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1HCF
Asym. Unit
Info
Asym.Unit (78 KB)
Biol.Unit 1 (73 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF TRKB-D5 BOUND TO NEUROTROPHIN-4/5
Authors
:
M. J. Banfield, R. L. Naylor, A. G. S. Robertson, S. J. Allen, D. Dawbarn, R. L. Brady
Date
:
03 May 01 (Deposition) - 06 Dec 01 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.70
Chains
:
Asym. Unit : A,B,X,Y
Biol. Unit 1: A,B,X,Y (1x)
Keywords
:
Transferase/Hormone, Complex(Transferase/Growth Factor), Neurotrophin-4/5, Trkb Receptor, Ngf-Beta Superfamily, Immunoglobulin Domain
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. J. Banfield, R. L. Naylor, A. G. S. Robertson, S. J. Allen, D. Dawbarn, R. L. Brady
Specificity In Trk-Receptor:Neurotrophin Interaction: The Crystal Structure Of Trkb-D5 In Complex With Neurotrophin-4/5
Structure V. 9 1191 2001
(for further references see the
PDB file header
)
[
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Hetero Components
(1, 4)
Info
All Hetero Components
1a: SULFATE ION (SO4a)
1b: SULFATE ION (SO4b)
1c: SULFATE ION (SO4c)
1d: SULFATE ION (SO4d)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
SO4
4
Ligand/Ion
SULFATE ION
[
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
ARG A:11
BINDING SITE FOR RESIDUE SO4 A1128
2
AC2
SOFTWARE
ARG B:34 , ARG B:36 , HIS B:85 , ARG B:111 , HOH B:2007 , HOH B:2015
BINDING SITE FOR RESIDUE SO4 B1129
3
AC3
SOFTWARE
ALA B:8 , ARG B:11 , HOH B:2018
BINDING SITE FOR RESIDUE SO4 B1130
4
AC4
SOFTWARE
ARG A:84 , ARG B:34 , HOH B:2019
BINDING SITE FOR RESIDUE SO4 B1131
[
close Site info
]
SAPs(SNPs)/Variants
(14, 27)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_063197 (E4K, chain A, )
02: VAR_063198 (A8V, chain A/B, )
03: VAR_063199 (S9N, chain A/B, )
04: VAR_063200 (R10C, chain A/B, )
05: VAR_063201 (R10H, chain A/B, )
06: VAR_063202 (R34G, chain A/B, )
07: VAR_063203 (R53H, chain A/B, )
08: VAR_063204 (R60C, chain A/B, )
09: VAR_063205 (R126Q, chain A/B, )
10: VAR_063206 (R126W, chain A/B, )
11: VAR_063207 (T127I, chain A/B, )
12: VAR_063208 (T127S, chain A/B, )
13: VAR_016320 (G309R, chain X/Y, )
14: VAR_011973 (N338Y, chain X/Y, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_063197
E
84
K
NTF4_HUMAN
Unclassified
---
A
E
4
K
02
UniProt
VAR_063198
A
88
V
NTF4_HUMAN
Polymorphism
---
A/B
A
8
V
03
UniProt
VAR_063199
S
89
N
NTF4_HUMAN
Polymorphism
---
A/B
S
9
N
04
UniProt
VAR_063200
R
90
C
NTF4_HUMAN
Polymorphism
---
A/B
R
10
C
05
UniProt
VAR_063201
R
90
H
NTF4_HUMAN
Unclassified
---
A/B
R
10
H
06
UniProt
VAR_063202
R
114
G
NTF4_HUMAN
Polymorphism
---
A/B
R
34
G
07
UniProt
VAR_063203
R
133
H
NTF4_HUMAN
Polymorphism
---
A/B
R
53
H
08
UniProt
VAR_063204
R
140
C
NTF4_HUMAN
Polymorphism
---
A/B
R
60
C
09
UniProt
VAR_063205
R
206
Q
NTF4_HUMAN
Unclassified
---
A/B
R
126
Q
10
UniProt
VAR_063206
R
206
W
NTF4_HUMAN
Unclassified
---
A/B
R
126
W
11
UniProt
VAR_063207
T
207
I
NTF4_HUMAN
Polymorphism
---
A/B
T
127
I
12
UniProt
VAR_063208
T
207
S
NTF4_HUMAN
Polymorphism
---
A/B
T
127
S
13
UniProt
VAR_016320
G
309
R
NTRK2_HUMAN
Polymorphism
---
X/Y
G
309
R
14
UniProt
VAR_011973
N
338
Y
NTRK2_HUMAN
Polymorphism
1047856
X/Y
N
338
Y
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: NGF_2 (A:7-127,B:7-128)
2: NGF_1 (A:77-90,B:77-90)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
NGF_2
PS50270
Nerve growth factor family profile.
NTF4_HUMAN
87-209
2
A:7-127
B:7-128
2
NGF_1
PS00248
Nerve growth factor family signature.
