997) The crystal structure of the designed trimeric coiled coil coil-V(a)L(d): Implications for engineering crystals and supramolecular assemblies. PROTEIN SCIENCE, V6 N1:80-88.	C,F/A	De Novo designed peptide, 29a.a.
T0009		PDB code 1JER	Hart, P.J., Nersissian, A.M., Herrmann, R.G., Nalbandyan, R.M., Valentine, J.S. and Eisenberg, D. (1996). A missing link in cupredoxins: Crystal structure of cucumber stellacyanin at 1.6 A resolution. Protein Science 5, 2175 - 2183.	C	Cucumber Stellacyanin, Cucumis sativus, 109a.a.
T0010		PDB code 1BP1	Beamer, L.J., Carroll, S.F. and Eisenberg, D. (1997) Crystal structure of human BPI and two bound phospholipids at 2.4 angstrom resolution. Science, 276:1861-4.	F/A	bactericial/permeablility-increasing protein, Human, 456a.a.
T0011		PDB code 1AH6	Prodromou, C; Roe, SM; Piper, PW; Pearl, LH. (1997) A molecular clamp in the crystal structure of the N-terminal domain of the yeast Hsp90 chaperone. Nat. Struct. Biol., 4:477-482.	F/A	Hsp-90 N-terminal domain, S.cerevisiae, 220a.a.
T0012		PDB code 1PCI	Groves, M.R., Taylor, M.A., Scott, M., Cummings, N.J., Pickersgill, R.W. and Jenkins, J.A. (1996) The prosequence of procaricain forms an alpha-helical domain that prevents access to the substrate-binding cleft. Structure, 4:1193-203.	C,F/A	Proregion of Procaricain, Carica papaya, 107a.a.
T0013		[**] Individual request	Please acknowledge pre-publication information from A.J. Kalb(Gilboa), F. Frolow and R. Ventura.	D	Complex of concanavalin A and methyl alpha-D-arabinofuranoside, 237a.a.
T0014		???	Annette K. Shrive, Igor Polikarpov, Tino Krell, Andrew Coulson, John R. Coggins, Alastair R. Hawkins & Lindsay Sawyer (1997) Three-dimensional structure of type I dehydroquinase - an enzyme recruited for a role in eukaryotic transcription regulation. Nature Structural Biology, submitted. An 'unpublished results' reference would be: Annette K. Shrive, Igor Polikarpov & Lindsay Sawyer	F/A	3-Dehydroquinase, Salmonella typhi, 252a.a.
T0015		PDB code 1CUM	Tanner, J. J., Lei, B., Tu, S-C. and Krause, K. L. (1996) Flavin reductase P: Structure of an enzyme that reduces flavin. Biochemistry, 35, 13531-13539.	C	NADPH:FMN oxidoreductase, vibrio harveyi, 240a.a.
T0016		PDB code 1PPR	Hofmann, E; Wrench, PM; Sharples, FP; Hiller, RG; Welte, W; Diederichs, K. (1996) Structural basis of light harvesting by carotenoids: peridinin-chlorophyll-protein from Amphidinium carterae. Science, 272:1788-1791.	F/A	Peridinin Chlorophyll Protein, Amphidinium carterae, 312a.a.
T0017		Early 1998	Gaoyi Xiao, Jihong Chen, Xinhua Ji, Gary L. Gilliland and Richard N. Armstrong	C	Glutathione transferase, rattus liver, 217a.a.
T0018		Released!	Fleury D., Bizebard T., Skehel J.J. & Knossow M.	D	Hemagglutinin-fab complex, influenza virus, 950a.a.
T0019	-			F/A	RepA1, E. coli, 340a.a.
T0020		PDB code 1AK1	Al-Karadaghi, S., Hansson, M., Nikonov, S., Jonsson, B. & Hederstedt, L. (1997) Crystal structure of ferrochelatase: the terminal enzyme in heme biosynthesis. Structure, 5:1501-1510.	F/A	Ferrochelatase, B. subtilis, 320a.a.
T0021	-			C,F/A	KorB C-terminal domain, E. coli, 64a.a.
T0022		PDB code 1FUI	Seemann, J.E. & Schulz, G.E. (1997) Structure and mechanism of L-fucose isomerase from Escherichia coli. J. Mol. Biol., 273:256-268.	F/A	L-Fucose-Isomerase, E. coli, 591a.a.
T0023	-			F/A	KDO8P Synthase, E. coli, 284a.a.
T0024		PDB code 1U9A	Tong, H., Hateboer, G., Perrakis, A., Bernards, R. and Sixma, T.K. (1997) Crystal structure of murine/human Ubc9 provides insight into the variability of the ubiquitin-conjugating system. J. Biol. Chem. 272:21381-21387.	C	UBC9, mouse/human, 158a.a.
