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Getting 'Biological Unit' information from database.
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Getting 'Hetero Component' information from database.
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Getting 'Site' information from database.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
4C2A
Asym. Unit
Info
Asym.Unit (170 KB)
Biol.Unit 1 (165 KB)
(using Jmol or JSmol)
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(1)
Title
:
CRYSTAL STRUCTURE OF HIGH-AFFINITY VON WILLEBRAND FACTOR A1 DOMAIN WITH R1306Q AND I1309V MUTATIONS IN COMPLEX WITH HIGH AFFINITY GPIB ALPHA
Authors
:
M. A. Blenner, X. Dong, T. A. Springer
Date
:
16 Aug 13 (Deposition) - 08 Jan 14 (Release) - 30 Sep 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.08
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Blood Clotting, Cell Adhesion, A1, Gpibalpha
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. A. Blenner, X. Dong, T. A. Springer
Towards The Structural Basis Of Regulation Of Von Willebrand Factor Binding To Glycoprotein Ib
J. Biol. Chem. V. 289 5565 2014
[
close entry info
]
Hetero Components
(4, 4)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
3a: CACODYLATE ION (CACa)
2a: CALCIUM ION (CAa)
4a: DI(HYDROXYETHYL)ETHER (PEGa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
1
Ligand/Ion
ACETATE ION
2
CA
1
Ligand/Ion
CALCIUM ION
3
CAC
1
Ligand/Ion
CACODYLATE ION
4
PEG
1
Ligand/Ion
DI(HYDROXYETHYL)ETHER
[
close Hetero Component info
]
Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
LEU A:1267 , HIS A:1268 , ARG A:1450 , HOH A:2009 , THR B:145
BINDING SITE FOR RESIDUE CAC A2468
2
AC2
SOFTWARE
SER A:1273 , ARG A:1308
BINDING SITE FOR RESIDUE ACT A2469
3
AC3
SOFTWARE
ASP A:1302 , HOH A:2024 , HOH A:2025 , HOH A:2026 , HOH A:2027 , HOH A:2105
BINDING SITE FOR RESIDUE CA A2470
4
AC4
SOFTWARE
ASP B:106
BINDING SITE FOR RESIDUE PEG B1267
[
close Site info
]
SAPs(SNPs)/Variants
(30, 30)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_011909 (R56H, chain B, )
02: VAR_014206 (L57F, chain B, )
03: VAR_005256 (C65R, chain B, )
04: VAR_013511 (L70F, chain B, )
05: VAR_014207 (L129P, chain B, )
06: VAR_005257 (T145M, chain B, )
07: VAR_005258 (A156V, chain B, )
08: VAR_005260 (C209S, chain B, )
09: VAR_019657 (V233S, chain B, )
10: VAR_005261 (V233V, chain B, )
11: VAR_011910 (A238S, chain B, )
12: VAR_005262 (V239V, chain B, )
13: VAR_005791 (P1266L, chain A, )
14: VAR_005792 (H1268D, chain A, )
15: VAR_067340 (C1272F, chain A, )
16: VAR_005793 (C1272R, chain A, )
17: VAR_005794 (Q1306W, chain A, )
18: VAR_005795 (R1308C, chain A, )
19: VAR_005796 (W1313C, chain A, )
20: VAR_005797 (V1314L, chain A, )
21: VAR_005798 (V1316M, chain A, )
22: VAR_005799 (V1318L, chain A, )
23: VAR_005800 (G1324S, chain A, )
