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.
1SG1
Asym. Unit
Info
Asym.Unit (71 KB)
Biol.Unit 1 (66 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CRYSTAL STRUCTURE OF THE RECEPTOR-LIGAND COMPLEX BETWEEN NERVE GROWTH FACTOR AND THE COMMON NEUROTROPHIN RECEPTOR P75
Authors
:
X. L. He, K. C. Garcia
Date
:
22 Feb 04 (Deposition) - 01 Jun 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A,B,X
Biol. Unit 1: A,B,X (1x)
Keywords
:
Nerve Growth Factor, Ngf, P75, Neurotrophin, Common Neurotrophin Receptor, Crystal Structure, Growth Factor Receptor, Receptor/Ligand Complex, Hormone/Growth Factor/Membrane Protein Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
X. L. He, K. C. Garcia
Structure Of Nerve Growth Factor Complexed With The Shared Neurotrophin Receptor P75
Science V. 304 870 2004
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(1, 1)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
1
Ligand/Ion
CHLORIDE ION
[
close Hetero Component info
]
Sites
(1, 1)
Info
All Sites
1: AC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
VAL A:109 , CYS A:110 , CYS B:110
BINDING SITE FOR RESIDUE CL A 551
[
close Site info
]
SAPs(SNPs)/Variants
(1, 2)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_030659 (R100W, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_030659
R
221
W
NGF_HUMAN
Disease (HSAN5)
11466112
A/B
R
100
W
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(3, 9)
Info
All PROSITE Patterns/Profiles
1: TNFR_NGFR_2 (X:3-36|X:38-79|X:80-118|X:120-160)
2: TNFR_NGFR_1 (X:39-79|X:79-118|X:121-160)
3: NGF_1 (A:67-80,B:67-80)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
TNFR_NGFR_2
PS50050
TNFR/NGFR family cysteine-rich region domain profile.
TNR16_RAT
32-65
67-108
109-147
149-189
4
X:3-36
X:38-79
X:80-118
X:120-160
2
TNFR_NGFR_1
PS00652
TNFR/NGFR family cysteine-rich region signature.
TNR16_RAT
68-108
108-147
150-189
3
X:39-79
X:79-118
X:121-160
3
NGF_1
PS00248
Nerve growth factor family signature.
NGF_HUMAN
188-201
2
A:67-80
B:67-80
[
close PROSITE info
]
Exons
(1, 2)
Info
All Exons
Exon 1.3 (A:11-115 (gaps) | B:9-116 (gaps))
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.2/1.3
2: Boundary 1.3/-
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
ENST00000369512
1
ENSE00001020911
chr1:
115880857-115880825
33
NGF_HUMAN
-
0
0
-
-
1.2
ENST00000369512
2
ENSE00001020912
chr1:
115836371-115836248
124
NGF_HUMAN
-
0
0
-
-
1.3
ENST00000369512
3
ENSE00001450208
chr1:
115829428-115828539
890
NGF_HUMAN
1-245
245
2
A:11-115 (gaps)
B:9-116 (gaps)
105
108
[
close EXON info
]
SCOP Domains
(2, 6)
Info
All SCOP Domains
1a: SCOP_d1sg1a_ (A:)
1b: SCOP_d1sg1b_ (B:)
2a: SCOP_d1sg1x1 (X:2-56)
2b: SCOP_d1sg1x2 (X:57-95)
2c: SCOP_d1sg1x3 (X:96-137)
2d: SCOP_d1sg1x4 (X:138-161)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Small proteins
(3458)
Fold
:
Cystine-knot cytokines
(124)
Superfamily
:
Cystine-knot cytokines
(124)
Family
:
Neurotrophin
(20)
Protein domain
:
beta-Nerve growth factor
(8)
Human (Homo sapiens) [TaxId: 9606]
(5)
1a
d1sg1a_
A:
1b
d1sg1b_
B:
Fold
:
TNF receptor-like
(25)
Superfamily
:
TNF receptor-like
(25)
Family
:
TNF receptor-like
(16)
Protein domain
:
Low affinity neurotrophin receptor p75NTR
(2)
Norway rat (Rattus norvegicus) [TaxId: 10116]
(2)
2a
d1sg1x1
X:2-56
2b
d1sg1x2
X:57-95
2c
d1sg1x3
X:96-137
2d
d1sg1x4
X:138-161
[
close SCOP info
]
CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1sg1B00 (B:9-116)
1b: CATH_1sg1A00 (A:11-115)
2a: CATH_1sg1X02 (X:83-161)
2b: CATH_1sg1X01 (X:2-82)
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
1sg1B00
B:9-116
1b
1sg1A00
A:11-115
Topology
:
Tumor Necrosis Factor Receptor, subunit A; domain 2
(17)
Homologous Superfamily
:
Tumor Necrosis Factor Receptor, subunit A, domain 2
(16)
Human (Homo sapiens)
(13)
2a
1sg1X02
X:83-161
2b
1sg1X01
X:2-82
[
close CATH info
]
Pfam Domains
(2, 5)
Info
all PFAM domains
1a: PFAM_NGF_1sg1B01 (B:9-116)
1b: PFAM_NGF_1sg1B02 (B:9-116)
2a: PFAM_TNFR_c6_1sg1X01 (X:121-160)
2b: PFAM_TNFR_c6_1sg1X02 (X:121-160)
2c: PFAM_TNFR_c6_1sg1X03 (X:121-160)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Cystine-knot
(56)
Family
:
NGF
(4)
Homo sapiens (Human)
(3)
1a
NGF-1sg1B01
B:9-116
1b
NGF-1sg1B02
B:9-116
Clan
:
no clan defined [family: TNFR_c6]
(13)
Family
:
TNFR_c6
(13)
Rattus norvegicus (Rat)
(1)
2a
TNFR_c6-1sg1X01
X:121-160
2b
TNFR_c6-1sg1X02
X:121-160
2c
TNFR_c6-1sg1X03
X:121-160
[
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
Chain X
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 (71 KB)
Header - Asym.Unit
Biol.Unit 1 (66 KB)
Header - Biol.Unit 1
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
1SG1
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help