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1YGC
Biol. Unit 2
Info
Asym.Unit (62 KB)
Biol.Unit 1 (56 KB)
Biol.Unit 2 (110 KB)
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(1)
Title
:
SHORT FACTOR VIIA WITH A SMALL MOLECULE INHIBITOR
Authors
:
A. G. Olivero, C. Eigenbrot, R. Goldsmith, K. Robarge, D. R. Artis, J. Flygare, T. Rawson, C. Refino, S. Bunting, D. Kirchhofer
Date
:
04 Jan 05 (Deposition) - 18 Jan 05 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : H,L
Biol. Unit 1: H,L (1x)
Biol. Unit 2: H,L (2x)
Keywords
:
Inverted Oxy-Anion Hole, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. G. Olivero, C. Eigenbrot, R. Goldsmith, K. Robarge, D. R. Artis, J. Flygare, T. Rawson, D. P. Sutherlin, S. Kadkhodayan, M. Beresini, L. O. Elliott, G. G. Deguzman, D. W. Banner, M. Ultsch, U. Marzec, S. R. Hanson, C. Refino, S. Bunting, D. Kirchhofer
A Selective, Slow Binding Inhibitor Of Factor Viia Binds To A Nonstandard Active Site Conformation And Attenuates Thrombus Formation In Vivo.
J. Biol. Chem. V. 280 9160 2005
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 16)
Info
All Hetero Components
1a: (R)-4-[2-(3-AMINO-BENZENESULFONYLA... (905a)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
3d: SULFATE ION (SO4d)
3e: SULFATE ION (SO4e)
3f: SULFATE ION (SO4f)
3g: SULFATE ION (SO4g)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
905
2
Ligand/Ion
(R)-4-[2-(3-AMINO-BENZENESULFONYLAMINO)-1-(3,5-DIETHOXY-2-FLUOROPHENYL)-2-OXO-ETHYLAMINO]-2-HYDROXY-BENZAMIDINE
2
CA
-1
Ligand/Ion
CALCIUM ION
3
SO4
14
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
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
GLU H:70 , ASP H:72 , GLU H:75 , GLU H:80 , HOH H:454 , HOH H:541
BINDING SITE FOR RESIDUE CA H 300
02
AC2
SOFTWARE
HOH H:438 , HOH H:553
BINDING SITE FOR RESIDUE CA H 538
03
AC3
SOFTWARE
MET H:164 , THR H:165 , ARG H:230 , HOH H:537 , HOH H:612 , HOH H:720 , HOH H:789
BINDING SITE FOR RESIDUE SO4 H 301
04
AC4
SOFTWARE
ARG H:129B , SER L:103 , ASP L:104 , HOH L:447
BINDING SITE FOR RESIDUE SO4 L 302
05
AC5
SOFTWARE
SER H:244 , GLU H:245 , HOH H:562 , HOH L:516
BINDING SITE FOR RESIDUE SO4 H 304
06
AC6
SOFTWARE
SER H:82 , ARG H:83 , ARG H:84 , HIS H:109 , GLN H:110
BINDING SITE FOR RESIDUE SO4 H 308
07
AC7
SOFTWARE
THR H:98 , THR H:99 , PRO H:170I , HOH H:605
BINDING SITE FOR RESIDUE SO4 H 310
08
AC8
SOFTWARE
SER H:170B , GLN H:217 , HIS H:224 , PHE H:225 , VAL H:227 , HOH H:634
BINDING SITE FOR RESIDUE SO4 H 311
09
AC9
SOFTWARE
THR H:115 , ASP H:116 , HIS H:117 , HOH H:621 , TYR L:133
BINDING SITE FOR RESIDUE SO4 H 312
10
BC1
SOFTWARE
HIS H:57 , ASP H:60 , THR H:98 , ASP H:102 , ASP H:189 , SER H:190 , LYS H:192 , SER H:195 , SER H:214 , TRP H:215 , GLY H:216 , GLY H:219 , CYS H:220 , GLY H:226 , HOH H:449 , HOH H:463 , HOH H:536 , HOH H:867 , HOH H:1013
BINDING SITE FOR RESIDUE 905 H 1
[
close Site info
]
SAPs(SNPs)/Variants
(93, 186)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
01: VAR_015138 (G19D, chain H, )