24: VAR_005801 (R1341Q, chain A, )
25: VAR_005802 (R1374C, chain A, )
26: VAR_005803 (R1374H, chain A, )
27: VAR_005804 (A1381A, chain A, )
28: VAR_005805 (R1399H, chain A, )
29: VAR_005806 (L1460V, chain A, )
30: VAR_005807 (A1461V, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_011909
R
72
H
GP1BA_HUMAN
Polymorphism
6068
B
R
56
H
02
UniProt
VAR_014206
L
73
F
GP1BA_HUMAN
Disease (BSS)
---
B
L
57
F
03
UniProt
VAR_005256
C
81
R
GP1BA_HUMAN
Disease (BSS)
---
B
C
65
R
04
UniProt
VAR_013511
L
86
F
GP1BA_HUMAN
Polymorphism
13306411
B
L
70
F
05
UniProt
VAR_014207
L
145
P
GP1BA_HUMAN
Disease (BSS)
---
B
L
129
P
06
UniProt
VAR_005257
T
161
M
GP1BA_HUMAN
Polymorphism
6065
B
T
145
M
07
UniProt
VAR_005258
A
172
V
GP1BA_HUMAN
Disease (BSS)
---
B
A
156
V
08
UniProt
VAR_005260
C
225
S
GP1BA_HUMAN
Disease (BSS)
---
B
C
209
S
09
UniProt
VAR_019657
G
249
S
GP1BA_HUMAN
Disease (VWDP)
---
B
V
233
S
10
UniProt
VAR_005261
G
249
V
GP1BA_HUMAN
Disease (VWDP)
---
B
V
233
V
11
UniProt
VAR_011910
A
254
S
GP1BA_HUMAN
Polymorphism
382524
B
A
238
S
12
UniProt
VAR_005262
M
255
V
GP1BA_HUMAN
Disease (VWDP)
---
B
V
239
V
13
UniProt
VAR_005791
P
1266
L
VWF_HUMAN
Disease (VWD2)
---
A
P
1266
L
14
UniProt
VAR_005792
H
1268
D
VWF_HUMAN
Disease (VWD2)
---
A
H
1268
D
15
UniProt
VAR_067340
C
1272
F
VWF_HUMAN
Disease (VWD2)
---
A
C
1272
F
16
UniProt
VAR_005793
C
1272
R
VWF_HUMAN
Disease (VWD2)
---
A
C
1272
R
17
UniProt
VAR_005794
R
1306
W
VWF_HUMAN
Disease (VWD2)
---
A
Q
1306
W
18
UniProt
VAR_005795
R
1308
C
VWF_HUMAN
Disease (VWD2)
---
A
R
1308
C
19
UniProt
VAR_005796
W
1313
C
VWF_HUMAN
Disease (VWD2)
---
A
W
1313
C
20
UniProt
VAR_005797
V
1314
L
VWF_HUMAN
Disease (VWD2)
---
A
V
1314
L
21
UniProt
VAR_005798
V
1316
M
VWF_HUMAN
Disease (VWD2)
---
A
V
1316
M
22
UniProt
VAR_005799
V
1318
L
VWF_HUMAN
Disease (VWD2)
---
A
V
1318
L
23
UniProt
VAR_005800
G
1324
S
VWF_HUMAN
Disease (VWD2)
---
A
G
1324
S
24
UniProt
VAR_005801
R
1341
Q
VWF_HUMAN
Disease (VWD2)
---
A
R
1341
Q
25
UniProt
VAR_005802
R
1374
C
VWF_HUMAN
Disease (VWD2)
---
A
R
1374
C
26
UniProt
VAR_005803
R
1374
H
VWF_HUMAN
Disease (VWD2)
---
A
R
1374
H
27
UniProt
VAR_005804
T
1381
A
VWF_HUMAN
Polymorphism
216311
A
A
1381
A
28
UniProt
VAR_005805
R
1399
H
VWF_HUMAN
Polymorphism
216312
A
R
1399
H
29
UniProt
VAR_005806
L
1460
V
VWF_HUMAN
Disease (VWD2)
---
A
L
1460
V
30
UniProt
VAR_005807
A
1461
V
VWF_HUMAN
Disease (VWD2)
---
A
A
1461
V
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 7)
Info
All PROSITE Patterns/Profiles
1: LRR (B:56-77|B:78-99|B:101-121|B:125-14...)
2: VWFA (-|A:1277-1453|-)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
LRR
PS51450
Leucine-rich repeat profile.
GP1BA_HUMAN
72-93
94-115
117-137
141-162
165-186
189-210
6
B:56-77
B:78-99
B:101-121
B:125-146
B:149-170
B:173-194
2
VWFA
PS50234
VWFA domain profile.
