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3BG8
Asym. Unit
Info
Asym.Unit (51 KB)
Biol.Unit 1 (46 KB)
Biol.Unit 2 (132 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF FACTOR XIA IN COMPLEX WITH CLAVATADINE A
Authors
:
Y. Xue, L. Oster
Date
:
26 Nov 07 (Deposition) - 09 Dec 08 (Release) - 09 Dec 08 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.60
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Biol. Unit 2: A (3x)
Keywords
:
Protease Inhibitor, Factor Xia Inhibitor Complex, Covalent Inhibitor, Alternative Splicing, Blood Coagulation, Disease Mutation, Glycoprotein, Heparin-Binding, Hydrolase, Polymorphism, Secreted, Serine Protease
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. S. Buchanan, A. R. Carroll, D. Wessling, M. Jobling, V. M. Avery, R. A. Davis, Y. Feng, Y. Xue, L. Oster, T. Fex, J. Deinum, J. N. Hooper, R. J. Quinn
Clavatadine A, A Natural Product With Selective Recognition And Irreversible Inhibition Of Factor Xia.
J. Med. Chem. V. 51 3583 2008
(for further references see the
PDB file header
)
[
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Hetero Components
(3, 7)
Info
All Hetero Components
1a: BENZAMIDINE (BENa)
2a: N-(R-CARBOXY-ETHYL)-ALPHA-(S)-(2-P... (INHa)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
3d: SULFATE ION (SO4d)
3e: SULFATE ION (SO4e)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BEN
1
Ligand/Ion
BENZAMIDINE
2
INH
1
Ligand/Ion
N-(R-CARBOXY-ETHYL)-ALPHA-(S)-(2-PHENYLETHYL)GLYCYL-L-ARGININE-N-PHENYLAMIDE
3
SO4
5
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(7, 7)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HIS A:413 , LYS A:554 , GLY A:555 , SER A:557 , INH A:612 , BEN A:613 , HOH A:702 , HOH A:812
BINDING SITE FOR RESIDUE SO4 A 1
2
AC2
SOFTWARE
HIS A:451 , TRP A:599 , HOH A:662 , HOH A:700 , HOH A:775 , HOH A:853
BINDING SITE FOR RESIDUE SO4 A 608
3
AC3
SOFTWARE
LYS A:486 , ARG A:489 , HOH A:856
BINDING SITE FOR RESIDUE SO4 A 609
4
AC4
SOFTWARE
ASN A:473 , TYR A:503 , ARG A:507 , LYS A:509 , LYS A:554 , HOH A:829
BINDING SITE FOR RESIDUE SO4 A 610
5
AC5
SOFTWARE
THR A:374 , ALA A:375 , GLN A:406 , GLN A:446 , LYS A:467 , ARG A:504 , HOH A:720 , HOH A:722
BINDING SITE FOR RESIDUE SO4 A 611
6
AC6
SOFTWARE
SO4 A:1 , HIS A:413 , ASP A:551 , ALA A:552 , CYS A:553 , LYS A:554 , GLY A:555 , ASP A:556 , SER A:557 , TRP A:577 , GLY A:578 , GLY A:580 , GLY A:588 , HOH A:629 , HOH A:671 , HOH A:766
BINDING SITE FOR RESIDUE INH A 612
7
AC7
SOFTWARE
SO4 A:1 , ASP A:551 , ALA A:552 , CYS A:553 , LYS A:554 , SER A:557 , THR A:575 , SER A:576 , TRP A:577 , GLY A:580 , GLY A:588 , HOH A:629 , HOH A:744
BINDING SITE FOR RESIDUE BEN A 613
[
close Site info
]
SAPs(SNPs)/Variants
(23, 23)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_011778 (W381R, chain A, )
02: VAR_067945 (W383R, chain A, )
03: VAR_067946 (V385M, chain A, )
04: VAR_012092 (T386N, chain A, )
05: VAR_054901 (G400V, chain A, )
06: VAR_012093 (A412V, chain A, )
07: VAR_067947 (I436K, chain A, )
08: VAR_012094 (F442V, chain A, )
09: VAR_067948 (I463S, chain A, )
10: VAR_012095 (T475I, chain A, )
11: VAR_067949 (S485P, chain A, )
12: VAR_067950 (E488G, chain A, )
13: VAR_054902 (Y493H, chain A, )
14: VAR_067951 (C496F, chain A, )
15: VAR_067952 (D508E, chain A, )
