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1XKB
Asym. Unit
Info
Asym.Unit (117 KB)
Biol.Unit 1 (58 KB)
Biol.Unit 2 (57 KB)
Biol.Unit 3 (112 KB)
Biol.Unit 4 (111 KB)
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(1)
Title
:
FACTOR XA COMPLEXED WITH A SYNTHETIC INHIBITOR FX-2212A,(2S)-(3'-AMIDINO-3-BIPHENYLYL)-5-(4-PYRIDYLAMINO)PENTANOIC ACID
Authors
:
K. Kamata, S. H. Kim
Date
:
19 Mar 98 (Deposition) - 23 Mar 99 (Release) - 20 Jun 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,C (1x)
Biol. Unit 2: B,D (1x)
Biol. Unit 3: A,B,C,D (1x)
Biol. Unit 4: A,B,C,D (1x)
Keywords
:
Blood Coagulation Factor, Serine Proteinase, Epidermal Growth Factor Like Domain
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. Kamata, H. Kawamoto, T. Honma, T. Iwama, S. H. Kim
Structural Basis For Chemical Inhibition Of Human Blood Coagulation Factor Xa.
Proc. Natl. Acad. Sci. Usa V. 95 6630 1998
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 7)
Info
All Hetero Components
1a: (2S)-(3'-AMIDINO-3-BIPHENYL)-5-(4-... (4PPa)
1b: (2S)-(3'-AMIDINO-3-BIPHENYL)-5-(4-... (4PPb)
2a: (3S)-3-HYDROXY-L-ASPARTIC ACID (BHDa)
2b: (3S)-3-HYDROXY-L-ASPARTIC ACID (BHDb)
3a: CALCIUM ION (CAa)
3b: CALCIUM ION (CAb)
3c: CALCIUM ION (CAc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
4PP
2
Ligand/Ion
(2S)-(3'-AMIDINO-3-BIPHENYL)-5-(4-PYRIDYLAMINO)PENTANOIC ACID
2
BHD
2
Mod. Amino Acid
(3S)-3-HYDROXY-L-ASPARTIC ACID
3
CA
3
Ligand/Ion
CALCIUM ION
[
close Hetero Component info
]
Sites
(5, 5)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLN A:49 , BHD A:63 , GLY A:64 , LEU A:65 , GLY A:66
BINDING SITE FOR RESIDUE CA A 501
2
AC2
SOFTWARE
ASP D:70 , ASN D:72 , GLN D:75 , GLU D:77 , GLU D:80
BINDING SITE FOR RESIDUE CA D 502
3
AC3
SOFTWARE
ASP C:70 , ASN C:72 , GLN C:75 , GLU C:76 , GLU C:77 , GLU C:80
BINDING SITE FOR RESIDUE CA C 503
4
AC4
SOFTWARE
GLU C:97 , THR C:98 , TYR C:99 , PHE C:174 , ASP C:189 , ALA C:190 , CYS C:191 , GLN C:192 , SER C:195 , VAL C:213 , GLY C:216 , GLY C:218 , GLY C:226 , HOH C:558 , HOH C:561 , HOH C:790 , HOH C:794
BINDING SITE FOR RESIDUE 4PP C 998
5
AC5
SOFTWARE
GLU D:97 , THR D:98 , TYR D:99 , PHE D:174 , ASP D:189 , ALA D:190 , CYS D:191 , GLN D:192 , SER D:195 , VAL D:213 , TRP D:215 , GLY D:216 , GLY D:218 , GLY D:226 , HOH D:647 , HOH D:650 , HOH D:670 , HOH D:672
BINDING SITE FOR RESIDUE 4PP D 999
[
close Site info
]
SAPs(SNPs)/Variants
(23, 46)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_065433 (E51K, chain A/B, )
02: VAR_065437 (G69R, chain C/D, )
03: VAR_065438 (E84K, chain C/D, )
04: VAR_065434 (E102K, chain A/B, )
05: VAR_065439 (D102N, chain C/D, )
06: VAR_065440 (R107W, chain C/D, )
07: VAR_065435 (C109Y, chain A/B, )
08: VAR_065436 (C111Y, chain A/B, )
09: VAR_020176 (A112T, chain A/B, )
10: VAR_065441 (V118M, chain C/D, )
11: VAR_065442 (E129K, chain C/D, )
12: VAR_065443 (T135M, chain C/D, )
13: VAR_065444 (G140S, chain C/D, )
14: VAR_065445 (R143C, chain C/D, )
15: VAR_065446 (S152P, chain C/D, )
