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2VYV
Asym. Unit
Info
Asym.Unit (235 KB)
Biol.Unit 1 (227 KB)
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(1)
Title
:
STRUCTURE OF E.COLI GAPDH RAT SPERM GAPDH HETEROTETRAMER
Authors
:
J. Frayne, A. Taylor, L. Hall, A. Hadfield
Date
:
29 Jul 08 (Deposition) - 05 Aug 08 (Release) - 25 Aug 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.38
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Contraceptive, Oxidoreductase, Alpha Chlorohydrin, Glyceraldehyde-3-Phosphate, Nad, Gapdh, Rat Sperm, Cytoplasm, Glycolysis
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Frayne, A. Taylor, G. Cameron, A. T. Hadfield
Structure Of Insoluble Rat Sperm Glyceraldehyde-3- Phosphate Dehydrogenase (Gapdh) Via Heterotetramer Formation With Escherichia Coli Gapdh Reveals Target For Contraceptive Design.
J. Biol. Chem. V. 284 22703 2009
[
close entry info
]
Hetero Components
(5, 27)
Info
All Hetero Components
1a: SN-GLYCEROL-1-PHOSPHATE (1GPa)
2a: 3-SULFINOALANINE (CSDa)
2b: 3-SULFINOALANINE (CSDb)
2c: 3-SULFINOALANINE (CSDc)
2d: 3-SULFINOALANINE (CSDd)
2e: 3-SULFINOALANINE (CSDe)
2f: 3-SULFINOALANINE (CSDf)
2g: 3-SULFINOALANINE (CSDg)
3a: S-OXY CYSTEINE (CSXa)
4a: FORMIC ACID (FMTa)
4b: FORMIC ACID (FMTb)
4c: FORMIC ACID (FMTc)
4d: FORMIC ACID (FMTd)
4e: FORMIC ACID (FMTe)
4f: FORMIC ACID (FMTf)
4g: FORMIC ACID (FMTg)
4h: FORMIC ACID (FMTh)
4i: FORMIC ACID (FMTi)
4j: FORMIC ACID (FMTj)
4k: FORMIC ACID (FMTk)
4l: FORMIC ACID (FMTl)
4m: FORMIC ACID (FMTm)
4n: FORMIC ACID (FMTn)
5a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
5b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
5c: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADc)
5d: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
1GP
1
Ligand/Ion
SN-GLYCEROL-1-PHOSPHATE
2
CSD
7
Mod. Amino Acid
3-SULFINOALANINE
3
CSX
1
Mod. Amino Acid
S-OXY CYSTEINE
4
FMT
14
Ligand/Ion
FORMIC ACID
5
NAD
4
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
[
close Hetero Component info
]
Sites
(19, 19)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
CSD D:149 , HIS D:176 , THR D:179 , THR D:181 , ARG D:231 , NAD D:1340 , HOH D:2210
BINDING SITE FOR RESIDUE 1GP D1334
02
AC2
SOFTWARE
MET A:127 , ASN A:133 , LYS A:215 , HOH A:2208
BINDING SITE FOR RESIDUE FMT A1330
03
AC3
SOFTWARE
PRO C:126 , MET C:127 , HOH C:2183
BINDING SITE FOR RESIDUE FMT C1330
04
AC4
SOFTWARE
MET D:126 , HOH D:2211 , HOH D:2212
BINDING SITE FOR RESIDUE FMT D1335
05
AC5
SOFTWARE
PRO B:126 , MET B:127 , LYS B:215 , HOH B:2197
BINDING SITE FOR RESIDUE FMT B1330
06
AC6
SOFTWARE
GLU C:285 , HOH C:2148 , ARG D:51
BINDING SITE FOR RESIDUE FMT D1336
07
AC7
SOFTWARE
ARG A:51 , ASN B:283 , GLU B:285
BINDING SITE FOR RESIDUE FMT B1331
08
AC8
SOFTWARE
PRO D:120 , SER D:148 , THR D:151 , GLY D:209 , ALA D:210 , ALA D:213 , HOH D:2213 , HOH D:2214 , HOH D:2215
