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3QB4
Asym. Unit
Info
Asym.Unit (139 KB)
Biol.Unit 1 (67 KB)
Biol.Unit 2 (67 KB)
Biol.Unit 3 (132 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF A TGF-BETA LIGAND-RECEPTOR COMPLEX
Authors
:
T. D. Mueller, J. Nickel, W. Sebald
Date
:
12 Jan 11 (Deposition) - 14 Mar 12 (Release) - 07 Oct 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.28
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: A,B,C,D (1x)
Keywords
:
Cystine-Knot, Ligand-Receptor Complex, Protein, Membrane/Extracellular, Cytokine-Transferase Receptor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
U. Klammert, T. D. Mueller, T. V. Hellmann, K. K. Wuerzler, A. Kotzsch, A. Schliermann, W. Schmitz, A. C. Kuebler, W. Sebald, J. Nickel
Gdf-5 Can Act As A Context-Dependent Bmp-2 Antagonist.
Bmc Biol. V. 13 77 2015
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Hetero Components
(0, 0)
Info
All Hetero Components
View:
Select:
Label:
Sorry, no Info available
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]
Sites
(0, 0)
Info
All Sites
View:
Select:
Label:
Sorry, no Info available
[
close Site info
]
SAPs(SNPs)/Variants
(17, 34)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_064416 (R18C, chain A/C, )
02: VAR_017407 (C19Y, chain A/C, )
03: VAR_073141 (W33R, chain A/C, )
04: VAR_041398 (F35Y, chain B/D, )
05: VAR_022828 (Y39D, chain B/D, )
06: VAR_054911 (P55T, chain A/C, )
07: VAR_026545 (A57L, chain A/C, )
08: VAR_037980 (S58T, chain A/C, )
09: VAR_037981 (H59L, chain A/C, )
10: VAR_022829 (C59Y, chain B/D, )
11: VAR_017408 (L60P, chain A/C, )
12: VAR_073142 (N64K, chain A/C, )
13: VAR_073143 (N64T, chain A/C, )
14: VAR_037982 (S94N, chain A/C, )
15: VAR_015533 (C101R, chain B/D, )
16: VAR_022830 (C107R, chain B/D, )
17: VAR_037983 (E110K, chain A/C, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_064416
R
399
C
GDF5_HUMAN
Disease (BDA1C)
---
A/C
R
18
C
02
UniProt
VAR_017407
C
400
Y
GDF5_HUMAN
Disease (AMDG)
---
A/C
C
19
Y
03
UniProt
VAR_073141
W
414
R
GDF5_HUMAN
Disease (SYNS2)
---
A/C
W
33
R
04
UniProt
VAR_041398
F
58
Y
BMR1A_HUMAN
Unclassified
---
B/D
F
35
Y
05
UniProt
VAR_022828
Y
62
D
BMR1A_HUMAN
Disease (JPS)
---
B/D
Y
39
D
06
UniProt
VAR_054911
P
436
T
GDF5_HUMAN
Disease (DPS)
---
A/C
P
55
T
07
UniProt
VAR_026545
R
438
L
GDF5_HUMAN
Disease (SYM1B)
---
A/C
A
57
L
08
UniProt
VAR_037980
S
439
T
GDF5_HUMAN
Disease (DPS)
---
A/C
S
58
T
09
UniProt
VAR_037981
H
440
L
GDF5_HUMAN
Disease (DPS)
---
A/C
H
59
L
10
UniProt
VAR_022829
C
82
Y
BMR1A_HUMAN
Disease (JPS)
---
B/D
C
59
Y
11
UniProt
VAR_017408
L
441
P
GDF5_HUMAN
Disease (DPS)
28936683
A/C
L
60
P
12
UniProt
VAR_073142
N
445
K
GDF5_HUMAN
Disease (SYNS2)
---
A/C
N
64
K
13
UniProt
VAR_073143
N
445
T
GDF5_HUMAN
Disease (SYNS2)
---
A/C
N
64
T
14
UniProt
VAR_037982
S
475
N
GDF5_HUMAN
Disease (SYNS2)
---
A/C
S
94
N
15
UniProt
VAR_015533
C
124
R
BMR1A_HUMAN
Disease (JPS)
---
B/D
C
101
R
16
UniProt
VAR_022830
C
130
R
BMR1A_HUMAN
Disease (JPS)
---
B/D
C
107
R
17
UniProt
VAR_037983
E
491
K
GDF5_HUMAN
Disease (SYM1B)
---
A/C
E
110
K
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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]
PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: TGF_BETA_1 (A:37-52,C:37-52)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
TGF_BETA_1
PS00250
TGF-beta family signature.