16: VAR_072751 (V160A, chain C/D, )
17: VAR_065447 (P161S, chain C/D, )
18: VAR_065448 (C168F, chain C/D, )
19: VAR_065449 (C182R, chain C/D, )
20: VAR_065450 (G184S, chain C/D, )
21: VAR_065451 (G196R, chain C/D, )
22: VAR_072752 (G197D, chain C/D, )
23: VAR_065452 (K224N, chain C/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_065433
E
91
K
FA10_HUMAN
Disease (FA10D)
---
A/B
E
51
K
02
UniProt
VAR_065437
G
289
R
FA10_HUMAN
Disease (FA10D)
---
C/D
G
69
R
03
UniProt
VAR_065438
E
304
K
FA10_HUMAN
Disease (FA10D)
---
C/D
E
84
K
04
UniProt
VAR_065434
E
142
K
FA10_HUMAN
Unclassified
61753266
A/B
E
102
K
05
UniProt
VAR_065439
D
322
N
FA10_HUMAN
Disease (FA10D)
---
C/D
D
102
N
06
UniProt
VAR_065440
R
327
W
FA10_HUMAN
Disease (FA10D)
---
C/D
R
107
W
07
UniProt
VAR_065435
C
149
Y
FA10_HUMAN
Disease (FA10D)
---
A/B
C
109
Y
08
UniProt
VAR_065436
C
151
Y
FA10_HUMAN
Disease (FA10D)
---
A/B
C
111
Y
09
UniProt
VAR_020176
A
152
T
FA10_HUMAN
Polymorphism
3211772
A/B
A
112
T
10
UniProt
VAR_065441
V
338
M
FA10_HUMAN
Disease (FA10D)
---
C/D
V
118
M
11
UniProt
VAR_065442
E
350
K
FA10_HUMAN
Disease (FA10D)
---
C/D
E
129
K
12
UniProt
VAR_065443
T
358
M
FA10_HUMAN
Disease (FA10D)
---
C/D
T
135
M
13
UniProt
VAR_065444
G
363
S
FA10_HUMAN
Disease (FA10D)
---
C/D
G
140
S
14
UniProt
VAR_065445
R
366
C
FA10_HUMAN
Disease (FA10D)
---
C/D
R
143
C
15
UniProt
VAR_065446
S
374
P
FA10_HUMAN
Disease (FA10D)
---
C/D
S
152
P
16
UniProt
VAR_072751
V
382
A
FA10_HUMAN
Disease (FA10D)
---
C/D
V
160
A
17
UniProt
VAR_065447
P
383
S
FA10_HUMAN
Disease (FA10D)
---
C/D
P
161
S
18
UniProt
VAR_065448
C
390
F
FA10_HUMAN
Disease (FA10D)
199778916
C/D
C
168
F
19
UniProt
VAR_065449
C
404
R
FA10_HUMAN
Disease (FA10D)
---
C/D
C
182
R
20
UniProt
VAR_065450
G
406
S
FA10_HUMAN
Disease (FA10D)
---
C/D
G
184
S
21
UniProt
VAR_065451
G
420
R
FA10_HUMAN
Disease (FA10D)
---
C/D
G
196
R
22
UniProt
VAR_072752
G
421
D
FA10_HUMAN
Disease (FA10D)
---
C/D
G
197
D
23
UniProt
VAR_065452
K
448
N
FA10_HUMAN
Disease (FA10D)
---
C/D
K
224
N
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(6, 12)
Info
All PROSITE Patterns/Profiles
1: ASX_HYDROXYL (A:61-72,B:61-72)
2: EGF_1 (A:70-81,B:70-81)
3: EGF_2 (A:70-81,B:70-81|A:109-124,B:109-12...)
4: TRYPSIN_DOM (C:16-243,D:16-243)
5: TRYPSIN_HIS (C:53-58,D:53-58)
6: TRYPSIN_SER (C:189-200,D:189-200)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ASX_HYDROXYL
PS00010
Aspartic acid and asparagine hydroxylation site.
FA10_HUMAN
101-112
2
A:61-72
B:61-72
2
EGF_1
PS00022
EGF-like domain signature 1.
FA10_HUMAN
110-121
2
A:70-81
B:70-81
3
EGF_2
PS01186
EGF-like domain signature 2.
FA10_HUMAN
110-121
149-164
4
A:70-81
B:70-81
A:109-124
B:109-124
4
TRYPSIN_DOM
PS50240
Serine proteases, trypsin domain profile.
FA10_HUMAN
235-467
2
C:16-243
D:16-243
5
TRYPSIN_HIS
PS00134
Serine proteases, trypsin family, histidine active site.
FA10_HUMAN
272-277
2
C:53-58
D:53-58
6
TRYPSIN_SER
PS00135
Serine proteases, trypsin family, serine active site.
