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3KQB
Asym. Unit
Info
Asym.Unit (54 KB)
Biol.Unit 1 (50 KB)
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Title
:
FACTOR XA IN COMPLEX WITH THE INHIBITOR N-(3-FLUORO-2'-(METHYLSULFONYL)BIPHENYL-4-YL)-1-(3-(5-OXO-4,5-DIHYDRO-1H- 1,2,4-TRIAZOL-3-YL)PHENYL)-3-(TRIFLUOROMETHYL)-1H- PYRAZOLE-5-CARBOXAMIDE
Authors
:
S. Sheriff
Date
:
17 Nov 09 (Deposition) - 23 Feb 10 (Release) - 28 Apr 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.25
Chains
:
Asym. Unit : A,L
Biol. Unit 1: A,L (1x)
Keywords
:
Glycoprotein, Serine Protease, Plasma, Blood Coagulation Factor, Protein Inhibitor Complex, Calcium- Binding, Blood Coagulation, Calcium, Protease, Secreted, Egf-Like Domain, Gamma-Carboxyglutamic Acid, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. L. Quan, D. J. Pinto, K. A. Rossi, S. Sheriff, R. S. Alexander, E. Amparo, K. Kish, R. M. Knabb, J. M. Luettgen, P. Morin, A. Smallwood, F. J. Woerner, R. R. Wexler
Phenyltriazolinones As Potent Factor Xa Inhibitors.
Bioorg. Med. Chem. Lett. V. 20 1373 2010
[
close entry info
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Hetero Components
(2, 3)
Info
All Hetero Components
1a: N-(3-FLUORO-2'-(METHYLSULFONYL)BIP... (LGJa)
2a: SODIUM ION (NAa)
2b: SODIUM ION (NAb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
LGJ
1
Ligand/Ion
N-(3-FLUORO-2'-(METHYLSULFONYL)BIPHENYL-4-YL)-1-(3-(5-OXO-4,5-DIHYDRO-1H-1,2,4-TRIAZOL-3-YL)PHENYL)-3-(TRIFLUOROMETHYL)-1H-PYRAZOLE-5-CARBOXAMIDE
2
NA
2
Ligand/Ion
SODIUM ION
[
close Hetero Component info
]
Sites
(3, 3)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
LYS A:96 , GLU A:97 , THR A:98 , ARG A:143 , GLU A:146 , PHE A:174 , ASP A:189 , ALA A:190 , CYS A:191 , GLN A:192 , SER A:195 , TRP A:215 , GLY A:216 , GLU A:217 , GLY A:218 , CYS A:220 , ALA A:221 , GLY A:226 , HOH A:403 , HOH A:419 , HOH A:424
BINDING SITE FOR RESIDUE LGJ A 301
2
AC2
SOFTWARE
TYR A:185 , ARG A:222 , LYS A:224 , HOH A:419 , HOH A:445 , HOH A:466
BINDING SITE FOR RESIDUE NA A 302
3
AC3
SOFTWARE
ASP A:70 , ASN A:72 , GLN A:75 , GLU A:77 , GLU A:80
BINDING SITE FOR RESIDUE NA A 303
[
close Site info
]
SAPs(SNPs)/Variants
(22, 22)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_065437 (G69R, chain A, )
02: VAR_065438 (E84K, chain A, )
03: VAR_065434 (E102K, chain L, )
04: VAR_065439 (D102N, chain A, )
05: VAR_065440 (R107W, chain A, )
06: VAR_065435 (C109Y, chain L, )
07: VAR_065436 (C111Y, chain L, )
08: VAR_020176 (A112T, chain L, )
09: VAR_065441 (V118M, chain A, )
10: VAR_065442 (E129K, chain A, )
11: VAR_065443 (T135M, chain A, )
12: VAR_065444 (G140S, chain A, )
13: VAR_065445 (R143C, chain A, )
14: VAR_065446 (S152P, chain A, )
15: VAR_072751 (V160A, chain A, )
16: VAR_065447 (P161S, chain A, )
17: VAR_065448 (C168F, chain A, )
18: VAR_065449 (C182R, chain A, )
19: VAR_065450 (G184S, chain A, )
20: VAR_065451 (G196R, chain A, )
21: VAR_072752 (G197D, chain A, )
22: VAR_065452 (K224N, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_065437
G
289
R
FA10_HUMAN
Disease (FA10D)
---
A
G
69
R
02
UniProt
VAR_065438
E
304
K
FA10_HUMAN
Disease (FA10D)
---
A
E
84
K
03
UniProt
VAR_065434
E
142
K
FA10_HUMAN
Unclassified
61753266
L
E
102
K
04
UniProt
VAR_065439
D
322
N
FA10_HUMAN
Disease (FA10D)
---
A
D
102
N
05
UniProt
VAR_065440
R
327
W
FA10_HUMAN
Disease (FA10D)
---
A
R
107
W
06
UniProt
VAR_065435
C
149
Y
FA10_HUMAN
Disease (FA10D)
---
L
C
109
Y
07
UniProt
VAR_065436
C
151
Y
FA10_HUMAN
Disease (FA10D)
---
L
C
111
Y
08
UniProt
VAR_020176
A
152
T
FA10_HUMAN
Polymorphism
3211772
L
A
112
T
09
UniProt
VAR_065441
V
338
M
FA10_HUMAN
Disease (FA10D)
---
A
V
118
M
10
UniProt
VAR_065442
E
350
K
FA10_HUMAN
Disease (FA10D)
---
A
E
129
K
11
UniProt
VAR_065443
T
358
M
FA10_HUMAN
Disease (FA10D)
---
A
T
135
M
12
UniProt
VAR_065444
G
363
S
FA10_HUMAN
Disease (FA10D)
---
A
G
140
S
13
UniProt
VAR_065445
