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1DX5
Biol. Unit 4
Info
Asym.Unit (298 KB)
Biol.Unit 1 (77 KB)
Biol.Unit 2 (77 KB)
Biol.Unit 3 (77 KB)
Biol.Unit 4 (77 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE THROMBIN-THROMBOMODULIN COMPLEX
Authors
:
P. Fuentes-Prior, Y. Iwanaga, R. Huber, R. Pagila, G. Rumennik, M. Seto J. Morser, D. R. Light, W. Bode
Date
:
20 Dec 99 (Deposition) - 10 Apr 00 (Release) - 21 Dec 16 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P
Biol. Unit 1: A,E,I,M (1x)
Biol. Unit 2: B,F,J,N (1x)
Biol. Unit 3: C,G,K,O (1x)
Biol. Unit 4: D,H,L,P (1x)
Keywords
:
Serine Proteinase, Egf-Like Domains, Anticoagulant Complex, Antifibrinolytic Complex, Hydrolase-Hydrolase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. Fuentes-Prior, Y. Iwanaga, R. Huber, R. Pagila, G. Rumennik, M. Seto, J. Morser, D. R. Light, W. Bode
Structural Basis For The Anticoagulant Activity Of The Thrombin-Thrombomodulin Complex
Nature V. 404 518 2000
[
close entry info
]
Hetero Components
(4, 5)
Info
All Hetero Components
1a: CHLOROMETHANE (0QEa)
1b: CHLOROMETHANE (0QEb)
1c: CHLOROMETHANE (0QEc)
1d: CHLOROMETHANE (0QEd)
2a: AMINO{[(4S)-4-AMINO-5,5-DIHYDROXYP... (AR7a)
2b: AMINO{[(4S)-4-AMINO-5,5-DIHYDROXYP... (AR7b)
2c: AMINO{[(4S)-4-AMINO-5,5-DIHYDROXYP... (AR7c)
2d: AMINO{[(4S)-4-AMINO-5,5-DIHYDROXYP... (AR7d)
3a: CALCIUM ION (CAa)
3b: CALCIUM ION (CAb)
3c: CALCIUM ION (CAc)
3d: CALCIUM ION (CAd)
4a: FORMIC ACID (FMTa)
4b: FORMIC ACID (FMTb)
4c: FORMIC ACID (FMTc)
4d: FORMIC ACID (FMTd)
4e: FORMIC ACID (FMTe)
6a: N-ACETYL-D-GLUCOSAMINE (NAGa)
6b: N-ACETYL-D-GLUCOSAMINE (NAGb)
6c: N-ACETYL-D-GLUCOSAMINE (NAGc)
6d: N-ACETYL-D-GLUCOSAMINE (NAGd)
5a: SODIUM ION (NAa)
5b: SODIUM ION (NAb)
5c: SODIUM ION (NAc)
5d: SODIUM ION (NAd)
5e: SODIUM ION (NAe)
5f: SODIUM ION (NAf)
5g: SODIUM ION (NAg)
6h: SODIUM ION (NAh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
0QE
1
Mod. Amino Acid
CHLOROMETHANE
2
AR7
1
Mod. Amino Acid
AMINO{[(4S)-4-AMINO-5,5-DIHYDROXYPENTYL]AMINO}METHANIMINIUM
3
CA
-1
Ligand/Ion
CALCIUM ION
4
FMT
2
Ligand/Ion
FORMIC ACID
5
NA
-1
Ligand/Ion
SODIUM ION
6
NAG
1
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: BC2 (SOFTWARE)
3: BC3 (SOFTWARE)
4: BC4 (SOFTWARE)
5: BC8 (SOFTWARE)
6: CC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLY H:2 , TYR P:60A
BINDING SITE FOR RESIDUE FMT H 502
2
BC2
SOFTWARE
GLU L:357 , NA L:2002