VWF_HUMAN
1498-1665
1277-1453
1691-1871
1
-
A:1277-1453
-
[
close PROSITE info
]
Exons
(2, 2)
Info
All Exons
Exon 1.29 (A:1266-1467)
Exon 2.2b (B:1-266)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.28/1.29
2: Boundary 1.29/1.30
3: Boundary -/2.2b
4: Boundary 2.2b/2.3a
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
1.1
ENST00000261405
1
ENSE00001184496
chr12:
6233836-6233587
250
VWF_HUMAN
-
0
0
-
-
1.2
ENST00000261405
2
ENSE00001653826
chr12:
6232362-6232308
55
VWF_HUMAN
1-19
19
0
-
-
1.4
ENST00000261405
4
ENSE00001261893
chr12:
6230504-6230340
165
VWF_HUMAN
19-74
56
0
-
-
1.5
ENST00000261405
5
ENSE00001261546
chr12:
6220134-6220032
103
VWF_HUMAN
74-108
35
0
-
-
1.6
ENST00000261405
6
ENSE00002152539
chr12:
6219748-6219540
209
VWF_HUMAN
108-178
71
0
-
-
1.7a
ENST00000261405
7a
ENSE00001676171
chr12:
6204750-6204626
125
VWF_HUMAN
178-219
42
0
-
-
1.8
ENST00000261405
8
ENSE00001682720
chr12:
6184717-6184501
217
VWF_HUMAN
220-292
73
0
-
-
1.9
ENST00000261405
9
ENSE00001640051
chr12:
6182907-6182785
123
VWF_HUMAN
292-333
42
0
-
-
1.10
ENST00000261405
10
ENSE00001656280
chr12:
6181608-6181497
112
VWF_HUMAN
333-370
38
0
-
-
1.11
ENST00000261405
11
ENSE00001700039
chr12:
6180509-6180463
47
VWF_HUMAN
370-386
17
0
-
-
1.12
ENST00000261405
12
ENSE00001674584
chr12:
6174439-6174303
137
VWF_HUMAN
386-431
46
0
-
-
1.13
ENST00000261405
13
ENSE00001645253
chr12:
6173550-6173412
139
VWF_HUMAN
432-478
47
0
-
-
1.14
ENST00000261405
14
ENSE00001679915
chr12:
6172220-6172120
101
VWF_HUMAN
478-511
34
0
-
-
1.15
ENST00000261405
15
ENSE00001640163
chr12:
6167210-6167015
196
VWF_HUMAN
512-577
66
0
-
-
1.16
ENST00000261405
16
ENSE00001727074
chr12:
6166238-6166023
216
VWF_HUMAN
577-649
73
0
-
-
1.17b
ENST00000261405
17b
ENSE00000936967
chr12:
6161949-6161709
241
VWF_HUMAN
649-729
81
0
-
-
1.18
ENST00000261405
18
ENSE00000936968
chr12:
6155983-6155889
95
VWF_HUMAN
729-761
33
0
-
-
1.19
ENST00000261405
19
ENSE00000936969
chr12:
6153617-6153457
161
VWF_HUMAN
761-814
54
0
-
-
1.20
ENST00000261405
20
ENSE00000936970
chr12:
6145657-6145554
104
VWF_HUMAN
815-849
35
0
-
-
1.21
ENST00000261405
21
ENSE00000936971
chr12:
6143992-6143854
139
VWF_HUMAN
849-895
47
0
-
-
1.22
ENST00000261405
22
ENSE00000936972
chr12:
6140744-6140610
135
VWF_HUMAN
896-940
45
0
-
-
1.23
ENST00000261405
23
ENSE00000936973
chr12:
6138654-6138508
147
VWF_HUMAN
941-989
49
0
-
-
1.24
ENST00000261405
24
ENSE00000936974
chr12:
6135212-6135072
141
VWF_HUMAN
990-1036
47
0
-
-
1.25
ENST00000261405
25
ENSE00001731504
chr12:
6134859-6134746
114
VWF_HUMAN
1037-1074
38
0
-
-
1.26
ENST00000261405
26
ENSE00000936976
chr12:
6132953-6132797
157
VWF_HUMAN
1075-1127
53
0
-
-
1.27
ENST00000261405
27
ENSE00001792722
chr12:
6132064-6131906
159
VWF_HUMAN
1127-1180
54
0
-
-
1.28
ENST00000261405
28
ENSE00001679248
chr12:
6131201-6131066
136
VWF_HUMAN
1180-1225
46
0
-
-
1.29
ENST00000261405
29
ENSE00001749068
chr12:
6128909-6127531
1379
VWF_HUMAN
1225-1685
461
1
A:1266-1467
202
1.30
ENST00000261405
30
ENSE00001676963
chr12:
6126036-6125920
117
VWF_HUMAN
1685-1724
40
0
-
-
1.31
ENST00000261405
31
ENSE00001646337
chr12:
6125822-6125682
141
VWF_HUMAN
1724-1771
48
0
-
-
1.32
ENST00000261405
32
ENSE00001603271
chr12:
6125398-6125255
144
VWF_HUMAN
1771-1819
49
0
-
-
1.33
ENST00000261405
33
ENSE00000936983
chr12:
6122811-6122647
165
VWF_HUMAN
1819-1874
56
0
-
-
1.34
ENST00000261405
34
ENSE00001761241
chr12:
6121296-6121253