R
366
C
FA10_HUMAN
Disease (FA10D)
---
A
R
143
C
14
UniProt
VAR_065446
S
374
P
FA10_HUMAN
Disease (FA10D)
---
A
S
152
P
15
UniProt
VAR_072751
V
382
A
FA10_HUMAN
Disease (FA10D)
---
A
V
160
A
16
UniProt
VAR_065447
P
383
S
FA10_HUMAN
Disease (FA10D)
---
A
P
161
S
17
UniProt
VAR_065448
C
390
F
FA10_HUMAN
Disease (FA10D)
199778916
A
C
168
F
18
UniProt
VAR_065449
C
404
R
FA10_HUMAN
Disease (FA10D)
---
A
C
182
R
19
UniProt
VAR_065450
G
406
S
FA10_HUMAN
Disease (FA10D)
---
A
G
184
S
20
UniProt
VAR_065451
G
420
R
FA10_HUMAN
Disease (FA10D)
---
A
G
196
R
21
UniProt
VAR_072752
G
421
D
FA10_HUMAN
Disease (FA10D)
---
A
G
197
D
22
UniProt
VAR_065452
K
448
N
FA10_HUMAN
Disease (FA10D)
---
A
K
224
N
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(4, 4)
Info
All PROSITE Patterns/Profiles
1: EGF_2 (-|L:109-124)
2: TRYPSIN_DOM (A:16-243)
3: TRYPSIN_HIS (A:53-58)
4: TRYPSIN_SER (A:189-200)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
EGF_2
PS01186
EGF-like domain signature 2.
FA10_HUMAN
110-121
149-164
1
-
L:109-124
2
TRYPSIN_DOM
PS50240
Serine proteases, trypsin domain profile.
FA10_HUMAN
235-467
1
A:16-243
3
TRYPSIN_HIS
PS00134
Serine proteases, trypsin family, histidine active site.
FA10_HUMAN
272-277
1
A:53-58
4
TRYPSIN_SER
PS00135
Serine proteases, trypsin family, serine active site.
FA10_HUMAN
413-424
1
A:189-200
[
close PROSITE info
]
Exons
(4, 5)
Info
All Exons
Exon 1.6c (- | L:87-128)
Exon 1.7a (A:16-30 | L:128-138)
Exon 1.8e (A:31-69 | -)
Exon 1.9c (A:69-244 (gaps) | -)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.5/1.6c
2: Boundary 1.6c/1.7a
3: Boundary 1.7a/1.8e
4: Boundary 1.8e/1.9c
5: Boundary 1.9c/-
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
1.1b
ENST00000375559
1b
ENSE00001885902
chr13:
113777132-113777239
108
FA10_HUMAN
1-24
24
0
-
-
1.2
ENST00000375559
2
ENSE00001757906
chr13:
113783766-113783926
161
FA10_HUMAN
24-77
54
0
-
-
1.4
ENST00000375559
4
ENSE00001666002
chr13:
113792771-113792795
25
FA10_HUMAN
78-86
9
0
-
-
1.5
ENST00000375559
5
ENSE00001614193
chr13:
113793671-113793784
114
FA10_HUMAN
86-124
39
0
-
-
1.6c
ENST00000375559
6c
ENSE00000862532
chr13:
113795233-113795364
132
FA10_HUMAN
124-168
45
1
-
L:87-128
-
42
1.7a
ENST00000375559
7a
ENSE00001710199
chr13:
113798165-113798409
245
FA10_HUMAN
168-249
82
2
A:16-30
L:128-138
15
11
1.8e
ENST00000375559
8e
ENSE00000862534
chr13:
113801693-113801810
118
FA10_HUMAN
250-289
40
1
A:31-69
-
40
-
1.9c
ENST00000375559
9c
ENSE00001616173
chr13:
113803230-113803843
614
FA10_HUMAN
289-488
200
1
A:69-244 (gaps)
-
182
-
[
close EXON info
]
SCOP Domains
(2, 2)
Info
All SCOP Domains
1a: SCOP_d3kqba_ (A:)
2a: SCOP_d3kqbl_ (L:)
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
:
automated matches
(162)
Human (Homo sapiens) [TaxId: 9606]
(132)
1a
d3kqba_
A:
Class
:
Small proteins
(3458)
Fold
:
Knottins (small inhibitors, toxins, lectins)
(761)
Superfamily
:
EGF/Laminin
(347)
Family
:
EGF-type module
(304)
Protein domain
:
automated matches
(66)
Human (Homo sapiens) [TaxId: 9606]
(66)
2a
d3kqbl_
L:
[
close SCOP info
]
CATH Domains
(2, 3)
Info
all CATH domains
1a: CATH_3kqbA01 (A:16-27,A:121-232)
1b: CATH_3kqbA02 (A:28-120,A:233-244)
2a: CATH_3kqbL00 (L:87-138)
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
3kqbA01
A:16-27,A:121-232
1b
3kqbA02
A:28-120,A:233-244
Architecture
:
Ribbon
(789)
Topology
:
Laminin
(270)
Homologous Superfamily
:
Laminin
(263)
Human (Homo sapiens)
(195)
2a
3kqbL00
L:87-138
[
close CATH info
]
Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_Trypsin_3kqbA01 (A:16-238)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Peptidase_PA
(797)
Family
:
Trypsin
(679)
Homo sapiens (Human)
(339)
1a
Trypsin-3kqbA01
A:16-238
[
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]
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Asymmetric Unit 1
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