BINDING SITE FOR RESIDUE FMT L 501
3
BC3
SOFTWARE
ASP L:423 , ILE L:424 , GLU L:426 , ASN L:439 , LEU L:440 , THR L:443 , HOH L:2051
BINDING SITE FOR RESIDUE CA L1001
4
BC4
SOFTWARE
TYR L:358 , CYS L:372 , ALA L:373 , PHE L:376 , FMT L:501
BINDING SITE FOR RESIDUE NA L2002
5
BC8
SOFTWARE
ARG P:221A , LYS P:224 , HOH P:2089 , HOH P:2090 , HOH P:2115
BINDING SITE FOR RESIDUE NA P2001
6
CC3
SOFTWARE
LEU P:60 , ASN P:60G , ILE P:60I , HOH P:2053
BINDING SITE FOR MONO-SACCHARIDE NAG P 600 BOUND TO ASN P 60G
[
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 P, )
2: VAR_011782 (P37T, chain P, )
3: VAR_006715 (R67C, chain P, )
4: VAR_006716 (R73H, chain P, )
5: VAR_006717 (R101W, chain P, )
6: VAR_006718 (E146A, chain P, )
7: VAR_068913 (E164Q, chain P, )
8: VAR_006719 (G226V, chain P, )
9: VAR_011370 (A455V, chain L, )
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)
---
P
M
32
T
2
UniProt
VAR_011782
P
386
T
THRB_HUMAN
Polymorphism
5897
P
P
37
T
3
UniProt
VAR_006715
R
425
C
THRB_HUMAN
Disease (FA2D)
---
P
R
67
C
4
UniProt
VAR_006716
R
431
H
THRB_HUMAN
Disease (FA2D)
---
P
R
73
H
5
UniProt
VAR_006717
R
461
W
THRB_HUMAN
Disease (FA2D)
---
P
R
101
W
6
UniProt
VAR_006718
E
509
A
THRB_HUMAN
Disease (FA2D)
---
P
E
146
A
7
UniProt
VAR_068913
E
532
Q
THRB_HUMAN
Polymorphism
---
P
E
164
Q
8
UniProt
VAR_006719
G
601
V
THRB_HUMAN
Disease (FA2D)
---
P
G
226
V
9
UniProt
VAR_011370
A
473
V
TRBM_HUMAN
Polymorphism
1042579
L
A
455
V
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(7, 8)
Info
All PROSITE Patterns/Profiles
1: EGF_3 (L:423-462)
2: EGF_2 (L:407-421)
3: EGF_CA (L:423-446)
4: ASX_HYDROXYL (L:437-448)
5: TRYPSIN_DOM (P:16-243)
6: TRYPSIN_HIS (P:53-58)
7: TRYPSIN_SER (P: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
2
-
-
-
-
-
L:347-387
-
-
-
L:423-462
2
EGF_2
PS01186
EGF-like domain signature 2.
TRBM_HUMAN
308-323
425-439
1
-
-
-
-
L:407-421
3
EGF_CA
PS01187
Calcium-binding EGF-like domain signature.
TRBM_HUMAN
325-349
441-464
1
-
-
-
-
L:423-446
4
ASX_HYDROXYL
PS00010
Aspartic acid and asparagine hydroxylation site.
TRBM_HUMAN
340-351
455-466
1
-
-
-
-
L:437-448
5
TRYPSIN_DOM
PS50240
Serine proteases, trypsin domain profile.
THRB_HUMAN
364-618
1
-
-
-
P:16-243
6
TRYPSIN_HIS
PS00134
Serine proteases, trypsin family, histidine active site.
THRB_HUMAN
402-407
1
-
-
-
P:53-58
7
TRYPSIN_SER
PS00135
Serine proteases, trypsin family, serine active site.
