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1SGF
Asym. Unit
Info
Asym.Unit (169 KB)
Biol.Unit 1 (161 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF 7S NGF: A COMPLEX OF NERVE GROWTH FACTOR WITH FOUR BINDING PROTEINS (SERINE PROTEINASES)
Authors
:
B. D. V. Bax, T. L. Blundell, J. Murray-Rust, N. Q. Mcdonald
Date
:
08 Aug 97 (Deposition) - 27 May 98 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.15
Chains
:
Asym. Unit : A,B,G,X,Y,Z
Biol. Unit 1: A,B,G,X,Y,Z (1x)
Keywords
:
Growth Factor (Beta-Ngf), Hydrolase - Serine Proteinase (Gamma-Ngf), Inactive Serine Proteinase (Alpha-Ngf), Growth Factor
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
B. Bax, T. L. Blundell, J. Murray-Rust, N. Q. Mcdonald
Structure Of Mouse 7S Ngf: A Complex Of Nerve Growth Factor With Four Binding Proteins.
Structure V. 5 1275 1997
(for further references see the
PDB file header
)
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Hetero Components
(3, 8)
Info
All Hetero Components
1a: N-ACETYL-D-GLUCOSAMINE (NAGa)
1b: N-ACETYL-D-GLUCOSAMINE (NAGb)
1c: N-ACETYL-D-GLUCOSAMINE (NAGc)
1d: N-ACETYL-D-GLUCOSAMINE (NAGd)
1e: N-ACETYL-D-GLUCOSAMINE (NAGe)
2a: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGa)
3a: ZINC ION (ZNa)
3b: ZINC ION (ZNb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NAG
5
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
2
NDG
1
Ligand/Ion
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
3
ZN
2
Ligand/Ion
ZINC ION
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Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASN A:95 , SER A:95B , ASP A:97
BINDING SITE FOR RESIDUE NAG A 11
2
AC2
SOFTWARE
ASN G:95 , NAG G:248
BINDING SITE FOR RESIDUE NAG G 247
3
AC3
SOFTWARE
PHE G:95J , NAG G:247
BINDING SITE FOR RESIDUE NAG G 248
4
AC4
SOFTWARE
ASN X:95 , SER X:95B , LEU X:95C
BINDING SITE FOR RESIDUE NAG X 511
5
AC5
SOFTWARE
LYS G:244 , ASN Z:95 , NAG Z:532
BINDING SITE FOR RESIDUE NDG Z 531
6
AC6
SOFTWARE
NDG Z:531
BINDING SITE FOR RESIDUE NAG Z 532
7
AC7
SOFTWARE
GLU A:75 , HIS A:82 , HIS G:217 , GLU G:222
BINDING SITE FOR RESIDUE ZN A 1
8
AC8
SOFTWARE
ASP X:77 , HIS X:82 , HIS Z:217 , GLU Z:222
BINDING SITE FOR RESIDUE ZN X 501
[
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SAPs(SNPs)/Variants
(1, 2)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_K1KB4_MOUSE_001 (E173K, chain A/X, )
View:
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Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_K1KB4_MOUSE_001
*
E
184
K
K1KB4_MOUSE
---
---
A/X
E
173
K
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(4, 10)
Info
All PROSITE Patterns/Profiles
1: TRYPSIN_DOM (G:16-243,Z:16-243)
2: TRYPSIN_HIS (A:53-58,X:53-58,G:53-58,Z:53-58)
3: NGF_1 (B:67-80,Y:67-80)
4: TRYPSIN_SER (G:189-200,Z:189-200)
;
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
TRYPSIN_DOM
PS50240
Serine proteases, trypsin domain profile.
K1KB3_MOUSE
25-258
2
G:16-243
Z:16-243
2
TRYPSIN_HIS
PS00134
Serine proteases, trypsin family, histidine active site.
K1KB4_MOUSE
56-61
2
A:53-58
X:53-58
K1KB3_MOUSE
61-66
2
G:53-58
Z:53-58
3
NGF_1
PS00248
Nerve growth factor family signature.
NGF_MOUSE
188-201
2
B:67-80
Y:67-80
4
TRYPSIN_SER
PS00135
Serine proteases, trypsin family, serine active site.