BINDING SITE FOR RESIDUE FMT D1337
09
AC9
SOFTWARE
GLY D:130 , GLU D:133 , PRO D:266
BINDING SITE FOR RESIDUE FMT D1338
10
BC1
SOFTWARE
ARG A:51 , THR B:273 , GLU B:285
BINDING SITE FOR RESIDUE FMT A1331
11
BC2
SOFTWARE
THR B:273 , GLU B:274
BINDING SITE FOR RESIDUE FMT B1332
12
BC3
SOFTWARE
GLY A:131 , ALA A:132 , PHE A:134 , HOH A:2209 , HOH A:2210
BINDING SITE FOR RESIDUE FMT A1332
13
BC4
SOFTWARE
GLY B:131 , PHE B:134 , ASP B:135 , HOH B:2069
BINDING SITE FOR RESIDUE FMT B1333
14
BC5
SOFTWARE
ARG D:17 , HOH D:2216
BINDING SITE FOR RESIDUE FMT D1339
15
BC6
SOFTWARE
GLY C:131 , ALA C:132 , ASN C:133 , PHE C:134
BINDING SITE FOR RESIDUE FMT C1331
16
BC7
SOFTWARE
GLY A:7 , PHE A:8 , GLY A:9 , ARG A:10 , ILE A:11 , ASN A:31 , ASP A:32 , ARG A:76 , ALA A:94 , THR A:95 , GLY A:96 , LEU A:97 , THR A:118 , CSD A:148 , ALA A:179 , ASN A:312 , HOH A:2097 , HOH A:2211 , HOH A:2213 , HOH A:2214 , HOH A:2216 , HOH A:2217 , HOH A:2218 , HOH A:2219
BINDING SITE FOR RESIDUE NAD A1333
17
BC8
SOFTWARE
ASN B:6 , GLY B:9 , ARG B:10 , ILE B:11 , ASN B:31 , ASP B:32 , LEU B:33 , ARG B:76 , ALA B:94 , THR B:95 , GLY B:96 , LEU B:97 , THR B:118 , CSD B:148 , ALA B:179 , ASN B:312 , GLU B:313 , TYR B:316 , HOH B:2049 , HOH B:2187 , HOH B:2198 , HOH B:2200 , HOH B:2202 , HOH B:2203 , HOH B:2204 , HOH B:2205 , HOH B:2206 , HOH B:2207 , PRO C:187
BINDING SITE FOR RESIDUE NAD B1334
18
BC9
SOFTWARE
GLY C:7 , PHE C:8 , GLY C:9 , ARG C:10 , ILE C:11 , ASN C:31 , ASP C:32 , ARG C:76 , ALA C:94 , THR C:95 , GLY C:96 , LEU C:97 , THR C:118 , CSD C:148 , ALA C:179 , ASN C:312 , TYR C:316 , HOH C:2003 , HOH C:2050 , HOH C:2057 , HOH C:2075 , HOH C:2087 , HOH C:2185 , HOH C:2186 , HOH C:2187 , HOH C:2188 , HOH C:2189 , HOH C:2190
BINDING SITE FOR RESIDUE NAD C1332
19
CC1
SOFTWARE
HOH A:2117 , ASN D:6 , GLY D:7 , PHE D:8 , GLY D:9 , ARG D:10 , ILE D:11 , ASN D:30 , ASP D:31 , PRO D:32 , PHE D:33 , LYS D:76 , ALA D:94 , THR D:95 , GLY D:96 , TYR D:98 , THR D:118 , ALA D:119 , CSD D:149 , ALA D:180 , ASN D:313 , TYR D:317 , 1GP D:1334 , HOH D:2063 , HOH D:2115 , HOH D:2210 , HOH D:2217 , HOH D:2218 , HOH D:2219 , HOH D:2220 , HOH D:2221 , HOH D:2222
BINDING SITE FOR RESIDUE NAD D1340
[
close Site info
]
SAPs(SNPs)/Variants
(3, 9)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_G3P1_ECOLI_001 (Y41I, chain A/B/C, )
2: VAR_G3P1_ECOLI_002 (G264D, chain A/B/C, )
3: VAR_G3P1_ECOLI_003 (E265A, chain A/B/C, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_G3P1_ECOLI_001
*
Y
43
I
G3P1_ECOLI
---
---
A/B/C
Y
41
I
2
UniProt
VAR_G3P1_ECOLI_002
*
G
266
D
G3P1_ECOLI
---
---
A/B/C
G
264
D
3
UniProt
VAR_G3P1_ECOLI_003
*
E
267
A
G3P1_ECOLI
---
---
A/B/C
E
265
A
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: GAPDH (A:146-153,B:146-153,C:146-153,D:14...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
GAPDH
PS00071
Glyceraldehyde 3-phosphate dehydrogenase active site.
