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2A5I
Biol. Unit 1
Info
Asym.Unit (63 KB)
Biol.Unit 1 (112 KB)
Biol.Unit 2 (57 KB)
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(1)
Title
:
CRYSTAL STRUCTURES OF SARS CORONAVIRUS MAIN PEPTIDASE INHIBITED BY AN AZA-PEPTIDE EPOXIDE IN THE SPACE GROUP C2
Authors
:
T. -W. Lee, M. M. Cherney, C. Huitema, J. Liu, K. E. James, J. C. Powers, L. M. N. James
Date
:
30 Jun 05 (Deposition) - 25 Oct 05 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.88
Chains
:
Asym. Unit : A
Biol. Unit 1: A (2x)
Biol. Unit 2: A (1x)
Keywords
:
Cysteine Peptidase, 3C-Like, N-Finger, Chymotrypsin-Like Fold, Long Loop, Alpha-Helical Domain, Dimer, Catalytic Dyad, Specificity Pockets, Aza-Peptide Epoxide, Substrate-Like Inhibitor, C-S Covalent Bond, Epoxide Stereochemistry, Hydrolase
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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Reference
:
T. -W. Lee, M. M. Cherney, C. Huitema, J. Liu, K. E. James, J. C. Powers, L. D. Eltis, M. N. James
Crystal Structures Of The Main Peptidase From The Sars Coronavirus Inhibited By A Substrate-Like Aza-Peptide Epoxide
J. Mol. Biol. V. 353 1137 2005
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Hetero Components
(3, 6)
Info
All Hetero Components
1a: (5S,8S,14R)-ETHYL 11-(3-AMINO-3-OX... (AZPa)
2a: 1,2-ETHANEDIOL (EDOa)
3a: GLYCEROL (GOLa)
View:
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Label:
No.
Name
Count
Type
Full Name
1
AZP
2
Ligand/Ion
(5S,8S,14R)-ETHYL 11-(3-AMINO-3-OXOPROPYL)-8-BENZYL-14-HYDROXY-5-ISOBUTYL-3,6,9,12-TETRAOXO-1-PHENYL-2-OXA-4,7,10,11-TETRAAZAPENTADECAN-15-OATE
2
EDO
2
Ligand/Ion
1,2-ETHANEDIOL
3
GOL
2
Ligand/Ion
GLYCEROL
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Sites
(3, 3)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
THR A:25 , HIS A:41 , MET A:49 , TYR A:54 , PHE A:140 , LEU A:141 , ASN A:142 , GLY A:143 , SER A:144 , CYS A:145 , HIS A:163 , HIS A:164 , MET A:165 , GLU A:166 , PRO A:168 , HIS A:172 , ASP A:187 , ARG A:188 , GLN A:189 , THR A:190 , GLN A:192 , HOH A:324 , HOH A:369 , HOH A:416
BINDING SITE FOR RESIDUE AZP A 307
2
AC2
SOFTWARE
ARG A:4 , LYS A:5 , GLN A:127 , GOL A:309
BINDING SITE FOR RESIDUE EDO A 308
3
AC3
SOFTWARE
LYS A:5 , ALA A:7 , VAL A:125 , TYR A:126 , GLN A:127 , EDO A:308
BINDING SITE FOR RESIDUE GOL A 309
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SAPs(SNPs)/Variants
(4, 8)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_R1AB_CVHSA_047 (Q189P, chain A, )
2: VAR_R1A_CVHSA_047 (Q189P, chain A, )
3: VAR_R1AB_CVHSA_048 (D248E, chain A, )
4: VAR_R1A_CVHSA_048 (D248E, chain A, )
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dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_R1AB_CVHSA_047
*
Q
3429
P
R1AB_CVHSA
---
---
A
Q
189
P
2
UniProt
VAR_R1A_CVHSA_047
*
Q
3429
P
R1A_CVHSA
---
---
A
Q
189
P
3
UniProt
VAR_R1AB_CVHSA_048
*
D
3488
E
R1AB_CVHSA
---
---
A
D
248
E
4
UniProt
VAR_R1A_CVHSA_048
*
D
3488
E
R1A_CVHSA
---
---
A
D
248
E
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: M_PRO (A:1-306)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
M_PRO
PS51442
Coronavirus main protease (M-pro) domain profile.
R1A_CVHSA
3241-3546
2
A:1-306
R1AB_CVHSA
3241-3546
2
A:1-306
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Exons
(0, 0)
Info
All Exons
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
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SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d2a5ia_ (A:)
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Class
:
All beta proteins
(24004)
Fold
:
Trypsin-like serine proteases
(1752)
Superfamily
:
Trypsin-like serine proteases
(1752)
Family
:
Viral cysteine protease of trypsin fold
(145)
Protein domain
:
Coronavirus main proteinase (3Cl-pro, putative coronavirus nsp2)
(75)
SARS coronavirus [TaxId: 227859]
(65)
1a
d2a5ia_
A:
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CATH Domains
(2, 3)
Info
all CATH domains
1a: CATH_2a5iA03 (A:198-301)
2a: CATH_2a5iA01 (A:1-14,A:100-197)
2b: CATH_2a5iA02 (A:15-99)
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Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
main proteinase (3clpro) structure, domain 3
(38)
Homologous Superfamily
:
main proteinase (3clpro) structure, domain 3
(38)
Sars coronavirus. Organism_taxid: 227859. Strain: sars.
(11)
1a
2a5iA03
A:198-301
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
Thrombin, subunit H
(1535)
Homologous Superfamily
:
Trypsin-like serine proteases
(1488)
Sars coronavirus. Organism_taxid: 227859. Strain: sars.
(11)
2a
2a5iA01
A:1-14,A:100-197
2b
2a5iA02
A:15-99
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Pfam Domains
(0, 0)
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Asym.Unit (63 KB)
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