K1KB3_MOUSE
207-218
2
G:189-200
Z:189-200
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(2, 6)
Info
All SCOP Domains
1a: SCOP_d1sgfa_ (A:)
1b: SCOP_d1sgfg_ (G:)
1c: SCOP_d1sgfx_ (X:)
1d: SCOP_d1sgfz_ (Z:)
2a: SCOP_d1sgfb_ (B:)
2b: SCOP_d1sgfy_ (Y:)
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)
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)
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Trypsin-like serine proteases
(1752)
Superfamily
:
Trypsin-like serine proteases
(1752)
Family
:
Eukaryotic proteases
(1343)
Protein domain
:
7S NGF protease subunits
(1)
Mouse (Mus musculus) [TaxId: 10090]
(1)
1a
d1sgfa_
A:
1b
d1sgfg_
G:
1c
d1sgfx_
X:
1d
d1sgfz_
Z:
Class
:
Small proteins
(3458)
Fold
:
Cystine-knot cytokines
(124)
Superfamily
:
Cystine-knot cytokines
(124)
Family
:
Neurotrophin
(20)
Protein domain
:
beta-Nerve growth factor
(8)
Mouse (Mus musculus) [TaxId: 10090]
(3)
2a
d1sgfb_
B:
2b
d1sgfy_
Y:
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CATH Domains
(2, 10)
Info
all CATH domains
1a: CATH_1sgfG02 (G:28-120,G:233-245)
1b: CATH_1sgfZ02 (Z:28-120,Z:233-245)
1c: CATH_1sgfA02 (A:28-120,A:233-246)
1d: CATH_1sgfX02 (X:28-120,X:233-244)
1e: CATH_1sgfG01 (G:16-27,G:121-232)
1f: CATH_1sgfZ01 (Z:16-27,Z:121-232)
1g: CATH_1sgfA01 (A:25-27,A:121-232)
1h: CATH_1sgfX01 (X:26-27,X:121-232)
2a: CATH_1sgfB00 (B:10-118)
2b: CATH_1sgfY00 (Y:8-118)
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)
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(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
Thrombin, subunit H
(1535)
Homologous Superfamily
:
Trypsin-like serine proteases
(1488)
House mouse (Mus musculus)
(6)
1a
1sgfG02
G:28-120,G:233-245
1b
1sgfZ02
Z:28-120,Z:233-245
1c
1sgfA02
A:28-120,A:233-246
1d
1sgfX02
X:28-120,X:233-244
1e
1sgfG01
G:16-27,G:121-232
1f
1sgfZ01
Z:16-27,Z:121-232
1g
1sgfA01
A:25-27,A:121-232
1h
1sgfX01
X:26-27,X:121-232
Architecture
:
Ribbon
(789)
Topology
:
Cystine Knot Cytokines, subunit B
(102)
Homologous Superfamily
:
Cystine-knot cytokines
(102)
House mouse (Mus musculus)
(6)
2a
1sgfB00
B:10-118
2b
1sgfY00
Y:8-118
[
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Pfam Domains
(2, 6)
Info
all PFAM domains
1a: PFAM_NGF_1sgfY01 (Y:8-118)
1b: PFAM_NGF_1sgfY02 (Y:8-118)
2a: PFAM_Trypsin_1sgfZ01 (Z:16-238)
2b: PFAM_Trypsin_1sgfZ02 (Z:16-238)
2c: PFAM_Trypsin_1sgfX01 (X:26-238)
2d: PFAM_Trypsin_1sgfX02 (X:26-238)
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Clans
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)
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Families
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)
(
)
Organisms
(
)
(
)
Clan
:
Cystine-knot
(56)
Family
:
NGF
(4)
Mus musculus (Mouse)
(1)
1a
NGF-1sgfY01
Y:8-118
1b
NGF-1sgfY02
Y:8-118
Clan
:
Peptidase_PA
(797)
Family
:
Trypsin
(679)
Mus musculus (Mouse)
(4)
2a
Trypsin-1sgfZ01
Z:16-238
2b
Trypsin-1sgfZ02
Z:16-238
2c
Trypsin-1sgfX01
X:26-238
2d
Trypsin-1sgfX02
X:26-238
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