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1GMY
Biol. Unit 3
Info
Asym.Unit (139 KB)
Biol.Unit 1 (47 KB)
Biol.Unit 2 (47 KB)
Biol.Unit 3 (47 KB)
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(1)
Title
:
CATHEPSIN B COMPLEXED WITH DIPEPTIDYL NITRILE INHIBITOR
Authors
:
P. D. Greenspan, K. L. Clark, R. A. Tommasi, S. D. Cowen, L. W. Mcquire, D. J. H. Van Duzer, R. L. Goldberg, H. Zhou, Z. Du, J. J. Fitt, D. E. Coppa, Z W. Macchia, L. Zhu, M. P. Capparelli, R. Goldstein, A. M. Wigg, J. R. Dou R. S. Bohacek, A. K. Knap
Date
:
25 Sep 01 (Deposition) - 19 Sep 02 (Release) - 05 Jul 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Keywords
:
Hydrolase/Inhibitor, Complex (Hydrolase-Inhibitor), Covalent Complex, Protease, Cathepsin B, Hydrolase, Thiol Protease, Hydrolase- Inhibitor Complex
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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Reference
:
P. D. Greenspan, K. L. Clark, R. A. Tommasi, S. D. Cowen, L. W. Mcquire, D. L. Farley, J. H. Van Duzer, R. L. Goldberg, H. Zhou, Z. Du, J. J. Fitt, D. E. Coppa, Z. Fang, W. Macchia, L. Zhu, M. P. Capparelli, R. Goldstein A. M. Wigg, J. R. Doughty, R. S Bohacek, A. K. Knap
Identification Of Dipeptidyl Nitriles As Potent And Selective Inhibitors Of Cathepsin B Through Structure-Based Drug Design
J. Med. Chem. V. 44 4524 2001
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Hetero Components
(3, 3)
Info
All Hetero Components
1a: 2-AMINOETHANIMIDIC ACID (AEMa)
1b: 2-AMINOETHANIMIDIC ACID (AEMb)
1c: 2-AMINOETHANIMIDIC ACID (AEMc)
2a: 3-METHYLPHENYLALANINE (APDa)
2b: 3-METHYLPHENYLALANINE (APDb)
2c: 3-METHYLPHENYLALANINE (APDc)
3a: DIPHENYLACETIC ACID (DFAa)
3b: DIPHENYLACETIC ACID (DFAb)
3c: DIPHENYLACETIC ACID (DFAc)
View:
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Label:
No.
Name
Count
Type
Full Name
1
AEM
1
Ligand/Ion
2-AMINOETHANIMIDIC ACID
2
APD
1
Ligand/Ion
3-METHYLPHENYLALANINE
3
DFA
1
Ligand/Ion
DIPHENYLACETIC ACID
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Sites
(3, 3)
Info
All Sites
1: AC5 (SOFTWARE)
2: AC6 (SOFTWARE)
3: AC9 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC5
SOFTWARE
GLN C:23 , GLY C:27 , SER C:28 , CYS C:29 , GLY C:198 , APD C:501 , HOH C:2213
BINDING SITE FOR RESIDUE AEM C 500
2
AC6
SOFTWARE
CYS C:29 , TRP C:30 , GLY C:73 , GLY C:74 , PRO C:76 , ALA C:173 , GLY C:198 , HIS C:199 , AEM C:500 , DFA C:502 , HOH C:2148 , HOH C:2150
BINDING SITE FOR RESIDUE APD C 501
3
AC9
SOFTWARE
ASN C:72 , GLY C:73 , GLY C:74 , TYR C:75 , APD C:501
BINDING SITE FOR RESIDUE DFA C 502
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SAPs(SNPs)/Variants
(2, 2)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_051512 (P12L, chain C, )
2: VAR_014696 (S156N, chain C, )
View:
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Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_051512
P
91
L
CATB_HUMAN
Polymorphism
11548596
C
P
12
L
2
UniProt
VAR_014696
S
235
N
CATB_HUMAN
Polymorphism
17573
C
S
156
N
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(3, 3)
Info
All PROSITE Patterns/Profiles
1: THIOL_PROTEASE_CYS (C:23-34)
2: THIOL_PROTEASE_HIS (C:197-207)
3: THIOL_PROTEASE_ASN (C:214-233)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
THIOL_PROTEASE_CYS
PS00139
Eukaryotic thiol (cysteine) proteases cysteine active site.
CATB_HUMAN
102-113
1
-
-
C:23-34
2
THIOL_PROTEASE_HIS
PS00639
Eukaryotic thiol (cysteine) proteases histidine active site.
CATB_HUMAN
276-286
1
-
-
C:197-207
3
THIOL_PROTEASE_ASN
PS00640
Eukaryotic thiol (cysteine) proteases asparagine active site.
CATB_HUMAN
293-312
1
-
-
C:214-233
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 3)
Info
All SCOP Domains
1a: SCOP_d1gmya_ (A:)
1b: SCOP_d1gmyb_ (B:)
1c: SCOP_d1gmyc_ (C:)
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Organisms
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(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Cysteine proteinases
(392)
Superfamily
:
Cysteine proteinases
(392)
Family
:
Papain-like
(200)
Protein domain
:
(Pro)cathepsin B
(13)
Human (Homo sapiens) [TaxId: 9606]
(6)
1a
d1gmya_
A:
1b
d1gmyb_
B:
1c
d1gmyc_
C:
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CATH Domains
(1, 3)
Info
all CATH domains
1a: CATH_1gmyB00 (B:0-252)
1b: CATH_1gmyC00 (C:0-252)
1c: CATH_1gmyA00 (A:0-253)
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Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Cathepsin B; Chain A
(207)
Homologous Superfamily
:
Cysteine proteinases
(207)
Human (Homo sapiens)
(92)
1a
1gmyB00
B:0-252
1b
1gmyC00
C:0-252
1c
1gmyA00
A:0-253
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Pfam Domains
(0, 0)
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Chain C
Asymmetric Unit 1
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Asym.Unit (139 KB)
Header - Asym.Unit
Biol.Unit 1 (47 KB)
Header - Biol.Unit 1
Biol.Unit 2 (47 KB)
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Biol.Unit 3 (47 KB)
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