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3TH3
Biol. Unit 1
Info
Asym.Unit (90 KB)
Biol.Unit 1 (84 KB)
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(1)
Title
:
MG2+ IS REQUIRED FOR OPTIMAL FOLDING OF THE GAMMA-CARBOXYGLUTAMIC ACID (GLA) DOMAINS OF VITAMIN K-DEPENDENT CLOTTING FACTORS AT PHYSIOLOGICAL CA2+
Authors
:
K. Vadivel, S. Agah, D. Cascio, K. Padmanabhan, S. P. Bajaj
Date
:
18 Aug 11 (Deposition) - 22 Aug 12 (Release) - 22 Aug 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.70
Chains
:
Asym. Unit : H,L,T
Biol. Unit 1: H,T (1x)
Keywords
:
Hydrolase, Blood Clotting, Serine Protease, Blood Coagulation, Soluble Tissue Factor, Hydrolase-Hydrolase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. Vadivel, Sayeh Agah, A. Messer, D. Cascio, M. S. Bajaj, S. Krishnaswamy, C. T. Esmon, K. Padmanabhan, S. P. Bajaj
Mg2+ Is Required For Optimal Folding Of The Gamma-Carboxyglutamic Acid (Gla) Domains Of Vitamin K-Dependent Clotting Factors At Physiological Ca2+
To Be Published
[
close entry info
]
Hetero Components
(3, 3)
Info
All Hetero Components
1a: N-{[5-(DIMETHYLAMINO)NAPHTHALEN-1-... (0GEa)
2a: BETA-D-GLUCOSE (BGCa)
3a: CALCIUM ION (CAa)
3b: CALCIUM ION (CAb)
4a: CHLORIDE ION (CLa)
5a: ALPHA-L-FUCOSE (FUCa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
0GE
1
Ligand/Ion
N-{[5-(DIMETHYLAMINO)NAPHTHALEN-1-YL]SULFONYL}-L-ALPHA-GLUTAMYL-N-[(2S,3S)-6-CARBAMIMIDAMIDO-1-CHLORO-2-HYDROXYHEXAN-3-YL]GLYCINAMIDE
2
BGC
1
Ligand/Ion
BETA-D-GLUCOSE
3
CA
-1
Ligand/Ion
CALCIUM ION
4
CL
-1
Ligand/Ion
CHLORIDE ION
5
FUC
1
Ligand/Ion
ALPHA-L-FUCOSE
[
close Hetero Component info
]
Sites
(4, 4)
Info
All Sites
1: AC2 (SOFTWARE)
2: AC4 (SOFTWARE)
3: AC5 (SOFTWARE)
4: AC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC2
SOFTWARE
SER L:60 , LEU L:73 , ARG T:131 , PHE T:140
BINDING SITE FOR RESIDUE FUC L 144
2
AC4
SOFTWARE
HIS H:57 , ASP H:189 , SER H:190 , CYS H:191 , LYS H:192 , SER H:195 , SER H:214 , TRP H:215 , GLY H:216 , GLN H:217 , GLY H:219 , HOH H:275
BINDING SITE FOR RESIDUE 0GE H 1
3
AC5
SOFTWARE
GLU H:70 , ASP H:72 , GLU H:75 , HIS H:76 , GLU H:80 , HOH H:295 , HOH H:296
BINDING SITE FOR RESIDUE CA H 258
4
AC6
SOFTWARE
ARG H:84 , HIS H:109
BINDING SITE FOR RESIDUE CL H 3
[
close Site info
]
SAPs(SNPs)/Variants
(76, 76)
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_013936 (V95D, chain H, )
16: VAR_065395 (T98I, chain H, )
17: VAR_065396 (H101Q, chain H, )
18: VAR_014414 (D102H, chain H, )
19: VAR_014415 (D102N, chain H, )
20: VAR_014416 (A104T, chain H, )
21: VAR_006508 (A104V, chain H, )
22: VAR_014417 (R107C, chain H, )
23: VAR_006509 (R107H, chain H, )
24: VAR_015141 (V112M, chain H, )
25: VAR_065397 (L114V, chain H, )
26: VAR_065398 (L121F, chain H, )
27: VAR_065399 (L123R, chain H, )
28: VAR_006510 (E125K, chain H, )
29: VAR_065400 (R126Q, chain H, )
30: VAR_012008 (R131W, chain T, )
31: VAR_065401 (R134C, chain H, )
32: VAR_015142 (V138F, chain H, )
33: VAR_065402 (G140S, chain H, )
34: VAR_065403 (W141R, chain H, )
35: VAR_065404 (G142S, chain H, )
36: VAR_065405 (R147C, chain H, )
37: VAR_013122 (A150T, chain H, )
38: VAR_006511 (A152V, chain H, )