G3P1_ECOLI
148-155
3
A:146-153
B:146-153
C:146-153
G3PT_RAT
246-253
1
D:147-154
[
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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.
SCOP Domains
(2, 6)
Info
All SCOP Domains
1a: SCOP_d2vyva2 (A:147-310)
1b: SCOP_d2vyvb2 (B:147-310)
1c: SCOP_d2vyvc2 (C:147-310)
2a: SCOP_d2vyva1 (A:0-146,A:311-329)
2b: SCOP_d2vyvb1 (B:0-146,B:311-329)
2c: SCOP_d2vyvc1 (C:0-146,C:311-329)
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(
)
(
)
Folds
(
)
(
)
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(
)
(
)
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(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
FwdE/GAPDH domain-like
(188)
Superfamily
:
Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
(179)
Family
:
GAPDH-like
(99)
Protein domain
:
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)
(61)
Escherichia coli [TaxId: 562]
(9)
1a
d2vyva2
A:147-310
1b
d2vyvb2
B:147-310
1c
d2vyvc2
C:147-310
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
NAD(P)-binding Rossmann-fold domains
(1604)
Superfamily
:
NAD(P)-binding Rossmann-fold domains
(1604)
Family
:
Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain
(179)
Protein domain
:
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)
(61)
Escherichia coli [TaxId: 562]
(9)
2a
d2vyva1
A:0-146,A:311-329
2b
d2vyvb1
B:0-146,B:311-329
2c
d2vyvc1
C:0-146,C:311-329
[
close SCOP info
]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_2vyvA02 (A:147-312)
1b: CATH_2vyvD02 (D:147-313)
1c: CATH_2vyvB02 (B:147-312)
1d: CATH_2vyvC02 (C:147-312)
2a: CATH_2vyvD01 (D:0-146,D:314-333)
2b: CATH_2vyvA01 (A:0-146,A:313-329)
2c: CATH_2vyvB01 (B:0-146,B:313-329)
2d: CATH_2vyvC01 (C:0-146,C:313-329)
View:
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(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Dihydrodipicolinate Reductase; domain 2
(182)
Homologous Superfamily
:
Dihydrodipicolinate Reductase; domain 2
(178)
Norway rat (Rattus norvegicus)
(5)
1a
2vyvA02
A:147-312
1b
2vyvD02
D:147-313
1c
2vyvB02
B:147-312
1d
2vyvC02
C:147-312
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Norway rat (Rattus norvegicus)
(18)
2a
2vyvD01
D:0-146,D:314-333
2b
2vyvA01
A:0-146,A:313-329
2c
2vyvB01
B:0-146,B:313-329
2d
2vyvC01
C:0-146,C:313-329
[
close CATH info
]
Pfam Domains
(4, 8)
Info
all PFAM domains
1a: PFAM_Gp_dh_C_2vyvC01 (C:153-310)
1b: PFAM_Gp_dh_C_2vyvC02 (C:153-310)
1c: PFAM_Gp_dh_C_2vyvC03 (C:153-310)
2a: PFAM_Gp_dh_C_2vyvD01 (D:154-311)
3a: PFAM_Gp_dh_N_2vyvC04 (C:1-148)
3b: PFAM_Gp_dh_N_2vyvC05 (C:1-148)
3c: PFAM_Gp_dh_N_2vyvC06 (C:1-148)
4a: PFAM_Gp_dh_N_2vyvD02 (D:3-149)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
GADPH_aa-bio_dh
(59)
Family
:
Gp_dh_C
(38)
Escherichia coli (strain K12)
(5)
1a
Gp_dh_C-2vyvC01
C:153-310
1b
Gp_dh_C-2vyvC02
C:153-310
1c
Gp_dh_C-2vyvC03
C:153-310
Rattus norvegicus (Rat)
(1)
2a
Gp_dh_C-2vyvD01
D:154-311
Clan
:
NADP_Rossmann
(1239)
Family
:
Gp_dh_N
(38)
Escherichia coli (strain K12)
(5)
3a
Gp_dh_N-2vyvC04
C:1-148
3b
Gp_dh_N-2vyvC05
C:1-148
3c
Gp_dh_N-2vyvC06
C:1-148
Rattus norvegicus (Rat)
(1)
4a
Gp_dh_N-2vyvD02
D:3-149
[
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]
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Asym.Unit (235 KB)
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