02: VAR_006506 (C42Y, chain H, )
03: VAR_065387 (G44R, chain H, )
04: VAR_014413 (T45N, chain H, )
05: VAR_065388 (S54F, chain H, )
06: VAR_065389 (A55P, chain H, )
07: VAR_065390 (A55T, chain H, )
08: VAR_065391 (C58R, chain H, )
09: VAR_015139 (C58Y, chain H, )
10: VAR_065392 (L64P, chain H, )
11: VAR_015140 (A66T, chain H, )
12: VAR_065393 (D72N, chain H, )
13: VAR_065394 (D77N, chain H, )
14: VAR_006507 (R83W, chain H, )
15: VAR_014410 (C91S, chain L, )
16: VAR_015137 (E94K, chain L, )
17: VAR_013936 (V95D, chain H, )
18: VAR_065378 (G96S, chain L, )
19: VAR_006501 (G97C, chain L, )
20: VAR_006500 (G97S, chain L, )
21: VAR_014411 (G97V, chain L, )
22: VAR_065395 (T98I, chain H, )
23: VAR_006502 (Q100R, chain L, )
24: VAR_065396 (H101Q, chain H, )
25: VAR_014414 (D102H, chain H, )
26: VAR_014415 (D102N, chain H, )
27: VAR_014416 (A104T, chain H, )
28: VAR_006508 (A104V, chain H, )
29: VAR_014417 (R107C, chain H, )
30: VAR_006509 (R107H, chain H, )
31: VAR_065379 (S111F, chain L, )
32: VAR_015141 (V112M, chain H, )
33: VAR_065397 (L114V, chain H, )
34: VAR_065380 (G117R, chain L, )
35: VAR_065398 (L121F, chain H, )
36: VAR_065381 (L121P, chain L, )
37: VAR_065382 (D123N, chain L, )
38: VAR_065399 (L123R, chain H, )
39: VAR_006510 (E125K, chain H, )
40: VAR_065383 (S126F, chain L, )
41: VAR_065400 (R126Q, chain H, )
42: VAR_065384 (P129S, chain L, )
43: VAR_065401 (R134C, chain H, )
44: VAR_065385 (P134L, chain L, )
45: VAR_006503 (P134T, chain L, )
46: VAR_014412 (C135R, chain L, )
47: VAR_006504 (K137E, chain L, )
48: VAR_015142 (V138F, chain H, )
49: VAR_065386 (I138T, chain L, )
50: VAR_065402 (G140S, chain H, )
51: VAR_065403 (W141R, chain H, )
52: VAR_065404 (G142S, chain H, )
53: VAR_065405 (R147C, chain H, )
54: VAR_013122 (A150T, chain H, )
55: VAR_006511 (A152V, chain H, )
56: VAR_006512 (M156I, chain H, )
57: VAR_006513 (M156V, chain H, )
58: VAR_065406 (L158P, chain H, )
59: VAR_065407 (P161H, chain H, )
60: VAR_015143 (P161R, chain H, )
61: VAR_006514 (R162Q, chain H, )
62: VAR_065408 (R162W, chain H, )
63: VAR_018671 (T165S, chain H, )
64: VAR_006515 (C168F, chain H, )
65: VAR_065410 (T177M, chain H, )
66: VAR_065411 (M180T, chain H, )
67: VAR_065412 (M180V, chain H, )
68: VAR_065413 (F181S, chain H, )
69: VAR_014392 (C182G, chain H, )
70: VAR_065415 (D189E, chain H, )
71: VAR_065416 (K192E, chain H, )
72: VAR_006517 (G193E, chain H, )
73: VAR_006516 (G193R, chain H, )
74: VAR_015144 (D194H, chain H, )
75: VAR_065417 (S195N, chain H, )
76: VAR_065418 (H199Q, chain H, )
77: VAR_065419 (H199R, chain H, )
78: VAR_065420 (R204G, chain H, )
79: VAR_006518 (R204Q, chain H, )
80: VAR_065421 (G205C, chain H, )
81: VAR_006519 (T210M, chain H, )
82: VAR_065422 (V213F, chain H, )
83: VAR_065423 (G216A, chain H, )
84: VAR_065424 (G216C, chain H, )
85: VAR_065426 (G223D, chain H, )
86: VAR_014420 (G226E, chain H, )
87: VAR_065427 (Y228F, chain H, )
88: VAR_013123 (E236K, chain H, )
89: VAR_014418 (T129CM, chain H, )
90: VAR_065409 (R170CW, chain H, )