39: VAR_006512 (M156I, chain H, )
40: VAR_006513 (M156V, chain H, )
41: VAR_065406 (L158P, chain H, )
42: VAR_065407 (P161H, chain H, )
43: VAR_015143 (P161R, chain H, )
44: VAR_006514 (R162Q, chain H, )
45: VAR_065408 (R162W, chain H, )
46: VAR_018671 (T165S, chain H, )
47: VAR_006515 (C168F, chain H, )
48: VAR_065410 (T177M, chain H, )
49: VAR_065411 (M180T, chain H, )
50: VAR_065412 (M180V, chain H, )
51: VAR_065413 (F181S, chain H, )
52: VAR_014392 (C182G, chain H, )
53: VAR_065415 (D189E, chain H, )
54: VAR_065416 (K192E, chain H, )
55: VAR_006517 (G193E, chain H, )
56: VAR_006516 (G193R, chain H, )
57: VAR_015144 (D194H, chain H, )
58: VAR_065417 (S195N, chain H, )
59: VAR_065418 (H199Q, chain H, )
60: VAR_065419 (H199R, chain H, )
61: VAR_065420 (R204G, chain H, )
62: VAR_006518 (R204Q, chain H, )
63: VAR_065421 (G205C, chain H, )
64: VAR_006519 (T210M, chain H, )
65: VAR_065422 (V213F, chain H, )
66: VAR_065423 (G216A, chain H, )
67: VAR_065424 (G216C, chain H, )
68: VAR_065426 (G223D, chain H, )
69: VAR_014420 (G226E, chain H, )
70: VAR_065427 (Y228F, chain H, )
71: VAR_013123 (E236K, chain H, )
72: VAR_014418 (T129CM, chain H, )
73: VAR_065409 (R170CW, chain H, )
74: VAR_065414 (G184AC, chain H, )
75: VAR_014419 (G184AS, chain H, )
76: VAR_065425 (A221AT, chain H, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
001
UniProt
VAR_015138
G
216
D
FA7_HUMAN
Disease (FA7D)
---
H
G
19
D
002
UniProt
VAR_006506
C
238
Y
FA7_HUMAN
Disease (FA7D)
---
H
C
42
Y
003
UniProt
VAR_065387
G
240
R
FA7_HUMAN
Disease (FA7D)
---
H
G
44
R
004
UniProt
VAR_014413
T
241
N
FA7_HUMAN
Disease (FA7D)
---
H
T
45
N
005
UniProt
VAR_065388
S
250
F
FA7_HUMAN
Disease (FA7D)
---
H
S
54
F
006
UniProt
VAR_065389
A
251
P
FA7_HUMAN
Disease (FA7D)
---
H
A
55
P
007
UniProt
VAR_065390
A
251
T
FA7_HUMAN
Disease (FA7D)
---
H
A
55
T
009
UniProt
VAR_065391
C
254
R
FA7_HUMAN
Disease (FA7D)
---
H
C
58
R
010
UniProt
VAR_015139
C
254
Y
FA7_HUMAN
Disease (FA7D)
---
H
C
58
Y
013
UniProt
VAR_065392
L
264
P
FA7_HUMAN
Disease (FA7D)
---
H
L
64
P
015
UniProt
VAR_015140
A
266
T
FA7_HUMAN
Disease (FA7D)
---
H
A
66
T
017
UniProt
VAR_065393
D
272
N
FA7_HUMAN
Disease (FA7D)
---
H
D
72
N
018
UniProt
VAR_065394
D
277
N
FA7_HUMAN
Disease (FA7D)
---
H
D
77
N
023
UniProt
VAR_006507
R
283
W
FA7_HUMAN
Disease (FA7D)
---
H
R
83
W
026
UniProt
VAR_013936
V
295
D
FA7_HUMAN
Polymorphism
6045
H
V
95
D
031
UniProt
VAR_065395
T
298
I
FA7_HUMAN
Disease (FA7D)
---
H
T
98
I
033
UniProt
VAR_065396
H
301
Q
FA7_HUMAN
Disease (FA7D)
---
H
H
101
Q
034
UniProt
VAR_014414
D
302
H
FA7_HUMAN
Disease (FA7D)
---
H
D
102
H
035
UniProt
VAR_014415
D
302
N
FA7_HUMAN
Disease (FA7D)
---
H
D
102
N
036
UniProt
VAR_014416
A
304
T
FA7_HUMAN
Disease (FA7D)
---
H
A
104
T
037
UniProt
VAR_006508
A
304
V
FA7_HUMAN
Disease (FA7D)
---
H
A
104
V
038
UniProt
VAR_014417
R
307
C
FA7_HUMAN
Disease (FA7D)
---
H
R
107
C
039
UniProt
VAR_006509
R
307
H
FA7_HUMAN
Disease (FA7D)
---
H
R
107
H
041
UniProt
VAR_015141
V
312
M
FA7_HUMAN
Disease (FA7D)
---
H
V
112
M
042
UniProt
VAR_065397
L
314
V
FA7_HUMAN
Disease (FA7D)
---
H
L
114
V
044
UniProt
VAR_065398
L
321
F
FA7_HUMAN
Disease (FA7D)
---
H
L
121
F
047
UniProt
VAR_065399
