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1GR3
Biol. Unit 1
Info
Asym.Unit (30 KB)
Biol.Unit 1 (70 KB)
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(1)
Title
:
STRUCTURE OF THE HUMAN COLLAGEN X NC1 TRIMER
Authors
:
O. Bogin, M. Kvansakul, E. Rom, J. Singer, A. Yayon, E. Hohenester
Date
:
12 Dec 01 (Deposition) - 14 Feb 02 (Release) - 05 Jul 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A
Biol. Unit 1: A (3x)
Keywords
:
Collagen, Extracellular Matrix, Connective Tissue
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
O. Bogin, M. Kvansakul, E. Rom, J. Singer, A. Yayon, E. Hohenester
Insight Into Schmid Metaphyseal Chondrodysplasia From The Crystal Structure Of The Collagen X Nc1 Domain Trimer.
Structure V. 10 165 2002
(for further references see the
PDB file header
)
[
close entry info
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Hetero Components
(1, 3)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
2a: 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMO... (CPSa)
3a: SODIUM ION (NAa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
-1
Ligand/Ion
CALCIUM ION
2
CPS
3
Ligand/Ion
3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE
3
NA
-1
Ligand/Ion
SODIUM ION
[
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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
ASP A:634 , HOH A:2024
BINDING SITE FOR RESIDUE CA A 901
2
AC2
SOFTWARE
GLN A:635 , HOH A:2021 , HOH A:2029
BINDING SITE FOR RESIDUE NA A 902
3
AC3
SOFTWARE
ASP A:626 , GLU A:627 , LEU A:633 , ASP A:634 , HOH A:2024
BINDING SITE FOR RESIDUE CA A 903
4
AC4
SOFTWARE
TRP A:611 , LYS A:616 , VAL A:621 , TYR A:625 , SER A:659 , TYR A:667
BINDING SITE FOR RESIDUE CPS A 800
[
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]
SAPs(SNPs)/Variants
(17, 51)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
01: VAR_023188 (Y582D, chain A, )
02: VAR_001841 (C591R, chain A, )
03: VAR_001842 (G595E, chain A, )
04: VAR_023189 (G595R, chain A, )
05: VAR_008039 (Y597C, chain A, )
06: VAR_001843 (Y597H, chain A, )
07: VAR_001844 (Y598D, chain A, )
08: VAR_001845 (S600P, chain A, )
09: VAR_023190 (V603M, chain A, )
10: VAR_001846 (L614P, chain A, )
11: VAR_001847 (N617K, chain A, )
12: VAR_001848 (G618V, chain A, )
13: VAR_001849 (L644R, chain A, )
14: VAR_001850 (D648G, chain A, )
15: VAR_023191 (W651R, chain A, )
16: VAR_023192 (Q653P, chain A, )
17: VAR_023193 (S671P, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_023188
Y
582
D
COAA1_HUMAN
Disease (SMCD)
---
A
Y
582
D
02
UniProt
VAR_001841
C
591
R
COAA1_HUMAN
Disease (SMCD)
---
A
C
591
R
03
UniProt
VAR_001842
G
595
E
COAA1_HUMAN
Disease (SMCD)
---
A
G
595
E
04
UniProt
VAR_023189
G
595
R
COAA1_HUMAN
Disease (SMCD)
---
A
G
595
R
05
UniProt
VAR_008039
Y
597
C
COAA1_HUMAN
Disease (SMCD)
---
A
Y
597
C
06
UniProt
VAR_001843
Y
597
H
COAA1_HUMAN
Disease (SMCD)
---
A
Y
597
H
07
UniProt
VAR_001844
Y
598
D
COAA1_HUMAN
Disease (SMCD)
---
A
Y
598
D
08
UniProt
VAR_001845
S
600
P
COAA1_HUMAN
Disease (SMCD)
---
A
S
600
P
09
UniProt
VAR_023190
V
603
M
COAA1_HUMAN
Polymorphism
---
A
V
603
M
10
UniProt
VAR_001846
L
614
P
COAA1_HUMAN
Disease (SMCD)
---
A
L
614
P
11
UniProt
VAR_001847
N
617
K
COAA1_HUMAN
Disease (SMCD)
---
A
N
617
K
12
UniProt
VAR_001848
G
618
V
COAA1_HUMAN
Disease (SMCD)
---
A
G
618
V
13
UniProt
VAR_001849
L
644
R
COAA1_HUMAN
Disease (SMCD)
---
A
L
644
R
14
UniProt
VAR_001850
D
648
G
COAA1_HUMAN
Disease (SMCD)
---
A
D
648
G
15
UniProt
VAR_023191
W
651
R
COAA1_HUMAN
Disease (SMCD)
---
A
W
651
R
16
UniProt
VAR_023192
Q
653
P
COAA1_HUMAN
Disease (SMCD)
---
A
Q
653
P
17
UniProt
VAR_023193
S
671
P
COAA1_HUMAN
Disease (SMCD)
---
A
S
671
P
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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]
PROSITE Patterns/Profiles
(, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
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]
Exons
(0, 0)
Info
All Exons
View:
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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
(1, 1)
Info
All SCOP Domains
1a: SCOP_d1gr3a_ (A:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
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(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
TNF-like
(100)
Superfamily
:
TNF-like
(100)
Family
:
TNF-like
(82)
Protein domain
:
Collagen NC1 trimerisation domain
(2)
Human (Homo sapiens), isoform X [TaxId: 9606]
(1)
1a
d1gr3a_
A:
[
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]
CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_1gr3A00 (A:549-680)
View:
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(
)
(
)
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)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Jelly Rolls
(1293)
Homologous Superfamily
:
[code=2.60.120.40, no name defined]
(56)
Human (Homo sapiens)
(38)
1a
1gr3A00
A:549-680
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Label:
Sorry, no Info available
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Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
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Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Asymmetric Unit 1
Asymmetric Unit 2
Asymmetric Unit 3
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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
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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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