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Asym. Unit
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
[
close entry info
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Hetero Components
(2, 18)
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
3
Ligand/Ion
CALCIUM ION
2
SO4
15
Ligand/Ion
SULFATE ION
[
close Hetero Component info
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Sites
(17, 17)
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: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (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
AC9
SOFTWARE
PHE C:1M , ASP D:125 , ARG D:126 , LYS D:235 , HOH D:440 , HOH D:525
BINDING SITE FOR RESIDUE SO4 D 3
10
BC1
SOFTWARE
ARG D:93 , ARG D:101 , ASN D:179
BINDING SITE FOR RESIDUE SO4 D 4
11
BC2
SOFTWARE
GLU D:164 , ARG D:165 , PRO D:166 , HOH D:266
BINDING SITE FOR RESIDUE SO4 D 5
12
BC3
SOFTWARE
ARG A:14D , LYS D:169 , ARG D:175 , HOH D:350
BINDING SITE FOR RESIDUE SO4 D 6
13
BC4
SOFTWARE
ALA E:1B , GLY E:1D , SER E:1E , HOH E:313
BINDING SITE FOR RESIDUE SO4 E 16
14
BC5
SOFTWARE
ASP F:125 , ARG F:126 , LYS F:235 , HOH F:291
BINDING SITE FOR RESIDUE SO4 F 7
15
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
16
BC7
SOFTWARE
ASP Y:423 , ILE Y:424 , GLU Y:426 , ASN Y:439 , LEU Y:440 , THR Y:443
BINDING SITE FOR RESIDUE CA Y 1002
17
BC8
SOFTWARE
HOH Z:256 , ASP Z:423 , ILE Z:424 , GLU Z:426 , ASN Z:439 , LEU Z:440 , THR Z:443
BINDING SITE FOR RESIDUE CA Z 1003
[
close Site info
]
SAPs(SNPs)/Variants
(9, 27)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_006714 (M32T, chain B/D/F, )
2: VAR_011782 (P37T, chain B/D/F, )
3: VAR_006715 (R67C, chain B/D/F, )
4: VAR_006716 (R73H, chain B/D/F, )
5: VAR_006717 (R101W, chain B/D/F, )
6: VAR_006718 (E146A, chain B/D/F, )
7: VAR_068913 (E164Q, chain B/D/F, )
8: VAR_006719 (G226V, chain B/D/F, )
9: VAR_011370 (A455V, chain X/Y/Z, )
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/D/F
M
32
T
2
UniProt
VAR_011782
P
386
T
THRB_HUMAN
Polymorphism
5897
B/D/F
P
37
T
3
UniProt
VAR_006715
R
425
C
THRB_HUMAN
Disease (FA2D)
---
B/D/F
R
67
C
4
UniProt
VAR_006716
R
431
H
THRB_HUMAN
Disease (FA2D)
---
B/D/F
R
73
H
5
UniProt
VAR_006717
R
461
W
THRB_HUMAN
Disease (FA2D)
---
B/D/F
R
101
W
6
UniProt
VAR_006718
E
509
A
THRB_HUMAN
Disease (FA2D)
---
B/D/F
E
146
A
7
UniProt
VAR_068913
E
532
Q
THRB_HUMAN
Polymorphism
---
B/D/F
E
164
Q
8
UniProt
VAR_006719
G
601
V
THRB_HUMAN
Disease (FA2D)
---
B/D/F
G
226
V
9
UniProt
VAR_011370
A
473
V
TRBM_HUMAN
Polymorphism
1042579
X/Y/Z
A
455
V
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(7, 21)
Info
All PROSITE Patterns/Profiles
1: EGF_3 (-|-|-|X:423-463,Y:423-463,Z:423-46...)
2: EGF_2 (-|X:407-421,Y:407-421,Z:407-421)
3: EGF_CA (-|X:423-446,Y:423-446,Z:423-446)
4: ASX_HYDROXYL (-|X:437-448,Y:437-448,Z:437-448)
5: TRYPSIN_DOM (B:16-243,D:16-243,F:16-243)
6: TRYPSIN_HIS (B:53-58,D:53-58,F:53-58)
7: TRYPSIN_SER (B:189-200,D:189-200,F: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
3
-
-
-
X:423-463
Y:423-463
Z:423-463
2
EGF_2
PS01186
EGF-like domain signature 2.
TRBM_HUMAN
308-323
425-439
3
-
X:407-421
Y:407-421
Z:407-421
3
EGF_CA
PS01187
Calcium-binding EGF-like domain signature.
TRBM_HUMAN
325-349
441-464
3
-
X:423-446
Y:423-446
Z:423-446
4
ASX_HYDROXYL
PS00010
Aspartic acid and asparagine hydroxylation site.
TRBM_HUMAN
340-351
455-466
3
-
X:437-448
Y:437-448
Z:437-448
5
TRYPSIN_DOM
PS50240
Serine proteases, trypsin domain profile.
THRB_HUMAN
364-618
3
B:16-243
D:16-243
F:16-243
6
TRYPSIN_HIS
PS00134
Serine proteases, trypsin family, histidine active site.