L
323
R
FA7_HUMAN
Disease (FA7D)
---
H
L
123
R
048
UniProt
VAR_006510
E
325
K
FA7_HUMAN
Disease (FA7D)
---
H
E
125
K
050
UniProt
VAR_065400
R
326
Q
FA7_HUMAN
Disease (FA7D)
---
H
R
126
Q
052
UniProt
VAR_012008
R
163
W
TF_HUMAN
Polymorphism
5901
T
R
131
W
053
UniProt
VAR_065401
R
337
C
FA7_HUMAN
Disease (FA7D)
---
H
R
134
C
058
UniProt
VAR_015142
V
341
F
FA7_HUMAN
Disease (FA7D)
---
H
V
138
F
060
UniProt
VAR_065402
G
343
S
FA7_HUMAN
Disease (FA7D)
---
H
G
140
S
061
UniProt
VAR_065403
W
344
R
FA7_HUMAN
Disease (FA7D)
---
H
W
141
R
062
UniProt
VAR_065404
G
345
S
FA7_HUMAN
Disease (FA7D)
---
H
G
142
S
063
UniProt
VAR_065405
R
350
C
FA7_HUMAN
Disease (FA7D)
---
H
R
147
C
064
UniProt
VAR_013122
A
352
T
FA7_HUMAN
Polymorphism
3093267
H
A
150
T
065
UniProt
VAR_006511
A
354
V
FA7_HUMAN
Disease (FA7D)
36209567
H
A
152
V
066
UniProt
VAR_006512
M
358
I
FA7_HUMAN
Disease (FA7D)
---
H
M
156
I
067
UniProt
VAR_006513
M
358
V
FA7_HUMAN
Disease (FA7D)
---
H
M
156
V
068
UniProt
VAR_065406
L
360
P
FA7_HUMAN
Disease (FA7D)
---
H
L
158
P
069
UniProt
VAR_065407
P
363
H
FA7_HUMAN
Disease (FA7D)
---
H
P
161
H
070
UniProt
VAR_015143
P
363
R
FA7_HUMAN
Disease (FA7D)
---
H
P
161
R
071
UniProt
VAR_006514
R
364
Q
FA7_HUMAN
Disease (FA7D)
121964926
H
R
162
Q
072
UniProt
VAR_065408
R
364
W
FA7_HUMAN
Disease (FA7D)
---
H
R
162
W
073
UniProt
VAR_018671
T
367
S
FA7_HUMAN
Polymorphism
---
H
T
165
S
074
UniProt
VAR_006515
C
370
F
FA7_HUMAN
Disease (FA7D)
---
H
C
168
F
075
UniProt
VAR_065410
T
384
M
FA7_HUMAN
Disease (FA7D)
---
H
T
177
M
076
UniProt
VAR_065411
M
387
T
FA7_HUMAN
Disease (FA7D)
---
H
M
180
T
077
UniProt
VAR_065412
M
387
V
FA7_HUMAN
Disease (FA7D)
---
H
M
180
V
078
UniProt
VAR_065413
F
388
S
FA7_HUMAN
Disease (FA7D)
---
H
F
181
S
079
UniProt
VAR_014392
C
389
G
FA7_HUMAN
Disease (FA7D)
---
H
C
182
G
080
UniProt
VAR_065415
D
398
E
FA7_HUMAN
Disease (FA7D)
---
H
D
189
E
081
UniProt
VAR_065416
K
401
E
FA7_HUMAN
Disease (FA7D)
---
H
K
192
E
082
UniProt
VAR_006517
G
402
E
FA7_HUMAN
Disease (FA7D)
---
H
G
193
E
083
UniProt
VAR_006516
G
402
R
FA7_HUMAN
Disease (FA7D)
---
H
G
193
R
084
UniProt
VAR_015144
D
403
H
FA7_HUMAN
Disease (FA7D)
---
H
D
194
H
085
UniProt
VAR_065417
S
404
N
FA7_HUMAN
Disease (FA7D)
---
H
S
195
N
086
UniProt
VAR_065418
H
408
Q
FA7_HUMAN
Disease (FA7D)
121964936
H
H
199
Q
087
UniProt
VAR_065419
H
408
R
FA7_HUMAN
Disease (FA7D)
---
H
H
199
R
088
UniProt
VAR_065420
R
413
G
FA7_HUMAN
Disease (FA7D)
---
H
R
204
G
089
UniProt
VAR_006518
R
413
Q
FA7_HUMAN
Polymorphism
6046
H
R
204
Q
090
UniProt
VAR_065421
G
414
C
FA7_HUMAN
Disease (FA7D)
---
H
G
205
C
091
UniProt
VAR_006519
T
419
M
FA7_HUMAN
Disease (FA7D)
---
H
T
210
M
092
UniProt
VAR_065422
V
422
F
FA7_HUMAN
Disease (FA7D)
---
H
V
213
F
093
UniProt
VAR_065423
G
425
A
FA7_HUMAN
Disease (FA7D)
---
H
G
216
A
094
UniProt
VAR_065424
G
425
C
FA7_HUMAN
Disease (FA7D)
---
H
G
216
C
095
UniProt
VAR_065426
G
432
D
FA7_HUMAN
Disease (FA7D)
---
H
G
223
D
096
UniProt
VAR_014420
G
435
E
FA7_HUMAN
Disease (FA7D)
---
H
G
226
E
097
UniProt
VAR_065427
Y
437
F
FA7_HUMAN
Disease (FA7D)
---
H
Y
228
F
098
UniProt
VAR_013123
E
445
K
FA7_HUMAN
Polymorphism
3093248
H
E
236
K
099
UniProt
