PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
1U5M
Asym. Unit
Info
Asym.Unit (363 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
Models
(20 )
Title
:
STRUCTURE OF A CHORDIN-LIKE CYSTEINE-RICH REPEAT (VWC MODULE) FROM COLLAGEN IIA
Authors
:
J. M. O'Leary, J. M. Hamilton, C. M. Deane, N. V. Valeyev, L. J. Sandell, A. K. Downing
Date
:
28 Jul 04 (Deposition) - 05 Oct 04 (Release) - 24 Feb 09 (Revision)
Method
:
SOLUTION NMR
Resolution
:
NOT APPLICABLE
Chains
:
Asym. Unit : A (20 x)
Keywords
:
5 Disulfide Bonds, Two Sub-Domain Architecture, Beta-Sheet, Structural Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. M. O'Leary, J. M. Hamilton, C. M. Deane, N. V. Valeyev, L. J. Sandell, A. K. Downing
Solution Structure And Dynamics Of A Prototypical Chordin-Like Cysteine-Rich Repeat (Von Willebrand Factor Type C Module) From Collagen Iia
J. Biol. Chem. V. 279 53857 2004
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(0, 0)
Info
All Hetero Components
View:
Select:
Label:
Sorry, no Info available
[
close Hetero component info
]
Sites
(0, 0)
Info
All Sites
View:
Select:
Label:
Sorry, no Info available
[
close Site info
]
SAPs(SNPs)/Variants
(1, 1)
Info
(mutated residues are not available in "Model" view)
All SNPs/Variants
1: VAR_063891 (C33Y, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_063891
C
57
Y
CO2A1_HUMAN
Disease (STL1O)
---
A
C
33
Y
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 2)
Info
All PROSITE Patterns/Profiles
1: VWFC_2 (A:8-66)
2: VWFC_1 (A:28-65)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
VWFC_2
PS50184
VWFC domain profile.
CO2A1_HUMAN
32-90
1
A:8-66
2
VWFC_1
PS01208
VWFC domain signature.
CO2A1_HUMAN
52-89
1
A:28-65
[
close PROSITE info
]
Exons
(2, 2)
Info
All Exons
Exon 1.1b (A:1-5)
Exon 1.4a (A:5-73)
View:
Select:
Label:
All Exon Boundaries
1: Boundary -/1.1b
2: Boundary 1.1b/1.4a
3: Boundary 1.4a/1.5b
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
ENST00000380518
1b
ENSE00002177316
chr12:
48398269-48398020
250
CO2A1_HUMAN
1-29
29
1
A:1-5
5
1.4a
ENST00000380518
4a
ENSE00001661130
chr12:
48393908-48393702
207
CO2A1_HUMAN
29-98
70
1
A:5-73
69
1.5b
ENST00000380518
5b
ENSE00001672257
chr12:
48392214-48392198
17
CO2A1_HUMAN
98-103
6
0
-
-
1.6
ENST00000380518
6
ENSE00001650589
chr12:
48391984-48391952
33
CO2A1_HUMAN
104-114
11
0
-
-
1.7
ENST00000380518
7
ENSE00001613103
chr12:
48391847-48391815
33
CO2A1_HUMAN
115-125
11
0
-
-
1.8
ENST00000380518
8
ENSE00001683942
chr12:
48391707-48391654
54
CO2A1_HUMAN
126-143
18
0
-
-
1.9b
ENST00000380518
9b
ENSE00001713001
chr12:
48391490-48391389
102
CO2A1_HUMAN
144-177
34
0
-
-
1.10
ENST00000380518
10
ENSE00001749051
chr12:
48390408-48390331
78
CO2A1_HUMAN
178-203
26
0
-
-
1.11
ENST00000380518
11
ENSE00001805624
chr12:
48389702-48389658
45
CO2A1_HUMAN
204-218
15
0
-
-
1.12
ENST00000380518
12
ENSE00001641870
chr12:
48389546-48389493
54
CO2A1_HUMAN
219-236
18
0
-
-
1.13
ENST00000380518
13
ENSE00001626662
chr12:
48389091-48389038
54
CO2A1_HUMAN
237-254
18
0
-
-
1.14
ENST00000380518
14
ENSE00001716055
chr12:
48388260-48388207
54
CO2A1_HUMAN
255-272
18
0
-
-
1.15
ENST00000380518
15
ENSE00001598832
chr12:
48387830-48387777
54
CO2A1_HUMAN
273-290
18
0
-
-
1.16
ENST00000380518
16
ENSE00001606284
chr12:
48387645-48387592
54
CO2A1_HUMAN
291-308
18
0
-
-
1.17
ENST00000380518
17
ENSE00001752481
chr12:
48387285-48387241
45
CO2A1_HUMAN
309-323
15
0
-
-
1.18
ENST00000380518
18
ENSE00001729865
chr12:
48386714-48386661
54
CO2A1_HUMAN
324-341
18
0
-
-
1.19
ENST00000380518
19
ENSE00001774985
chr12:
48383588-48383544
45
CO2A1_HUMAN
342-356
15
0
-
-
1.20
ENST00000380518
20
ENSE00001763552
chr12:
48383064-48383011
54
CO2A1_HUMAN
357-374
18
0
-
-
1.22
ENST00000380518
22
ENSE00001668796
chr12:
48381492-48381394
99
CO2A1_HUMAN
375-407
33
0
-
-
1.23
ENST00000380518
23
ENSE00001662817
chr12:
48381096-48381052
45
CO2A1_HUMAN
408-422
15
0
-
-
1.24
ENST00000380518
24
ENSE00001723909
chr12:
48380959-48380861
99
CO2A1_HUMAN
423-455
33
0
-
-
1.25
ENST00000380518
25
ENSE00001692548
chr12:
48380671-48380618
54
CO2A1_HUMAN
456-473
18
0
-
-
1.26
ENST00000380518
26
ENSE00001740201
chr12:
48380226-48380119
108
CO2A1_HUMAN
474-509
36
0
-
-
1.27
ENST00000380518
27
ENSE00001767237
chr12:
48379748-48379695
54
CO2A1_HUMAN
510-527
18
0
-
-
1.28
ENST00000380518
28
ENSE00001599090
chr12:
48379609-48379511
99
CO2A1_HUMAN
528-560
33
0
-
-
1.29
ENST00000380518
29
ENSE00001757919
chr12:
48379370-48379317
54
CO2A1_HUMAN
561-578
18
0
-
-
1.30
ENST00000380518
30
ENSE00001716482
chr12:
48378876-48378778
99
CO2A1_HUMAN
579-611
33
0
-
-
1.31
ENST00000380518
31
ENSE00001622932
chr12:
48378382-48378329
54
CO2A1_HUMAN
612-629
18
0
-
-
1.32
ENST00000380518
32
ENSE00001644701
chr12:
48377923-48377870
54
CO2A1_HUMAN
630-647
18
0
-
-
1.33b
ENST00000380518
33b
ENSE00001796614
chr12:
48377519-48377466
54
CO2A1_HUMAN
648-665
18
0
-
-
1.34
ENST00000380518
34
ENSE00001710088
chr12:
48377221-48377168
54
CO2A1_HUMAN
666-683
18
0
-
-
1.35
ENST00000380518
35
ENSE00001621432
chr12:
48376920-48376876
45
CO2A1_HUMAN
684-698
15
0
-
-
1.36
ENST00000380518
36
ENSE00001633545
chr12:
48376729-48376631
99
CO2A1_HUMAN
699-731
33
0
-
-
1.37
ENST00000380518
37
ENSE00001803753
chr12:
48376392-48376285
108
CO2A1_HUMAN
732-767
36
0
-
-
1.38a
ENST00000380518
38a
ENSE00001681804
chr12:
48375943-48375890
54
CO2A1_HUMAN
768-785
18
0
-
-
1.39
ENST00000380518
39
ENSE00001607745
chr12:
48375612-48375559
54
CO2A1_HUMAN
786-803
18
0
-
-
1.40
ENST00000380518
40
ENSE00001635649
chr12:
48375179-48375126
54
CO2A1_HUMAN
804-821
18
0
-
-
1.41
ENST00000380518
41
ENSE00001669107
chr12:
48374751-48374698
54
CO2A1_HUMAN
822-839
18
0
-
-
1.42
ENST00000380518
42
ENSE00001772729
chr12:
48374444-48374337
108
CO2A1_HUMAN
840-875
36
0
-
-
1.43