NTF4_HUMAN
157-170
2
A:77-90
B:77-90
[
close PROSITE info
]
Exons
(2, 4)
Info
All Exons
Exon 1.10 (X:283-285 | Y:283-285)
Exon 1.11 (X:285-383 | Y:285-383)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.9/1.10
2: Boundary 1.10/1.11
3: Boundary 1.11/1.12
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
ENST00000376213
1
ENSE00001469814
chr9:
87283466-87283700
235
NTRK2_HUMAN
-
0
0
-
-
1.2
ENST00000376213
2
ENSE00001469812
chr9:
87284217-87284338
122
NTRK2_HUMAN
-
0
0
-
-
1.3a
ENST00000376213
3a
ENSE00001469810
chr9:
87284595-87284803
209
NTRK2_HUMAN
-
0
0
-
-
1.4a
ENST00000376213
4a
ENSE00001343633
chr9:
87285292-87285875
584
NTRK2_HUMAN
1-71
71
0
-
-
1.5
ENST00000376213
5
ENSE00001264558
chr9:
87317074-87317148
75
NTRK2_HUMAN
71-96
26
0
-
-
1.6
ENST00000376213
6
ENSE00000982953
chr9:
87317263-87317334
72
NTRK2_HUMAN
96-120
25
0
-
-
1.7
ENST00000376213
7
ENSE00001264539
chr9:
87322759-87322827
69
NTRK2_HUMAN
120-143
24
0
-
-
1.8
ENST00000376213
8
ENSE00001264532
chr9:
87325552-87325706
155
NTRK2_HUMAN
143-195
53
0
-
-
1.9
ENST00000376213
9
ENSE00000982956
chr9:
87338488-87338624
137
NTRK2_HUMAN
195-240
46
0
-
-
1.10
ENST00000376213
10
ENSE00001264518
chr9:
87339139-87339271
133
NTRK2_HUMAN
241-285
45
2
X:283-285
Y:283-285
3
3
1.11
ENST00000376213
11
ENSE00001264511
chr9:
87342569-87342874
306
NTRK2_HUMAN
285-387
103
2
X:285-383
Y:285-383
99
99
1.12
ENST00000376213
12
ENSE00001025534
chr9:
87356807-87356842
36
NTRK2_HUMAN
387-399
13
0
-
-
1.13
ENST00000376213
13
ENSE00001264498
chr9:
87359888-87359988
101
NTRK2_HUMAN
399-432
34
0
-
-
1.14
ENST00000376213
14
ENSE00000982960
chr9:
87366901-87367000
100
NTRK2_HUMAN
433-466
34
0
-
-
1.17
ENST00000376213
17
ENSE00001090519
chr9:
87482158-87482346
189
NTRK2_HUMAN
466-529
64
0
-
-
1.19
ENST00000376213
19
ENSE00001090518
chr9:
87549077-87549207
131
NTRK2_HUMAN
529-572
44
0
-
-
1.20
ENST00000376213
20
ENSE00001090522
chr9:
87563377-87563549
173
NTRK2_HUMAN
573-630
58
0
-
-
1.21
ENST00000376213
21
ENSE00001090521
chr9:
87570198-87570432
235
NTRK2_HUMAN
630-708
79
0
-
-
1.22
ENST00000376213
22
ENSE00001714994
chr9:
87635121-87635279
159
NTRK2_HUMAN
709-761
53
0
-
-
1.23c
ENST00000376213
23c
ENSE00001469734
chr9:
87636167-87638505
2339
NTRK2_HUMAN
762-822
61
0
-
-
[
close EXON info
]
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d1hcfx_ (X:)
1b: SCOP_d1hcfy_ (Y:)
2a: SCOP_d1hcfa_ (A:)
2b: SCOP_d1hcfb_ (B:)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
Immunoglobulin
(5995)
Family
:
I set domains
(152)
Protein domain
:
Ligand binding domain of trkB receptor
(2)
Human (Homo sapiens) [TaxId: 9606]
(2)
1a
d1hcfx_
X:
1b
d1hcfy_
Y:
Class
:
Small proteins
(3458)
Fold
:
Cystine-knot cytokines
(124)
Superfamily
:
Cystine-knot cytokines
(124)
Family
:
Neurotrophin
(20)
Protein domain
:
Neurotrophin 4, NT4
(3)
Human (Homo sapiens) [TaxId: 9606]
(3)
2a
d1hcfa_
A:
2b
d1hcfb_
B:
[
close SCOP info
]
CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1hcfA00 (A:1-127)
1b: CATH_1hcfB00 (B:5-128)
2a: CATH_1hcfX00 (X:283-383)
2b: CATH_1hcfY00 (Y:283-383)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Ribbon
(789)
Topology
:
Cystine Knot Cytokines, subunit B
(102)
Homologous Superfamily
:
Cystine-knot cytokines
(102)
Human (Homo sapiens)
(84)
1a
1hcfA00
A:1-127
1b
1hcfB00
B:5-128
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Human (Homo sapiens)
(912)
2a
1hcfX00
X:283-383
2b
1hcfY00
Y:283-383
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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]
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(currently selected atoms:
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)
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Sidechain
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Protein & NOT Site
Protein & NOT PROSITE
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Chain X
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Asymmetric Unit 1
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