91: VAR_065414 (G184AC, chain H, )
92: VAR_014419 (G184AS, chain H, )
93: VAR_065425 (A221AT, chain H, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_015138
G
216
D
FA7_HUMAN
Disease (FA7D)
---
H
G
19
D
02
UniProt
VAR_006506
C
238
Y
FA7_HUMAN
Disease (FA7D)
---
H
C
42
Y
03
UniProt
VAR_065387
G
240
R
FA7_HUMAN
Disease (FA7D)
---
H
G
44
R
04
UniProt
VAR_014413
T
241
N
FA7_HUMAN
Disease (FA7D)
---
H
T
45
N
05
UniProt
VAR_065388
S
250
F
FA7_HUMAN
Disease (FA7D)
---
H
S
54
F
06
UniProt
VAR_065389
A
251
P
FA7_HUMAN
Disease (FA7D)
---
H
A
55
P
07
UniProt
VAR_065390
A
251
T
FA7_HUMAN
Disease (FA7D)
---
H
A
55
T
08
UniProt
VAR_065391
C
254
R
FA7_HUMAN
Disease (FA7D)
---
H
C
58
R
09
UniProt
VAR_015139
C
254
Y
FA7_HUMAN
Disease (FA7D)
---
H
C
58
Y
10
UniProt
VAR_065392
L
264
P
FA7_HUMAN
Disease (FA7D)
---
H
L
64
P
11
UniProt
VAR_015140
A
266
T
FA7_HUMAN
Disease (FA7D)
---
H
A
66
T
12
UniProt
VAR_065393
D
272
N
FA7_HUMAN
Disease (FA7D)
---
H
D
72
N
13
UniProt
VAR_065394
D
277
N
FA7_HUMAN
Disease (FA7D)
---
H
D
77
N
14
UniProt
VAR_006507
R
283
W
FA7_HUMAN
Disease (FA7D)
---
H
R
83
W
15
UniProt
VAR_014410
C
151
S
FA7_HUMAN
Disease (FA7D)
---
L
C
91
S
16
UniProt
VAR_015137
E
154
K
FA7_HUMAN
Disease (FA7D)
146795869
L
E
94
K
17
UniProt
VAR_013936
V
295
D
FA7_HUMAN
Polymorphism
6045
H
V
95
D
18
UniProt
VAR_065378
G
156
S
FA7_HUMAN
Disease (FA7D)
---
L
G
96
S
19
UniProt
VAR_006501
G
157
C
FA7_HUMAN
Disease (FA7D)
---
L
G
97
C
20
UniProt
VAR_006500
G
157
S
FA7_HUMAN
Disease (FA7D)
---
L
G
97
S
21
UniProt
VAR_014411
G
157
V
FA7_HUMAN
Disease (FA7D)
---
L
G
97
V
22
UniProt
VAR_065395
T
298
I
FA7_HUMAN
Disease (FA7D)
---
H
T
98
I
23
UniProt
VAR_006502
Q
160
R
FA7_HUMAN
Disease (FA7D)
---
L
Q
100
R
24
UniProt
VAR_065396
H
301
Q
FA7_HUMAN
Disease (FA7D)
---
H
H
101
Q
25
UniProt
VAR_014414
D
302
H
FA7_HUMAN
Disease (FA7D)
---
H
D
102
H
26
UniProt
VAR_014415
D
302
N
FA7_HUMAN
Disease (FA7D)
---
H
D
102
N
27
UniProt
VAR_014416
A
304
T
FA7_HUMAN
Disease (FA7D)
---
H
A
104
T
28
UniProt
VAR_006508
A
304
V
FA7_HUMAN
Disease (FA7D)
---
H
A
104
V
29
UniProt
VAR_014417
R
307
C
FA7_HUMAN
Disease (FA7D)
---
H
R
107
C
30
UniProt
VAR_006509
R
307
H
FA7_HUMAN
Disease (FA7D)
---
H
R
107
H
31
UniProt
VAR_065379
S
171
F
FA7_HUMAN
Disease (FA7D)
---
L
S
111
F
32
UniProt
VAR_015141
V
312
M
FA7_HUMAN
Disease (FA7D)
---
H
V
112
M
33
UniProt
VAR_065397
L
314
V
FA7_HUMAN
Disease (FA7D)
---
H
L
114
V
34
UniProt
VAR_065380
G
177
R
FA7_HUMAN
Disease (FA7D)
---
L
G
117
R
35
UniProt
VAR_065398
L
321
F
FA7_HUMAN
Disease (FA7D)
---
H
L
121
F
36
UniProt
VAR_065381
L
181
P
FA7_HUMAN
Disease (FA7D)
---
L
L
121
P
37
UniProt
VAR_065382
D
183
N
FA7_HUMAN
Disease (FA7D)
---
L
D
123
N
38
UniProt
VAR_065399
L
323
R
FA7_HUMAN
Disease (FA7D)
---
H
L
123
R
39
UniProt
VAR_006510
E
325
K
FA7_HUMAN
Disease (FA7D)
---
H
E
125
K
40
UniProt
VAR_065383
S
186
F
FA7_HUMAN
Disease (FA7D)
---
L
S
126
F
41
UniProt
VAR_065400
R
326
Q
FA7_HUMAN
Disease (FA7D)
---
H
R
126
Q
42
UniProt
VAR_065384
P
189
S
