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1SG8
Biol. Unit 2
Info
Asym.Unit (106 KB)
Biol.Unit 1 (52 KB)
Biol.Unit 2 (51 KB)
Biol.Unit 3 (100 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE PROCOAGULANT FAST FORM OF THROMBIN
Authors
:
A. O. Pineda, C. J. Carrell, L. A. Bush, S. Prasad, S. Caccia, Z. W. Chen, F. S. Mathews, E. Di Cera
Date
:
23 Feb 04 (Deposition) - 08 Jun 04 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B,D,E
Biol. Unit 1: A,B (1x)
Biol. Unit 2: D,E (1x)
Biol. Unit 3: A,B,D,E (1x)
Keywords
:
Thrombin, Allostery, Hydrolase
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. O. Pineda, C. J. Carrell, L. A. Bush, S. Prasad, S. Caccia, Z. W. Chen, F. S. Mathews, E. Di Cera
Molecular Dissection Of Na+ Binding To Thrombin.
J. Biol. Chem. V. 279 31842 2004
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Hetero Components
(1, 1)
Info
All Hetero Components
2a: N-ACETYL-D-GLUCOSAMINE (NAGa)
2b: N-ACETYL-D-GLUCOSAMINE (NAGb)
1a: SODIUM ION (NAa)
1b: SODIUM ION (NAb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NA
-1
Ligand/Ion
SODIUM ION
2
NAG
1
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
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Sites
(2, 2)
Info
All Sites
1: AC3 (SOFTWARE)
2: AC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC3
SOFTWARE
LYS A:14A , HOH B:783 , ASN E:60G , HOH E:657 , HOH E:679
BINDING SITE FOR RESIDUE NAG E 500
2
AC4
SOFTWARE
TYR E:184A , ARG E:221A , LYS E:224 , HOH E:649 , HOH E:651 , HOH E:663 , HOH E:664
BINDING SITE FOR RESIDUE NA E 1702
[
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SAPs(SNPs)/Variants
(8, 8)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_006714 (M32T, chain E, )
2: VAR_011782 (P37T, chain E, )
3: VAR_006715 (R67C, chain E, )
4: VAR_006716 (R73H, chain E, )
5: VAR_006717 (R101W, chain E, )
6: VAR_006718 (E146A, chain E, )
7: VAR_068913 (E164Q, chain E, )
8: VAR_006719 (G226V, chain E, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_006714
M
380
T
THRB_HUMAN
Disease (FA2D)
---
E
M
32
T
2
UniProt
VAR_011782
P
386
T
THRB_HUMAN
Polymorphism
5897
E
P
37
T
3
UniProt
VAR_006715
R
425
C
THRB_HUMAN
Disease (FA2D)
---
E
R
67
C
4
UniProt
VAR_006716
R
431
H
THRB_HUMAN
Disease (FA2D)
---
E
R
73
H
5
UniProt
VAR_006717
R
461
W
THRB_HUMAN
Disease (FA2D)
---
E
R
101
W
6
UniProt
VAR_006718
E
509
A
THRB_HUMAN
Disease (FA2D)
---
E
E
146
A
7
UniProt
VAR_068913
E
532
Q
THRB_HUMAN
Polymorphism
---
E
E
164
Q
8
UniProt
VAR_006719
G
601
V
THRB_HUMAN
Disease (FA2D)
---
E
G
226
V
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(3, 3)
Info
All PROSITE Patterns/Profiles
1: TRYPSIN_DOM (E:16-243)
2: TRYPSIN_HIS (E:53-58)
3: TRYPSIN_SER (E:189-200)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
TRYPSIN_DOM
PS50240
Serine proteases, trypsin domain profile.
THRB_HUMAN
364-618
1
-
E:16-243
2
TRYPSIN_HIS
PS00134
Serine proteases, trypsin family, histidine active site.
THRB_HUMAN
402-407
1
-
E:53-58
3
TRYPSIN_SER
PS00135
Serine proteases, trypsin family, serine active site.
THRB_HUMAN
562-573
1
-
E:189-200
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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, 2)
Info
All SCOP Domains
1a: SCOP_d1sg8_1 (A:,B:)
1b: SCOP_d1sg8_2 (D:,E:)
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Classes
(
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)
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)
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Trypsin-like serine proteases
(1752)
Superfamily
:
Trypsin-like serine proteases
(1752)
Family
:
Eukaryotic proteases
(1343)
Protein domain
:
Thrombin
(188)
Human (Homo sapiens) [TaxId: 9606]
(169)
1a
d1sg8.1
A:,B:
1b
d1sg8.2
D:,E:
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CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_1sg8B02 (B:28-120,B:233-245)
1b: CATH_1sg8B01 (B:16-27,B:121-232)
1c: CATH_1sg8E01 (E:16-27,E:121-232)
1d: CATH_1sg8E02 (E:28-120,E:233-245)
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(
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)
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)
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(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
Thrombin, subunit H
(1535)
Homologous Superfamily
:
Trypsin-like serine proteases
(1488)
Human (Homo sapiens)
(615)
1a
1sg8B02
B:28-120,B:233-245
1b
1sg8B01
B:16-27,B:121-232
1c
1sg8E01
E:16-27,E:121-232
1d
1sg8E02
E:28-120,E:233-245
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Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_Trypsin_1sg8E01 (E:16-238)
1b: PFAM_Trypsin_1sg8E02 (E:16-238)
2a: PFAM_Thrombin_light_1sg8D01 (D:1B-14K)
2b: PFAM_Thrombin_light_1sg8D02 (D:1B-14K)
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(
)
Organisms
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)
(
)
Clan
:
Peptidase_PA
(797)
Family
:
Trypsin
(679)
Homo sapiens (Human)
(339)
1a
Trypsin-1sg8E01
E:16-238
1b
Trypsin-1sg8E02
E:16-238
Clan
:
no clan defined [family: Thrombin_light]
(136)
Family
:
Thrombin_light
(136)
Homo sapiens (Human)
(124)
2a
Thrombin_light-1sg8D01
D:1B-14K
2b
Thrombin_light-1sg8D02
D:1B-14K
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Asymmetric Unit 1
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Asym.Unit (106 KB)
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