THRB_HUMAN
402-407
3
B:53-58
D:53-58
F:53-58
7
TRYPSIN_SER
PS00135
Serine proteases, trypsin family, serine active site.
THRB_HUMAN
562-573
3
B:189-200
D:189-200
F:189-200
[
close PROSITE info
]
Exons
(8, 27)
Info
All Exons
Exon 1.8 (A:1R-1A | - | C:1S-1A | - | E:1R-1...)
Exon 1.9 (A:1A-15 | B:16-29 | C:1A-15 | D:16...)
Exon 1.10 (- | B:29-75 | - | D:29-75 | - | F:...)
Exon 1.11b (- | B:75-129B | - | D:75-129B | - ...)
Exon 1.12 (- | B:129B-184 (gaps) | - | D:129B...)
Exon 1.13 (- | B:184-202 | - | D:184-202 | - ...)
Exon 1.14c (- | B:203-247 (gaps) | - | D:203-2...)
Exon 2.1 (X:349-463 (gaps) | Y:348-463 (gaps...)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.7b/1.8
02: Boundary 1.8/1.9
03: Boundary 1.9/1.10
04: Boundary 1.10/1.11b
05: Boundary 1.11b/1.12
06: Boundary 1.12/1.13
07: Boundary 1.13/1.14c
08: Boundary 1.14c/-
09: Boundary -/2.1
10: Boundary 2.1/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1a
ENST00000311907
1a
ENSE00001931088
chr11:
46740730-46740864
135
THRB_HUMAN
1-27
27
0
-
-
1.2a
ENST00000311907
2a
ENSE00001181543
chr11:
46741252-46741412
161
THRB_HUMAN
27-80
54
0
-
-
1.3
ENST00000311907
3
ENSE00001181538
chr11:
46742073-46742097
25
THRB_HUMAN
81-89
9
0
-
-
1.4
ENST00000311907
4
ENSE00001181532
chr11:
46742340-46742390
51
THRB_HUMAN
89-106
18
0
-
-
1.6a
ENST00000311907
6a
ENSE00001181527
chr11:
46744730-46744835
106
THRB_HUMAN
106-141
36
0
-
-
1.6c
ENST00000311907
6c
ENSE00001181524
chr11:
46744932-46745068
137
THRB_HUMAN
141-187
47
0
-
-
1.7b
ENST00000311907
7b
ENSE00001688723
chr11:
46747409-46747723
315
THRB_HUMAN
187-292
106
0
-
-
1.8
ENST00000311907
8
ENSE00002179953
chr11:
46748048-46748176
129
THRB_HUMAN
292-335
44
3
A:1R-1A
-
C:1S-1A
-
E:1R-1A
-
18
-
18
-
18
-
1.9
ENST00000311907
9
ENSE00001770269
chr11:
46748261-46748387
127
THRB_HUMAN
335-377
43
6
A:1A-15
B:16-29
C:1A-15
D:16-29
E:1A-15
F:16-29
29
14
29
14
29
14
1.10
ENST00000311907
10
ENSE00001650441
chr11:
46749546-46749713
168
THRB_HUMAN
377-433
57
3
-
B:29-75
-
D:29-75
-
F:29-75
-
57
-
57
-
57
1.11b
ENST00000311907
11b
ENSE00001657931
chr11:
46750214-46750387
174
THRB_HUMAN
433-491
59
3
-
B:75-129B
-
D:75-129B
-
F:75-129B
-
59
-
59
-
59
1.12
ENST00000311907
12
ENSE00001646362
chr11:
46750930-46751111
182
THRB_HUMAN
491-552
62
3
-
B:129B-184 (gaps)
-
D:129B-184 (gaps)
-
F:129B-184 (gaps)
-
62
-
62
-
62
1.13
ENST00000311907
13
ENSE00001680217
chr11:
46760598-46760668
71
THRB_HUMAN
552-575
24
3
-
B:184-202
-
D:184-202
-
F:184-202
-
24
-
24
-
24
1.14c
ENST00000311907
14c
ENSE00001227030
chr11:
46760815-46761056
242
THRB_HUMAN
576-622
47
3
-
B:203-247 (gaps)
-
D:203-246 (gaps)
-
F:203-244 (gaps)
-
48
-
47
-
45
2.1
ENST00000377103
1
ENSE00001472793
chr20:
23030378-23026270
4109
TRBM_HUMAN
1-654
654
3
X:349-463 (gaps)
Y:348-463 (gaps)
Z:350-463 (gaps)
115
116
114
[
close EXON info
]
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)
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Folds
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Superfamilies
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)
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)
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
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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)
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Topologies
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Homologous Superfamilies
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(
)
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:
Select:
Label:
Sorry, no Info available
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Atom Selection
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Asym.Unit (216 KB)
Header - Asym.Unit
Biol.Unit 1 (75 KB)
Header - Biol.Unit 1
Biol.Unit 2 (73 KB)
Header - Biol.Unit 2
Biol.Unit 3 (71 KB)
Header - Biol.Unit 3
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