FA7_HUMAN
Disease (FA7D)
---
L
P
129
S
43
UniProt
VAR_065401
R
337
C
FA7_HUMAN
Disease (FA7D)
---
H
R
134
C
44
UniProt
VAR_065385
P
194
L
FA7_HUMAN
Disease (FA7D)
---
L
P
134
L
45
UniProt
VAR_006503
P
194
T
FA7_HUMAN
Disease (FA7D)
---
L
P
134
T
46
UniProt
VAR_014412
C
195
R
FA7_HUMAN
Disease (FA7D)
---
L
C
135
R
47
UniProt
VAR_006504
K
197
E
FA7_HUMAN
Disease (FA7D)
---
L
K
137
E
48
UniProt
VAR_015142
V
341
F
FA7_HUMAN
Disease (FA7D)
---
H
V
138
F
49
UniProt
VAR_065386
I
198
T
FA7_HUMAN
Disease (FA7D)
---
L
I
138
T
50
UniProt
VAR_065402
G
343
S
FA7_HUMAN
Disease (FA7D)
---
H
G
140
S
51
UniProt
VAR_065403
W
344
R
FA7_HUMAN
Disease (FA7D)
---
H
W
141
R
52
UniProt
VAR_065404
G
345
S
FA7_HUMAN
Disease (FA7D)
---
H
G
142
S
53
UniProt
VAR_065405
R
350
C
FA7_HUMAN
Disease (FA7D)
---
H
R
147
C
54
UniProt
VAR_013122
A
352
T
FA7_HUMAN
Polymorphism
3093267
H
A
150
T
55
UniProt
VAR_006511
A
354
V
FA7_HUMAN
Disease (FA7D)
36209567
H
A
152
V
56
UniProt
VAR_006512
M
358
I
FA7_HUMAN
Disease (FA7D)
---
H
M
156
I
57
UniProt
VAR_006513
M
358
V
FA7_HUMAN
Disease (FA7D)
---
H
M
156
V
58
UniProt
VAR_065406
L
360
P
FA7_HUMAN
Disease (FA7D)
---
H
L
158
P
59
UniProt
VAR_065407
P
363
H
FA7_HUMAN
Disease (FA7D)
---
H
P
161
H
60
UniProt
VAR_015143
P
363
R
FA7_HUMAN
Disease (FA7D)
---
H
P
161
R
61
UniProt
VAR_006514
R
364
Q
FA7_HUMAN
Disease (FA7D)
121964926
H
R
162
Q
62
UniProt
VAR_065408
R
364
W
FA7_HUMAN
Disease (FA7D)
---
H
R
162
W
63
UniProt
VAR_018671
T
367
S
FA7_HUMAN
Polymorphism
---
H
T
165
S
64
UniProt
VAR_006515
C
370
F
FA7_HUMAN
Disease (FA7D)
---
H
C
168
F
65
UniProt
VAR_065410
T
384
M
FA7_HUMAN
Disease (FA7D)
---
H
T
177
M
66
UniProt
VAR_065411
M
387
T
FA7_HUMAN
Disease (FA7D)
---
H
M
180
T
67
UniProt
VAR_065412
M
387
V
FA7_HUMAN
Disease (FA7D)
---
H
M
180
V
68
UniProt
VAR_065413
F
388
S
FA7_HUMAN
Disease (FA7D)
---
H
F
181
S
69
UniProt
VAR_014392
C
389
G
FA7_HUMAN
Disease (FA7D)
---
H
C
182
G
70
UniProt
VAR_065415
D
398
E
FA7_HUMAN
Disease (FA7D)
---
H
D
189
E
71
UniProt
VAR_065416
K
401
E
FA7_HUMAN
Disease (FA7D)
---
H
K
192
E
72
UniProt
VAR_006517
G
402
E
FA7_HUMAN
Disease (FA7D)
---
H
G
193
E
73
UniProt
VAR_006516
G
402
R
FA7_HUMAN
Disease (FA7D)
---
H
G
193
R
74
UniProt
VAR_015144
D
403
H
FA7_HUMAN
Disease (FA7D)
---
H
D
194
H
75
UniProt
VAR_065417
S
404
N
FA7_HUMAN
Disease (FA7D)
---
H
S
195
N
76
UniProt
VAR_065418
H
408
Q
FA7_HUMAN
Disease (FA7D)
121964936
H
H
199
Q
77
UniProt
VAR_065419
H
408
R
FA7_HUMAN
Disease (FA7D)
---
H
H
199
R
78
UniProt
VAR_065420
R
413
G
FA7_HUMAN
Disease (FA7D)
---
H
R
204
G
79
UniProt
VAR_006518
R
413
Q
FA7_HUMAN
Polymorphism
6046
H
R
204
Q
80
UniProt
VAR_065421
G
414
C
FA7_HUMAN
Disease (FA7D)
---
H
G
205
C
81
UniProt
VAR_006519
T
419
M
FA7_HUMAN
Disease (FA7D)
---
H
T
210
M
82
UniProt
VAR_065422
V
422
F
FA7_HUMAN
Disease (FA7D)
---
H
V
213
F
83
UniProt
VAR_065423
G
425
A
FA7_HUMAN
Disease (FA7D)
---
H
G
216
A
84
UniProt
VAR_065424
G
425
C
FA7_HUMAN
Disease (FA7D)
---
H
G
216
C
85
UniProt
VAR_065426
G
432
D
FA7_HUMAN
Disease (FA7D)