GDF5_HUMAN
418-433
2
A:37-52
C:37-52
[
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Exons
(4, 8)
Info
All Exons
Exon 1.5c (B:31-54 | D:31-54)
Exon 1.6 (B:54-88 | D:54-88)
Exon 1.7 (B:89-118 | D:89-119)
Exon 2.4 (A:16-120 | C:15-120)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.4a/1.5c
2: Boundary 1.5c/1.6
3: Boundary 1.6/1.7
4: Boundary 1.7/1.8
5: Boundary 2.3a/2.4
6: Boundary 2.4/-
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
ENST00000372037
1b
ENSE00001456788
chr10:
88516407-88516676
270
BMR1A_HUMAN
-
0
0
-
-
1.2a
ENST00000372037
2a
ENSE00001456787
chr10:
88598622-88598736
115
BMR1A_HUMAN
-
0
0
-
-
1.4a
ENST00000372037
4a
ENSE00001456785
chr10:
88635616-88635842
227
BMR1A_HUMAN
1-23
23
0
-
-
1.5c
ENST00000372037
5c
ENSE00000711713
chr10:
88649819-88649981
163
BMR1A_HUMAN
23-77
55
2
B:31-54
D:31-54
24
24
1.6
ENST00000372037
6
ENSE00000711717
chr10:
88651884-88651986
103
BMR1A_HUMAN
77-111
35
2
B:54-88
D:54-88
35
35
1.7
ENST00000372037
7
ENSE00000711722
chr10:
88659551-88659647
97
BMR1A_HUMAN
112-144
33
2
B:89-118
D:89-119
30
31
1.8
ENST00000372037
8
ENSE00000711728
chr10:
88659784-88659883
100
BMR1A_HUMAN
144-177
34
0
-
-
1.9
ENST00000372037
9
ENSE00000711732
chr10:
88671997-88672141
145
BMR1A_HUMAN
177-225
49
0
-
-
1.10a
ENST00000372037
10a
ENSE00000711737
chr10:
88676891-88677083
193
BMR1A_HUMAN
226-290
65
0
-
-
1.11b
ENST00000372037
11b
ENSE00000711742
chr10:
88678929-88679226
298
BMR1A_HUMAN
290-389
100
0
-
-
1.12
ENST00000372037
12
ENSE00001646386
chr10:
88681277-88681452
176
BMR1A_HUMAN
389-448
60
0
-
-
1.13
ENST00000372037
13
ENSE00000830582
chr10:
88683133-88683263
131
BMR1A_HUMAN
448-491
44
0
-
-
1.14b
ENST00000372037
14b
ENSE00001456760
chr10:
88683351-88684945
1595
BMR1A_HUMAN
492-532
41
0
-
-
2.3a
ENST00000374369
3a
ENSE00001463316
chr20:
34026023-34025078
946
GDF5_HUMAN
1-211
211
0
-
-
2.4
ENST00000374369
4
ENSE00001463322
chr20:
34022581-34021145
1437
GDF5_HUMAN
211-501
291
2
A:16-120
C:15-120
105
106
[
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]
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d3qb4a_ (A:)
1b: SCOP_d3qb4c_ (C:)
2a: SCOP_d3qb4b_ (B:)
2b: SCOP_d3qb4d_ (D:)
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Protein Domains
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Organisms
(
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(
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Class
:
Small proteins
(3458)
Fold
:
Cystine-knot cytokines
(124)
Superfamily
:
Cystine-knot cytokines
(124)
Family
:
automated matches
(18)
Protein domain
:
automated matches
(18)
Human (Homo sapiens) [TaxId: 9606]
(15)
1a
d3qb4a_
A:
1b
d3qb4c_
C:
Fold
:
Snake toxin-like
(152)
Superfamily
:
Snake toxin-like
(152)
Family
:
Extracellular domain of cell surface receptors
(39)
Protein domain
:
BMP receptor Ia ectodomain
(11)
Human (Homo sapiens) [TaxId: 9606]
(11)
2a
d3qb4b_
B:
2b
d3qb4d_
D:
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CATH Domains
(0, 0)
Info
all CATH domains
View:
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Sorry, no Info available
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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