16: VAR_054903 (P520L, chain A, )
17: VAR_054904 (E547K, chain A, )
18: VAR_067953 (S557L, chain A, )
19: VAR_054905 (W569S, chain A, )
20: VAR_012096 (S576R, chain A, )
21: VAR_067954 (E579K, chain A, )
22: VAR_067955 (Y590H, chain A, )
23: VAR_054906 (I600S, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_011778
W
399
R
FA11_HUMAN
Polymorphism
1800439
A
W
381
R
02
UniProt
VAR_067945
W
401
R
FA11_HUMAN
Disease (FA11D)
281875262
A
W
383
R
03
UniProt
VAR_067946
V
403
M
FA11_HUMAN
Disease (FA11D)
281875266
A
V
385
M
04
UniProt
VAR_012092
T
404
N
FA11_HUMAN
Disease (FA11D)
121965067
A
T
386
N
05
UniProt
VAR_054901
G
418
V
FA11_HUMAN
Disease (FA11D)
121965071
A
G
400
V
06
UniProt
VAR_012093
A
430
V
FA11_HUMAN
Disease (FA11D)
121965068
A
A
412
V
07
UniProt
VAR_067947
I
454
K
FA11_HUMAN
Disease (FA11D)
281875241
A
I
436
K
08
UniProt
VAR_012094
F
460
V
FA11_HUMAN
Disease (FA11D)
121965065
A
F
442
V
09
UniProt
VAR_067948
I
481
S
FA11_HUMAN
Disease (FA11D)
281875242
A
I
463
S
10
UniProt
VAR_012095
T
493
I
FA11_HUMAN
Disease (FA11D)
---
A
T
475
I
11
UniProt
VAR_067949
S
503
P
FA11_HUMAN
Disease (FA11D)
140068026
A
S
485
P
12
UniProt
VAR_067950
D
506
G
FA11_HUMAN
Disease (FA11D)
281875258
A
E
488
G
13
UniProt
VAR_054902
Y
511
H
FA11_HUMAN
Disease (FA11D)
281875278
A
Y
493
H
14
UniProt
VAR_067951
C
514
F
FA11_HUMAN
Disease (FA11D)
281875249
A
C
496
F
15
UniProt
VAR_067952
D
526
E
FA11_HUMAN
Disease (FA11D)
281875263
A
D
508
E
16
UniProt
VAR_054903
P
538
L
FA11_HUMAN
Disease (FA11D)
139695003
A
P
520
L
17
UniProt
VAR_054904
E
565
K
FA11_HUMAN
Disease (FA11D)
281875275
A
E
547
K
18
UniProt
VAR_067953
S
575
L
FA11_HUMAN
Disease (FA11D)
281875250
A
S
557
L
19
UniProt
VAR_054905
W
587
S
FA11_HUMAN
Disease (FA11D)
121965072
A
W
569
S
20
UniProt
VAR_012096
S
594
R
FA11_HUMAN
Disease (FA11D)
28934609
A
S
576
R
21
UniProt
VAR_067954
E
597
K
FA11_HUMAN
Disease (FA11D)
281875251
A
E
579
K
22
UniProt
VAR_067955
Y
608
H
FA11_HUMAN
Disease (FA11D)
281875255
A
Y
590
H
23
UniProt
VAR_054906
I
618
S
FA11_HUMAN
Disease (FA11D)
281875276
A
I
600
S
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(3, 3)
Info
All PROSITE Patterns/Profiles
1: TRYPSIN_DOM (A:370-605)
2: TRYPSIN_HIS (A:409-414)
3: TRYPSIN_SER (A:551-562)
;
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.
FA11_HUMAN
388-623
1
A:370-605
2
TRYPSIN_HIS
PS00134
Serine proteases, trypsin family, histidine active site.
FA11_HUMAN
427-432
1
A:409-414
3
TRYPSIN_SER
PS00135
Serine proteases, trypsin family, serine active site.
FA11_HUMAN
569-580
1
A:551-562
[
close PROSITE info
]
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.
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d3bg8a_ (A:)
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
:
Coagulation factor XI
(26)
Human (Homo sapiens) [TaxId: 9606]
(26)
1a
d3bg8a_
A:
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_3bg8A02 (A:382-480,A:596-607)
1b: CATH_3bg8A01 (A:370-381,A:481-595)
View:
Select:
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
3bg8A02
A:382-480,A:596-607
1b
3bg8A01
A:370-381,A:481-595
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
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Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Asymmetric Unit 1
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