44
VWF_HUMAN
1874-1888
15
0
-
-
1.35
ENST00000261405
35
ENSE00001622286
chr12:
6120960-6120783
178
VWF_HUMAN
1889-1948
60
0
-
-
1.36
ENST00000261405
36
ENSE00001261636
chr12:
6105388-6105168
221
VWF_HUMAN
1948-2021
74
0
-
-
1.37
ENST00000261405
37
ENSE00000866874
chr12:
6103773-6103581
193
VWF_HUMAN
2022-2086
65
0
-
-
1.38
ENST00000261405
38
ENSE00000866873
chr12:
6103369-6103028
342
VWF_HUMAN
2086-2200
115
0
-
-
1.39
ENST00000261405
39
ENSE00001328745
chr12:
6101184-6100985
200
VWF_HUMAN
2200-2266
67
0
-
-
1.40
ENST00000261405
40
ENSE00001261609
chr12:
6094831-6094729
103
VWF_HUMAN
2267-2301
35
0
-
-
1.41
ENST00000261405
41
ENSE00001261603
chr12:
6094285-6094211
75
VWF_HUMAN
2301-2326
26
0
-
-
1.42
ENST00000261405
42
ENSE00000866869
chr12:
6092420-6092316
105
VWF_HUMAN
2326-2361
36
0
-
-
1.43
ENST00000261405
43
ENSE00001309185
chr12:
6091157-6090952
206
VWF_HUMAN
2361-2429
69
0
-
-
1.44
ENST00000261405
44
ENSE00000866867
chr12:
6085426-6085277
150
VWF_HUMAN
2430-2479
50
0
-
-
1.45
ENST00000261405
45
ENSE00001261579
chr12:
6080875-6080765
111
VWF_HUMAN
2480-2516
37
0
-
-
1.46
ENST00000261405
46
ENSE00001316394
chr12:
6078557-6078377
181
VWF_HUMAN
2517-2577
61
0
-
-
1.47
ENST00000261405
47
ENSE00000866864
chr12:
6077333-6077293
41
VWF_HUMAN
2577-2590
14
0
-
-
1.48
ENST00000261405
48
ENSE00001289624
chr12:
6076768-6076652
117
VWF_HUMAN
2591-2629
39
0
-
-
1.49
ENST00000261405
49
ENSE00001312819
chr12:
6062760-6062662
99
VWF_HUMAN
2630-2662
33
0
-
-
1.50
ENST00000261405
50
ENSE00001326641
chr12:
6061685-6061557
129
VWF_HUMAN
2663-2705
43
0
-
-
1.51
ENST00000261405
51
ENSE00001307387
chr12:
6061049-6061010
40
VWF_HUMAN
2706-2719
14
0
-
-
1.52a
ENST00000261405
52a
ENSE00001293437
chr12:
6059049-6058952
98
VWF_HUMAN
2719-2751
33
0
-
-
1.53b
ENST00000261405
53b
ENSE00001314535
chr12:
6058369-6058040
330
VWF_HUMAN
2752-2813
62
0
-
-
2.2b
ENST00000329125
2b
ENSE00001299958
chr17:
4835900-4837150
1251
GP1BA_HUMAN
1-417
417
1
B:1-266
266
2.3a
ENST00000329125
3a
ENSE00001488421
chr17:
4837187-4837858
672
GP1BA_HUMAN
418-640
223
0
-
-
[
close EXON info
]
SCOP Domains
(2, 2)
Info
All SCOP Domains
1a: SCOP_d4c2ab_ (B:)
2a: SCOP_d4c2aa_ (A:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
(112)
Superfamily
:
L domain-like
(93)
Family
:
Ngr ectodomain-like
(21)
Protein domain
:
automated matches
(3)
Human (Homo sapiens) [TaxId: 9606]
(2)
1a
d4c2ab_
B:
Fold
:
vWA-like
(111)
Superfamily
:
vWA-like
(111)
Family
:
Integrin A (or I) domain
(84)
Protein domain
:
automated matches
(11)
Human (Homo sapiens) [TaxId: 9606]
(11)
2a
d4c2aa_
A:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
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(e.g.: "#3cb371" or "60,179,113")
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Graphics Window
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Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
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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close Script example commands
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Log
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") .
Note:
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") .
QuickSearch:
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Asym.Unit (170 KB)
Header - Asym.Unit
Biol.Unit 1 (165 KB)
Header - Biol.Unit 1
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