FA10_HUMAN
413-424
2
C:189-200
D:189-200
[
close PROSITE info
]
Exons
(5, 12)
Info
All Exons
Exon 1.5 (A:48-84 | B:50-84 | - | -)
Exon 1.6c (A:84-128 | B:84-128 | - | -)
Exon 1.7a (A:128-138 | B:128-139 | C:16-30 | ...)
Exon 1.8e (- | - | C:31-69 | D:31-69)
Exon 1.9c (- | - | C:69-245 (gaps) | D:69-244...)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.4/1.5
2: Boundary 1.5/1.6c
3: Boundary 1.6c/1.7a
4: Boundary 1.7a/1.8e
5: Boundary 1.8e/1.9c
6: 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
2
A:48-84
B:50-84
-
-
37
35
-
-
1.6c
ENST00000375559
6c
ENSE00000862532
chr13:
113795233-113795364
132
FA10_HUMAN
124-168
45
2
A:84-128
B:84-128
-
-
45
45
-
-
1.7a
ENST00000375559
7a
ENSE00001710199
chr13:
113798165-113798409
245
FA10_HUMAN
168-249
82
4
A:128-138
B:128-139
C:16-30
D:16-30
11
12
15
15
1.8e
ENST00000375559
8e
ENSE00000862534
chr13:
113801693-113801810
118
FA10_HUMAN
250-289
40
2
-
-
C:31-69
D:31-69
-
-
40
40
1.9c
ENST00000375559
9c
ENSE00001616173
chr13:
113803230-113803843
614
FA10_HUMAN
289-488
200
2
-
-
C:69-245 (gaps)
D:69-244 (gaps)
-
-
183
182
[
close EXON info
]
SCOP Domains
(2, 6)
Info
All SCOP Domains
1a: SCOP_d1xkbc_ (C:)
1b: SCOP_d1xkbd_ (D:)
2a: SCOP_d1xkba1 (A:48-86)
2b: SCOP_d1xkba2 (A:87-138)
2c: SCOP_d1xkbb1 (B:50-86)
2d: SCOP_d1xkbb2 (B:87-139)
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(
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Organisms
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(
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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 Xa, protease domain
(48)
Human (Homo sapiens) [TaxId: 9606]
(47)
1a
d1xkbc_
C:
1b
d1xkbd_
D:
Class
:
Small proteins
(3458)
Fold
:
Knottins (small inhibitors, toxins, lectins)
(761)
Superfamily
:
EGF/Laminin
(347)
Family
:
EGF-type module
(304)
Protein domain
:
Factor X, N-terminal module
(81)
Human (Homo sapiens) [TaxId: 9606]
(76)
2a
d1xkba1
A:48-86
2b
d1xkba2
A:87-138
2c
d1xkbb1
B:50-86
2d
d1xkbb2
B:87-139
[
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CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1xkbC01 (C:16-27,C:121-232)
1b: CATH_1xkbC02 (C:28-120,C:233-245)
1c: CATH_1xkbD02 (D:28-120,D:233-244)
1d: CATH_1xkbD01 (D:16-27,D:121-232)
2a: CATH_1xkbA02 (A:87-135)
2b: CATH_1xkbB02 (B:87-135)
2c: CATH_1xkbA01 (A:48-86)
2d: CATH_1xkbB01 (B:50-86)
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)
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
1xkbC01
C:16-27,C:121-232
1b
1xkbC02
C:28-120,C:233-245
1c
1xkbD02
D:28-120,D:233-244
1d
1xkbD01
D:16-27,D:121-232
Architecture
:
Ribbon
(789)
Topology
:
Laminin
(270)
Homologous Superfamily
:
Laminin
(263)
Human (Homo sapiens)
(195)
2a
1xkbA02
A:87-135
2b
1xkbB02
B:87-135
2c
1xkbA01
A:48-86
2d
1xkbB01
B:50-86
[
close CATH info
]
Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_EGF_1xkbB01 (B:50-80)
1b: PFAM_EGF_1xkbB02 (B:50-80)
2a: PFAM_Trypsin_1xkbD01 (D:16-238)
2b: PFAM_Trypsin_1xkbD02 (D:16-238)
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Clan
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EGF
(60)
Family
:
EGF
(31)
Homo sapiens (Human)
(25)
1a
EGF-1xkbB01
B:50-80
1b
EGF-1xkbB02
B:50-80
Clan
:
Peptidase_PA
(797)
Family
:
Trypsin
(679)
Homo sapiens (Human)
(339)
2a
Trypsin-1xkbD01
D:16-238
2b
Trypsin-1xkbD02
D:16-238
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