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3B9F
Asym. Unit
Info
Asym.Unit (132 KB)
Biol.Unit 1 (126 KB)
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(1)
Title
:
1.6 A STRUCTURE OF THE PCI-THROMBIN-HEPARIN COMPLEX
Authors
:
W. Li, T. E. Adams, J. A. Huntington
Date
:
05 Nov 07 (Deposition) - 22 Apr 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.60
Chains
:
Asym. Unit : H,I,L
Biol. Unit 1: H,I,L (1x)
Keywords
:
Michaelis Complex, Acute Phase, Blood Coagulation, Cleavage On Pair Of Basic Residues, Disease Mutation, Gamma-Carboxyglutamic Acid, Glycoprotein, Hydrolase, Kringle, Protease, Secreted, Serine Protease, Zymogen, Hydrolase-Hydrolase Inhibitor Complex
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
W. Li, T. E. Adams, J. Nangalia, C. T. Esmon, J. A. Huntington
Molecular Basis Of Thrombin Recognition By Protein C Inhibitor Revealed By The 1. 6-A Structure Of The Heparin-Bridged Complex.
Proc. Natl. Acad. Sci. Usa V. 105 4661 2008
[
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Hetero Components
(6, 12)
Info
All Hetero Components
1a: ALPHA-L-FUCOSE (FUCa)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
3a: 2-O-SULFO-ALPHA-L-IDOPYRANURONIC A... (IDSa)
4a: N-ACETYL-D-GLUCOSAMINE (NAGa)
5a: N,O6-DISULFO-GLUCOSAMINE (SGNa)
6a: SULFATE ION (SO4a)
6b: SULFATE ION (SO4b)
6c: SULFATE ION (SO4c)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FUC
1
Ligand/Ion
ALPHA-L-FUCOSE
2
GOL
5
Ligand/Ion
GLYCEROL
3
IDS
1
Ligand/Ion
2-O-SULFO-ALPHA-L-IDOPYRANURONIC ACID
4
NAG
1
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
5
SGN
1
Ligand/Ion
N,O6-DISULFO-GLUCOSAMINE
6
SO4
3
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: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN H:60G , HOH H:1013 , HOH H:1014 , HOH H:1035
BINDING SITE FOR RESIDUE NAG H 778
02
AC2
SOFTWARE
HIS H:91 , ARG H:93 , ARG H:101 , ASN H:179 , ARG H:233 , LEU H:234 , LYS H:236 , TRP H:237 , HOH H:824 , HOH H:981
BINDING SITE FOR RESIDUE SGN H 1
03
AC3
SOFTWARE
HIS H:91 , PRO H:92 , ARG H:93 , LYS H:236 , TRP H:237 , LYS H:240
BINDING SITE FOR RESIDUE IDS H 2
04
AC4
SOFTWARE
GLN H:38 , ARG H:165 , ASP H:178 , ARG H:233
BINDING SITE FOR RESIDUE SO4 H 781
05
AC5
SOFTWARE
LYS H:169 , HOH H:854 , ARG I:362
BINDING SITE FOR RESIDUE SO4 I 388
06
AC6
SOFTWARE
ARG H:165 , CYS H:168 , PHE H:181 , CYS H:182 , HOH H:894
BINDING SITE FOR RESIDUE GOL H 782
07
AC7
SOFTWARE
TRP H:60D , THR I:349 , THR I:352 , PHE I:353 , HOH I:402
BINDING SITE FOR RESIDUE GOL I 390
08
AC8
SOFTWARE
ARG H:75 , TYR H:76 , GLU H:77 , ARG H:77A , GLN H:131 , TYR H:134 , PHE H:204A , HOH I:486
BINDING SITE FOR RESIDUE GOL H 3
09
AC9
SOFTWARE
ARG H:50 , LYS H:107 , PRO H:111 , GLY H:246 , GLU H:247 , HOH H:999
BINDING SITE FOR RESIDUE GOL H 4
10
BC1
SOFTWARE
PHE I:29 , THR I:30 , GLY I:75
BINDING SITE FOR RESIDUE GOL I 391
[
close Site info
]
SAPs(SNPs)/Variants
(8, 8)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_006714 (M32T, chain H, )
2: VAR_011782 (P37T, chain H, )
3: VAR_006715 (R67C, chain H, )
4: VAR_006716 (R73H, chain H, )
5: VAR_006717 (R101W, chain H, )
6: VAR_006718 (E146A, chain H, )
7: VAR_068913 (E164Q, chain H, )
8: VAR_006719 (G226V, chain H, )
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)
---
H
M
32
T
2
UniProt
VAR_011782
P
386
T
THRB_HUMAN
Polymorphism
5897
H
P
37
T
3
UniProt
VAR_006715
R
425
C
THRB_HUMAN
Disease (FA2D)
---
H
R
67
C
4
UniProt
VAR_006716
R
431
H
THRB_HUMAN
Disease (FA2D)
---
H
R
73
H
5
UniProt
VAR_006717
R
461
W
THRB_HUMAN
Disease (FA2D)
---
H
R
101
W
6
UniProt
VAR_006718
E
509
A
THRB_HUMAN
Disease (FA2D)
---
H
E
146
A
7
UniProt
VAR_068913
E
532
Q
THRB_HUMAN
Polymorphism
---
H
E
164
Q
8
UniProt
VAR_006719
G
601
V
THRB_HUMAN
Disease (FA2D)
---
H
G
226
V
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(4, 4)
Info
All PROSITE Patterns/Profiles
1: TRYPSIN_DOM (H:16-243)
2: SERPIN (I:364-373)
3: TRYPSIN_HIS (H:53-58)
4: TRYPSIN_SER (H: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
H:16-243
2
SERPIN
PS00284
Serpins signature.