ENST00000380518
43
ENSE00001591943
chr12:
48373845-48373792
54
CO2A1_HUMAN
876-893
18
0
-
-
1.44
ENST00000380518
44
ENSE00001766798
chr12:
48373347-48373294
54
CO2A1_HUMAN
894-911
18
0
-
-
1.45
ENST00000380518
45
ENSE00001647246
chr12:
48372541-48372380
162
CO2A1_HUMAN
912-965
54
0
-
-
1.46
ENST00000380518
46
ENSE00001632799
chr12:
48372181-48372074
108
CO2A1_HUMAN
966-1001
36
0
-
-
1.47
ENST00000380518
47
ENSE00001687971
chr12:
48371900-48371793
108
CO2A1_HUMAN
1002-1037
36
0
-
-
1.48
ENST00000380518
48
ENSE00001745083
chr12:
48371436-48371383
54
CO2A1_HUMAN
1038-1055
18
0
-
-
1.49
ENST00000380518
49
ENSE00001771216
chr12:
48371210-48371103
108
CO2A1_HUMAN
1056-1091
36
0
-
-
1.50
ENST00000380518
50
ENSE00001800326
chr12:
48370938-48370885
54
CO2A1_HUMAN
1092-1109
18
0
-
-
1.51
ENST00000380518
51
ENSE00001628024
chr12:
48370702-48370595
108
CO2A1_HUMAN
1110-1145
36
0
-
-
1.52
ENST00000380518
52
ENSE00001632016
chr12:
48370350-48370297
54
CO2A1_HUMAN
1146-1163
18
0
-
-
1.53
ENST00000380518
53
ENSE00001755795
chr12:
48369853-48369746
108
CO2A1_HUMAN
1164-1199
36
0
-
-
1.54
ENST00000380518
54
ENSE00001632936
chr12:
48369388-48369100
289
CO2A1_HUMAN
1200-1296
97
0
-
-
1.55
ENST00000380518
55
ENSE00001165399
chr12:
48368645-48368458
188
CO2A1_HUMAN
1296-1358
63
0
-
-
1.56
ENST00000380518
56
ENSE00001005948
chr12:
48368114-48367872
243
CO2A1_HUMAN
1359-1439
81
0
-
-
1.57b
ENST00000380518
57b
ENSE00001521209
chr12:
48367336-48366748
589
CO2A1_HUMAN
1440-1487
48
0
-
-
[
close EXON info
]
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d1u5ma_ (A:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Small proteins
(3458)
Fold
:
FnI-like domain
(17)
Superfamily
:
FnI-like domain
(17)
Family
:
VWC domain
(1)
Protein domain
:
Collagen alpha 1(II) chain precursor
(1)
Human (Homo sapiens) [TaxId: 9606]
(1)
1a
d1u5ma_
A:
[
close SCOP info
]
CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_1u5mA01 (A:9-44)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Ribbon
(789)
Topology
:
Complement Module; domain 1
(62)
Homologous Superfamily
:
Complement Module, domain 1
(60)
Human (Homo sapiens)
(46)
1a
1u5mA01
A:9-44
[
close CATH info
]
Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_VWC_1u5mA01 (A:10-65)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
FnI-like
(2)
Family
:
VWC
(1)
Homo sapiens (Human)
(1)
1a
VWC-1u5mA01
A:10-65
[
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
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
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
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)
[
close Script example commands
]
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:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (363 KB)
Header - Asym.Unit
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
1U5M
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