VAR_014418
T
332
M
FA7_HUMAN
Disease (FA7D)
---
H
T
129C
M
100
UniProt
VAR_065409
R
375
W
FA7_HUMAN
Disease (FA7D)
137919286
H
R
170C
W
101
UniProt
VAR_065414
G
391
C
FA7_HUMAN
Disease (FA7D)
---
H
G
184A
C
102
UniProt
VAR_014419
G
391
S
FA7_HUMAN
Disease (FA7D)
190485816
H
G
184A
S
103
UniProt
VAR_065425
A
429
T
FA7_HUMAN
Disease (FA7D)
---
H
A
221A
T
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(4, 4)
Info
All PROSITE Patterns/Profiles
1: TISSUE_FACTOR (T:45-62)
5: TRYPSIN_DOM (H:16-243)
6: TRYPSIN_HIS (H:53-58)
7: TRYPSIN_SER (H:189-200)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
TISSUE_FACTOR
PS00621
Tissue factor signature.
TF_HUMAN
77-94
1
T:45-62
2
ASX_HYDROXYL
PS00010
Aspartic acid and asparagine hydroxylation site.
FA7_HUMAN
121-132
0
-
3
EGF_1
PS00022
EGF-like domain signature 1.
FA7_HUMAN
130-141
0
-
4
EGF_2
PS01186
EGF-like domain signature 2.
FA7_HUMAN
172-187
0
-
5
TRYPSIN_DOM
PS50240
Serine proteases, trypsin domain profile.
FA7_HUMAN
213-452
1
H:16-243
6
TRYPSIN_HIS
PS00134
Serine proteases, trypsin family, histidine active site.
FA7_HUMAN
249-254
1
H:53-58
7
TRYPSIN_SER
PS00135
Serine proteases, trypsin family, serine active site.
FA7_HUMAN
398-409
1
H:189-200
[
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.
(no "Exon" information available for biological units yet)
SCOP Domains
(4, 5)
Info
All SCOP Domains
1a: SCOP_d3th3t1 (T:6-106)
1b: SCOP_d3th3t2 (T:107-209)
2a: SCOP_d3th3h_ (H:)
3a: SCOP_d3th3l1 (L:47-86)
4a: SCOP_d3th3l2 (L:87-142)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
Fibronectin type III
(212)
Family
:
Fibronectin type III
(180)
Protein domain
:
Extracellular region of human tissue factor
(33)
Human (Homo sapiens) [TaxId: 9606]
(32)
1a
d3th3t1
T:6-106
1b
d3th3t2
T:107-209
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)
2a
d3th3h_
H:
Class
:
Small proteins
(3458)
Fold
:
Knottins (small inhibitors, toxins, lectins)
(761)
Superfamily
:
EGF/Laminin
(347)
Family
:
automated matches
(19)
Protein domain
:
automated matches
(19)
Human (Homo sapiens) [TaxId: 9606]
(17)
3a
d3th3l1
L:47-86
Family
:
EGF-type module
(304)
Protein domain
:
automated matches
(66)
Human (Homo sapiens) [TaxId: 9606]
(66)
4a
d3th3l2
L:87-142
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Asymmetric Unit 1
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select :A, :C
select chains 'A' and 'C'
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select all 'ALA' residues (Alanines) in chain 'A'
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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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select non-helix/non-sheet protein parts
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set label size to 20 (allowed range: 1-58)
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show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
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Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
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In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
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