IPSP_BOVIN
378-388
1
I:364-373
3
TRYPSIN_HIS
PS00134
Serine proteases, trypsin family, histidine active site.
THRB_HUMAN
402-407
1
H:53-58
4
TRYPSIN_SER
PS00135
Serine proteases, trypsin family, serine active site.
THRB_HUMAN
562-573
1
H:189-200
[
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]
Exons
(7, 8)
Info
All Exons
Exon 1.8 (- | L:1R-1A)
Exon 1.9 (H:16-29 | L:1A-14L)
Exon 1.10 (H:29-75 | -)
Exon 1.11b (H:75-129B | -)
Exon 1.12 (H:129B-184 (gaps) | -)
Exon 1.13 (H:184-202 | -)
Exon 1.14c (H:203-247 (gaps) | -)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.7b/1.8
2: Boundary 1.8/1.9
3: Boundary 1.9/1.10
4: Boundary 1.10/1.11b
5: Boundary 1.11b/1.12
6: Boundary 1.12/1.13
7: Boundary 1.13/1.14c
8: Boundary 1.14c/-
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
1
-
L:1R-1A
-
18
1.9
ENST00000311907
9
ENSE00001770269
chr11:
46748261-46748387
127
THRB_HUMAN
335-377
43
2
H:16-29
L:1A-14L
14
27
1.10
ENST00000311907
10
ENSE00001650441
chr11:
46749546-46749713
168
THRB_HUMAN
377-433
57
1
H:29-75
-
57
-
1.11b
ENST00000311907
11b
ENSE00001657931
chr11:
46750214-46750387
174
THRB_HUMAN
433-491
59
1
H:75-129B
-
59
-
1.12
ENST00000311907
12
ENSE00001646362
chr11:
46750930-46751111
182
THRB_HUMAN
491-552
62
1
H:129B-184 (gaps)
-
62
-
1.13
ENST00000311907
13
ENSE00001680217
chr11:
46760598-46760668
71
THRB_HUMAN
552-575
24
1
H:184-202
-
24
-
1.14c
ENST00000311907
14c
ENSE00001227030
chr11:
46760815-46761056
242
THRB_HUMAN
576-622
47
1
H:203-247 (gaps)
-
48
-
[
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]
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
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CATH Domains
(4, 5)
Info
all CATH domains
1a: CATH_3b9fI01 (I:28-189,I:285-338)
2a: CATH_3b9fL00 (L:1R-14L)
3a: CATH_3b9fH02 (H:28-120,H:233-245)
3b: CATH_3b9fH01 (H:16-27,H:121-232)
4a: CATH_3b9fI02 (I:190-284,I:344-387)
View:
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Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Antithrombin; Chain I, domain 2
(100)
Homologous Superfamily
:
Antithrombin, subunit I, domain 2
(100)
Human (Homo sapiens)
(80)
1a
3b9fI01
I:28-189,I:285-338
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)
2a
3b9fL00
L:1R-14L
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
Thrombin, subunit H
(1535)
Homologous Superfamily
:
Trypsin-like serine proteases
(1488)
Human (Homo sapiens)
(615)
3a
3b9fH02
H:28-120,H:233-245
3b
3b9fH01
H:16-27,H:121-232
Architecture
:
Roll
(1513)
Topology
:
Alpha-1-antitrypsin; domain 1
(101)
Homologous Superfamily
:
Alpha-1-antitrypsin, domain 1
(101)
Human (Homo sapiens)
(81)
4a
3b9fI02
I:190-284,I:344-387
[
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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
(currently selected atoms:
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Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain H
Chain I
Chain L
Asymmetric Unit 1
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Asym.Unit (132 KB)
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