THRB_HUMAN
562-573
1
-
-
-
P:189-200
[
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]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
All Exon Boundaries
View:
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
(2, 16)
Info
All SCOP Domains
1a: SCOP_d1dx5_1 (A:,M:)
1b: SCOP_d1dx5_2 (B:,N:)
1c: SCOP_d1dx5_3 (C:,O:)
1d: SCOP_d1dx5_4 (D:,P:)
2a: SCOP_d1dx5i1 (I:345-387)
2b: SCOP_d1dx5i2 (I:388-422)
2c: SCOP_d1dx5l2 (L:388-422)
2d: SCOP_d1dx5l3 (L:423-462)
2e: SCOP_d1dx5i3 (I:423-462)
2f: SCOP_d1dx5j1 (J:345-387)
2g: SCOP_d1dx5j2 (J:388-422)
2h: SCOP_d1dx5j3 (J:423-462)
2i: SCOP_d1dx5k1 (K:345-387)
2j: SCOP_d1dx5k2 (K:388-422)
2k: SCOP_d1dx5k3 (K:423-462)
2l: SCOP_d1dx5l1 (L:345-387)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
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
d1dx5.1
A:,M:
1b
d1dx5.2
B:,N:
1c
d1dx5.3
C:,O:
1d
d1dx5.4
D:,P:
Class
:
Small proteins
(3458)
Fold
:
Knottins (small inhibitors, toxins, lectins)
(761)
Superfamily
:
EGF/Laminin
(347)
Family
:
EGF-type module
(304)
Protein domain
:
Thrombomodulin, different EGF-like domains
(6)
Human (Homo sapiens) [TaxId: 9606]
(6)
2a
d1dx5i1
I:345-387
2b
d1dx5i2
I:388-422
2c
d1dx5l2
L:388-422
2d
d1dx5l3
L:423-462
2e
d1dx5i3
I:423-462
2f
d1dx5j1
J:345-387
2g
d1dx5j2
J:388-422
2h
d1dx5j3
J:423-462
2i
d1dx5k1
K:345-387
2j
d1dx5k2
K:388-422
2k
d1dx5k3
K:423-462
2l
d1dx5l1
L:345-387
[
close SCOP info
]
CATH Domains
(2, 20)
Info
all CATH domains
1a: CATH_1dx5M02 (M:28-120,M:233-246)
1b: CATH_1dx5M01 (M:16-27,M:121-232)
1c: CATH_1dx5N01 (N:16-27,N:121-232)
1d: CATH_1dx5O01 (O:16-27,O:121-232)
1e: CATH_1dx5P01 (P:16-27,P:121-232)
1f: CATH_1dx5N02 (N:28-120,N:233-246)
1g: CATH_1dx5O02 (O:28-120,O:233-246)
1h: CATH_1dx5P02 (P:28-120,P:233-246)
2a: CATH_1dx5I01 (I:345-389)
2b: CATH_1dx5J01 (J:345-389)
2c: CATH_1dx5K01 (K:345-389)
2d: CATH_1dx5L01 (L:345-389)
2e: CATH_1dx5I03 (I:423-462)
2f: CATH_1dx5J03 (J:423-462)
2g: CATH_1dx5K03 (K:423-462)
2h: CATH_1dx5L03 (L:423-462)
2i: CATH_1dx5I02 (I:390-422)
2j: CATH_1dx5J02 (J:390-422)
2k: CATH_1dx5K02 (K:390-422)
2l: CATH_1dx5L02 (L:390-422)
View:
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Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
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
1dx5M02
M:28-120,M:233-246
1b
1dx5M01
M:16-27,M:121-232
1c
1dx5N01
N:16-27,N:121-232
1d
1dx5O01
O:16-27,O:121-232
1e
1dx5P01
P:16-27,P:121-232
1f
1dx5N02
N:28-120,N:233-246
1g
1dx5O02
O:28-120,O:233-246
1h
1dx5P02
P:28-120,P:233-246
Architecture
:
Ribbon
(789)
Topology
:
Laminin
(270)
Homologous Superfamily
:
Laminin
(263)
Human (Homo sapiens)
(195)
2a
1dx5I01
I:345-389
2b
1dx5J01
J:345-389
2c
1dx5K01
K:345-389
2d
1dx5L01
L:345-389
2e
1dx5I03
I:423-462
2f
1dx5J03
J:423-462
2g
1dx5K03
K:423-462
2h
1dx5L03
L:423-462
2i
1dx5I02
I:390-422
2j
1dx5J02
J:390-422
2k
1dx5K02
K:390-422
2l
1dx5L02
L: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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