---
H
G
223
D
86
UniProt
VAR_014420
G
435
E
FA7_HUMAN
Disease (FA7D)
---
H
G
226
E
87
UniProt
VAR_065427
Y
437
F
FA7_HUMAN
Disease (FA7D)
---
H
Y
228
F
88
UniProt
VAR_013123
E
445
K
FA7_HUMAN
Polymorphism
3093248
H
E
236
K
89
UniProt
VAR_014418
T
332
M
FA7_HUMAN
Disease (FA7D)
---
H
T
129C
M
90
UniProt
VAR_065409
R
375
W
FA7_HUMAN
Disease (FA7D)
137919286
H
R
170C
W
91
UniProt
VAR_065414
G
391
C
FA7_HUMAN
Disease (FA7D)
---
H
G
184A
C
92
UniProt
VAR_014419
G
391
S
FA7_HUMAN
Disease (FA7D)
190485816
H
G
184A
S
93
UniProt
VAR_065425
A
429
T
FA7_HUMAN
Disease (FA7D)
---
H
A
221A
T
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(4, 8)
Info
All PROSITE Patterns/Profiles
1: EGF_2 (L:112-127)
2: TRYPSIN_DOM (H:16-243)
3: TRYPSIN_HIS (H:53-58)
4: TRYPSIN_SER (H:189-200)
;
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PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
EGF_2
PS01186
EGF-like domain signature 2.
FA7_HUMAN
172-187
2
L:112-127
2
TRYPSIN_DOM
PS50240
Serine proteases, trypsin domain profile.
FA7_HUMAN
213-452
2
H:16-243
3
TRYPSIN_HIS
PS00134
Serine proteases, trypsin family, histidine active site.
FA7_HUMAN
249-254
2
H:53-58
4
TRYPSIN_SER
PS00135
Serine proteases, trypsin family, serine active site.
FA7_HUMAN
398-409
2
H:189-200
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Exons
(0, 0)
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SCOP Domains
(2, 2)
Info
All SCOP Domains
1a: SCOP_d1ygch_ (H:)
2a: SCOP_d1ygcl_ (L:)
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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 VIIa
(39)
Human (Homo sapiens) [TaxId: 9606]
(39)
1a
d1ygch_
H:
Class
:
Small proteins
(3458)
Fold
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Knottins (small inhibitors, toxins, lectins)
(761)
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:
EGF/Laminin
(347)
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:
EGF-type module
(304)
Protein domain
:
Coagulation factor VIIa
(45)
Human (Homo sapiens) [TaxId: 9606]
(45)
2a
d1ygcl_
L:
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CATH Domains
(2, 3)
Info
all CATH domains
1a: CATH_1ygcH01 (H:16-27,H:121-232)
1b: CATH_1ygcH02 (H:28-120,H:233-246)
2a: CATH_1ygcL00 (L:90-142)
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)
Organisms
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)
(
)
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
1ygcH01
H:16-27,H:121-232
1b
1ygcH02
H:28-120,H:233-246
Architecture
:
Ribbon
(789)
Topology
:
Laminin
(270)
Homologous Superfamily
:
Laminin
(263)
Human (Homo sapiens)
(195)
2a
1ygcL00
L:90-142
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Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_Trypsin_1ygcH01 (H:16-238)
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Peptidase_PA
(797)
Family
:
Trypsin
(679)
Homo sapiens (Human)
(339)
1a
Trypsin-1ygcH01
H:16-238
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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