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Biol. Unit 1
Info
Asym.Unit (216 KB)
Biol.Unit 1 (75 KB)
Biol.Unit 2 (73 KB)
Biol.Unit 3 (71 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF NA-FREE THROMBIN IN COMPLEX WITH THROMBOMODULIN
Authors
:
T. E. Adams, J. A. Huntington
Date
:
06 Mar 09 (Deposition) - 18 Aug 09 (Release) - 17 Feb 16 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A,B,C,D,E,F,X,Y,Z
Biol. Unit 1: A,B,X (1x)
Biol. Unit 2: C,D,Y (1x)
Biol. Unit 3: E,F,Z (1x)
Keywords
:
Protein-Protein Complex, Coagulation, Acute Phase, Blood Coagulation, Cleavage On Pair Of Basic Residues, Disease Mutation, Disulfide Bond, Gamma-Carboxyglutamic Acid, Glycoprotein, Hydrolase, Kringle, Protease, Secreted, Serine Protease, Zymogen, Egf-Like Domain, Hydroxylation, Membrane, Receptor, Thrombophilia, Transmembrane, Blood Clotting
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. E. Adams, W. Li, J. A. Huntington
Molecular Basis Of Thrombomodulin Activation Of Slow Thrombin
J. Thromb. Haemost. V. 7 1688 2009
[
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Hetero Components
(1, 7)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
2a: SULFATE ION (SO4a)
2b: SULFATE ION (SO4b)
2c: SULFATE ION (SO4c)
2d: SULFATE ION (SO4d)
2e: SULFATE ION (SO4e)
2f: SULFATE ION (SO4f)
2g: SULFATE ION (SO4g)
2h: SULFATE ION (SO4h)
2i: SULFATE ION (SO4i)
2j: SULFATE ION (SO4j)
2k: SULFATE ION (SO4k)
2l: SULFATE ION (SO4l)
2m: SULFATE ION (SO4m)
2n: SULFATE ION (SO4n)
2o: SULFATE ION (SO4o)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
-1
Ligand/Ion
CALCIUM ION
2
SO4
7
Ligand/Ion
SULFATE ION
[
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Sites
(10, 10)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: BC3 (SOFTWARE)
10: BC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ALA A:1B , GLU A:1C , GLY A:1D , SER A:1E , HOH A:384
BINDING SITE FOR RESIDUE SO4 A 16
02
AC2
SOFTWARE
ARG A:1I , ASN A:1K , HOH A:111
BINDING SITE FOR RESIDUE SO4 A 17
03
AC3
SOFTWARE
PHE A:1M , ASP B:125 , ARG B:126 , PHE B:232 , LYS B:235
BINDING SITE FOR RESIDUE SO4 B 1
04
AC4
SOFTWARE
ARG B:101 , ASN B:179 , HOH B:558
BINDING SITE FOR RESIDUE SO4 B 2
05
AC5
SOFTWARE
ALA B:132 , GLU B:164 , ARG B:165 , PRO B:166
BINDING SITE FOR RESIDUE SO4 B 11
06
AC6
SOFTWARE
TRP B:96 , ARG B:97
BINDING SITE FOR RESIDUE SO4 B 13
07
AC7
SOFTWARE
ARG B:101 , HOH B:515
BINDING SITE FOR RESIDUE SO4 B 14
08
AC8
SOFTWARE
HOH B:250 , ARG C:14D
BINDING SITE FOR RESIDUE SO4 C 16
09
BC3
SOFTWARE
ARG A:14D , LYS D:169 , ARG D:175 , HOH D:350
BINDING SITE FOR RESIDUE SO4 D 6
10
BC6
SOFTWARE
HOH X:148 , ASP X:423 , ILE X:424 , GLU X:426 , ASN X:439 , LEU X:440 , THR X:443
BINDING SITE FOR RESIDUE CA X 1001
[
close Site info
]
SAPs(SNPs)/Variants
(9, 9)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_006714 (M32T, chain B, )
2: VAR_011782 (P37T, chain B, )
3: VAR_006715 (R67C, chain B, )
4: VAR_006716 (R73H, chain B, )
5: VAR_006717 (R101W, chain B, )
6: VAR_006718 (E146A, chain B, )
7: VAR_068913 (E164Q, chain B, )
8: VAR_006719 (G226V, chain B, )
9: VAR_011370 (A455V, chain X, )
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)
---
B
M
32
T
2
UniProt
VAR_011782
P
386
T
THRB_HUMAN
Polymorphism
5897
B
P
37
T
3
UniProt
VAR_006715
R
425
C
THRB_HUMAN
Disease (FA2D)
---
B
R
67
C
4
UniProt
VAR_006716
R
431
H
THRB_HUMAN
Disease (FA2D)
---
B
R
73
H
5
UniProt
VAR_006717
R
461
W
THRB_HUMAN
Disease (FA2D)
---
B
R
101
W
6
UniProt
VAR_006718
E
509
A
THRB_HUMAN
Disease (FA2D)
---
B
E
146
A
7
UniProt
VAR_068913
E
532
Q
THRB_HUMAN
Polymorphism
---
B
E
164
Q
8
UniProt
VAR_006719
G
601
V
THRB_HUMAN
Disease (FA2D)
---
B
G
226
V
9
UniProt
VAR_011370
A
473
V
TRBM_HUMAN
Polymorphism
1042579
X
A
455
V
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(7, 7)
Info
All PROSITE Patterns/Profiles
1: EGF_3 ()
2: EGF_2 ()
3: EGF_CA ()
4: ASX_HYDROXYL ()
5: TRYPSIN_DOM (B:16-243)
6: TRYPSIN_HIS (B:53-58)
7: TRYPSIN_SER (B:189-200)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
EGF_3
PS50026
EGF-like domain profile.