T0025	-			C	Adrenodoxin, mitochondria of bovine adrenal cortex, 128a.a.
T0026	-			F/A	ArgR N-term domain, E. coli, 79a.a.
T0027		PDB code 1IDK	Mayans, O., Scott, M., Connerton, I., Gravesen, T., Benen, J., Visser, J., Pickersgill, R. & Jenkins, J. (1997) Two crystal structures of pectin lyase A from Aspergillus reveal a pH driven conformational change and striking divergence in the substrate-binding clefts of pectin and pectate lyases. Structure, 5:677-689.	C	Pectin lyase A, Aspergillus niger, 359a.a.
T0028		PDB code 1EG1	Kleywegt, GJ, Zou, J-Y, Divne, C, Davies, GJ, Sinning, I, Stahlberg, J, Reinikainen, T, Srisodsuk, M, Teeri, TT & Jones TA. (1997) The crystal structure of the catalytic core domain of endoglucanase I from Trichoderma reesei at 3.6 A resolution, and a comparison with related enzymes. J. Mol. Biol., 272:383-397.	C	Endoglucanase I (catalytic domain), Trichoderma reesei, 371a.a.
T0029	-			C	Enolpyruvyltransferase, Enterobacter cloacae, 419a.a.
T0030		PDB code 1FGP	Holliger, P. and Riechmann, L. (1997) A conserved infection pathway for filamentous bacteriophages is suggested by the structure of the membrane penetration domain of the minor coat protein g3p from phage fd. Structure, 5:265-75.	F/A	domain 1 of protein g3, filamentous phage fd, 66a.a.
T0031		PDB code 1AGJ	Vath, G.M., Earhart, C.A., Rago, J.V., Kim, M.H., Bohach, G.A., Schlievert, P.M., and Ohlendorf, D.H. (1997) The Structure of the Superantigen Exfoliative Toxin A Suggests a Novel Regulation as a Serine Protease. Biochemistry 36, 1559-1566.	F/A	Exfoliative toxin A, S. aureus, 242a.a.
T0032		PDB code 1BEO	Boissy, G., de La Fortelle, E., Kahn, R., Huet, J.C., Bricogne, G., Pernollet, J.C., Brunie, S. (1996) Crystal structure of a fungal elicitor secreted by Phytophthora cryptogea, a member of a novel class of plant necrotic proteins. Structure, 4:1429-39.	F/A	beta-cryptogein, fungus phytophthora cryptogea, 98a.a.
T0033		???	Kurinov Igor V. and Harrison Robert W. (1996) unpublished	D	trypsin/pentamidine complex, 231a.a.
T0034		???	Kurinov Igor V. and Harrison Robert W. (1996) unpublished	D	trypsin/amiloride complex, 231a.a.
T0035		???		D	pancreatic elastase/SBA complex, 240a.a.
T0036		???		D	pancreatic elastase/SBB complex, 240a.a.
T0037		PDB code 1AA2	Carugo, K.D., Banuelos, S. & Saraste, M. (1997) Crystal structure of a calponin homology domain. Nature Struct. Biol., 4:175-179.	F/A	calponon homology domain of beta-spectrin, Homo sapiens, 109a.a.
T0038		PDB code 1ULO	Philip E. Johnson, Manish D. Joshi, Peter Tomme, Douglas G. Kilburn, Lawrence P. McIntosh. "Structure of the N-Terminal Cellulose-Binding Domain of Cellulomonas fimi CenC Determined by Nuclear Magnetic Resonance Spectroscopy", Biochemistry 35, 14381-14394, (1996).	F/A	CBDN1, Cellulomonas fimi, 152a.a.
T0039		???		D	Fructose-1,6-Bisphosphatase, Human/Aica-Riboside Phosphate complex, 335a.a.
T0040		???		D	Pancreatic trypsin, Bovine/INH complex, 245a.a.
T0041		???		D	Pancreatic trypsin, Bovine/INI complex, 245a.a.
T0042		PDB code 1NKL	Liepinsh,E., Andersson, M., Ruysschaert, J.-M. and Otting, G. (1997) Saposin fold revealed by the NMR structure of NK-lysin. Nature Struct. Biol., 4:793-795.	F/A	NK-lysin, pig, 78a.a.

**Well justified requests to acquire the coordinates on individual basis may be sent directly to the experimentalists:

T0013 - Dr. Gilboa Frolow (bfgilboa@weizmann.weizmann.ac.il)

Updated on March 29, 1999

Protein Structure Prediction Center