TRBM_HUMAN
284-324
325-361
365-405
441-481
1
-
-
-
X:423-463
-
-
2
EGF_2
PS01186
EGF-like domain signature 2.
TRBM_HUMAN
308-323
425-439
1
-
X:407-421
-
-
3
EGF_CA
PS01187
Calcium-binding EGF-like domain signature.
TRBM_HUMAN
325-349
441-464
1
-
X:423-446
-
-
4
ASX_HYDROXYL
PS00010
Aspartic acid and asparagine hydroxylation site.
TRBM_HUMAN
340-351
455-466
1
-
X:437-448
-
-
5
TRYPSIN_DOM
PS50240
Serine proteases, trypsin domain profile.
THRB_HUMAN
364-618
1
B:16-243
-
-
6
TRYPSIN_HIS
PS00134
Serine proteases, trypsin family, histidine active site.
THRB_HUMAN
402-407
1
B:53-58
-
-
7
TRYPSIN_SER
PS00135
Serine proteases, trypsin family, serine active site.
THRB_HUMAN
562-573
1
B:189-200
-
-
[
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]
Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Label:
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, 9)
Info
All SCOP Domains
1a: SCOP_d3gisx1 (X:349-387)
1b: SCOP_d3gisx2 (X:388-422)
1c: SCOP_d3gisx3 (X:423-463)
1d: SCOP_d3gisy1 (Y:348-387)
1e: SCOP_d3gisy2 (Y:388-422)
1f: SCOP_d3gisy3 (Y:423-463)
1g: SCOP_d3gisz1 (Z:350-387)
1h: SCOP_d3gisz2 (Z:388-422)
1i: SCOP_d3gisz3 (Z:423-463)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Small proteins
(3458)
Fold
:
Knottins (small inhibitors, toxins, lectins)
(761)
Superfamily
:
EGF/Laminin
(347)
Family
:
automated matches
(19)
Protein domain
:
automated matches
(19)
Human (Homo sapiens) [TaxId: 9606]
(17)
1a
d3gisx1
X:349-387
1b
d3gisx2
X:388-422
1c
d3gisx3
X:423-463
1d
d3gisy1
Y:348-387
1e
d3gisy2
Y:388-422
1f
d3gisy3
Y:423-463
1g
d3gisz1
Z:350-387
1h
d3gisz2
Z:388-422
1i
d3gisz3
Z:423-463
[
close SCOP info
]
CATH Domains
(3, 18)
Info
all CATH domains
1a: CATH_3gisA00 (A:1R-15)
1b: CATH_3gisC00 (C:1S-15)
1c: CATH_3gisE00 (E:1R-15)
2a: CATH_3gisF02 (F:28-120,F:233-244)
2b: CATH_3gisF01 (F:16-27,F:121-232)
2c: CATH_3gisB01 (B:16-27,B:121-232)
2d: CATH_3gisD01 (D:16-27,D:121-232)
2e: CATH_3gisB02 (B:28-120,B:233-245)
2f: CATH_3gisD02 (D:28-120,D:233-245)
3a: CATH_3gisY01 (Y:348-389)
3b: CATH_3gisX01 (X:349-389)
3c: CATH_3gisZ01 (Z:350-389)
3d: CATH_3gisX03 (X:423-463)
3e: CATH_3gisY03 (Y:423-463)
3f: CATH_3gisZ03 (Z:423-463)
3g: CATH_3gisZ02 (Z:390-422)
3h: CATH_3gisX02 (X:390-422)
3i: CATH_3gisY02 (Y:390-422)
View:
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Classes
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)
(
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Architectures
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Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Few Secondary Structures
(1120)
Architecture
:
Irregular
(1120)
Topology
:
Epsilon-Thrombin; Chain L
(37)
Homologous Superfamily
:
Epsilon-Thrombin, subunit L
(37)
Human (Homo sapiens)
(11)
1a
3gisA00
A:1R-15
1b
3gisC00
C:1S-15
1c
3gisE00
E:1R-15
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
Thrombin, subunit H
(1535)
Homologous Superfamily
:
Trypsin-like serine proteases
(1488)
Human (Homo sapiens)
(615)
2a
3gisF02
F:28-120,F:233-244
2b
3gisF01
F:16-27,F:121-232
2c
3gisB01
B:16-27,B:121-232
2d
3gisD01
D:16-27,D:121-232
2e
3gisB02
B:28-120,B:233-245
2f
3gisD02
D:28-120,D:233-245
Architecture
:
Ribbon
(789)
Topology
:
Laminin
(270)
Homologous Superfamily
:
Laminin
(263)
Human (Homo sapiens)
(195)
3a
3gisY01
Y:348-389
3b
3gisX01
X:349-389
3c
3gisZ01
Z:350-389
3d
3gisX03
X:423-463
3e
3gisY03
Y:423-463
3f
3gisZ03
Z:423-463
3g
3gisZ02
Z:390-422
3h
3gisX02
X:390-422
3i
3gisY02
Y:390-422
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Label:
Sorry, no Info available
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