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3GPD
Biol. Unit 1
Info
Asym.Unit (93 KB)
Biol.Unit 1 (176 KB)
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(1)
Title
:
TWINNING IN CRYSTALS OF HUMAN SKELETAL MUSCLE D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
Authors
:
H. C. Watson, J. C. Campbell
Date
:
20 Jun 83 (Deposition) - 27 Oct 83 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.50
Chains
:
Asym. Unit : G,R
Biol. Unit 1: G,R (2x)
Keywords
:
Oxidoreductase (Nad(A)-Aldehyde(D))
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
W. D. Mercer, S. I. Winn, H. C. Watson
Twinning In Crystals Of Human Skeletal Muscle D-Glyceraldehyde-3-Phosphate Dehydrogenase.
J. Mol. Biol. V. 104 277 1976
(for further references see the
PDB file header
)
[
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Hetero Components
(2, 12)
Info
All Hetero Components
1a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
1b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
2a: SULFATE ION (SO4a)
2b: SULFATE ION (SO4b)
2c: SULFATE ION (SO4c)
2d: SULFATE ION (SO4d)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NAD
4
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
2
SO4
8
Ligand/Ion
SULFATE ION
[
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Sites
(14, 14)
Info
All Sites
01: ABR (AUTHOR)
02: AC1 (SOFTWARE)
03: AC2 (SOFTWARE)
04: AC3 (SOFTWARE)
05: AC4 (SOFTWARE)
06: AC5 (SOFTWARE)
07: AC6 (SOFTWARE)
08: APR (AUTHOR)
09: ARR (AUTHOR)
10: IPR (AUTHOR)
11: NBR (AUTHOR)
12: NPR (AUTHOR)
13: NRR (AUTHOR)
14: SPR (AUTHOR)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
ABR
AUTHOR
ASP R:8 , GLY R:9 , ASN R:33 , ASP R:34 , PRO R:35 , GLU R:78 , ARG R:79 , ASP R:80
RESIDUES INTERACTING WITH THE ADENINE BASE OF THE NAD COFACTOR IN THE RED SUBUNIT
02
AC1
SOFTWARE
THR R:181 , THR R:183 , NAD R:336
BINDING SITE FOR RESIDUE SO4 R 338
03
AC2
SOFTWARE
SER R:150 , CYS R:151 , THR R:210 , GLY R:211
BINDING SITE FOR RESIDUE SO4 R 340
04
AC3
SOFTWARE
THR G:181 , THR G:183 , NAD G:336
BINDING SITE FOR RESIDUE SO4 G 338
05
AC4
SOFTWARE
SER G:150 , CYS G:151 , THR G:152 , THR G:210 , GLY G:211
BINDING SITE FOR RESIDUE SO4 G 340
06
AC5
SOFTWARE
GLY R:9 , GLY R:11 , ARG R:12 , ILE R:13 , ASN R:33 , ASP R:34 , PRO R:35 , PHE R:36 , GLU R:78 , ASP R:80 , SER R:97 , THR R:98 , SER R:121 , ALA R:122 , CYS R:151 , ILE R:180 , ALA R:182 , ASN R:315 , GLU R:316 , SO4 R:338
BINDING SITE FOR RESIDUE NAD R 336
07
AC6
SOFTWARE
GLY G:9 , GLY G:11 , ARG G:12 , ILE G:13 , PRO G:35 , ARG G:79 , SER G:97 , THR G:98 , GLY G:99 , PHE G:101 , SER G:121 , ALA G:122 , CYS G:151 , ALA G:182 , ASN G:315 , SO4 G:338
BINDING SITE FOR RESIDUE NAD G 336
08
APR
AUTHOR
GLY R:11 , ARG R:12
RESIDUES INTERACTING WITH THE PHOSPHATE OF THE ADENOSINE NUCLEOTIDE OF THE NAD COFACTOR IN THE RED SUBUNIT
09
ARR
AUTHOR
PHE R:36 , SER R:97 , THR R:98
RESIDUES INTERACTING WITH THE ADENOSINE RIBOSE OF THE NAD COFACTOR IN THE RED SUBUNIT
10
IPR
AUTHOR
THR R:181 , ALA R:182 , THR R:183 , ARG R:233
RESIDUES INTERACTING WITH THE SUBSTRATE AND THE INORGANIC PHOSPHATE GROUPS RESPECTIVELY OF THE RED SUBUNIT
11
NBR
AUTHOR
CYS R:151 , ILE R:180 , ASN R:315 , GLU R:316
RESIDUES INTERACTING WITH THE NICOTINAMIDE BASE OF THE NAD COFACTOR IN THE RED SUBUNIT
12
NPR
AUTHOR
ARG R:12 , ILE R:13
RESIDUES INTERACTING WITH THE PHOSPHATE OF THE NICOTINAMIDE NUCLEOTIDE OF THE NAD COFACTOR IN THE RED SUBUNIT
13
NRR
AUTHOR
ILE R:13 , SER R:121 , ALA R:122
RESIDUES INTERACTING WITH THE RIBOSE OF THE NICOTINAMIDE NUCLEOTIDE OF THE NAD COFACTOR IN THE RED SUBUNIT
14
SPR
AUTHOR
SER R:150 , CYS R:151 , THR R:152 , THR R:210
RESIDUES INTERACTING WITH THE SUBSTRATE AND THE INORGANIC PHOSPHATE GROUPS RESPECTIVELY OF THE RED SUBUNIT
[
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SAPs(SNPs)/Variants
(2, 8)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_018889 (A21G, chain G/R, )
2: VAR_049218 (K250N, chain G/R, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_018889
A
22
G
G3P_HUMAN
Polymorphism
45541435
G/R
A
21
G
2
UniProt
VAR_049218
K
251
N
G3P_HUMAN
Polymorphism
1062429
G/R
K
250
N
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: GAPDH (G:149-156,R:149-156)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
GAPDH
PS00071
Glyceraldehyde 3-phosphate dehydrogenase active site.
G3P_HUMAN
150-157
4
G:149-156
R:149-156
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d3gpdg2 (G:151-314)
1b: SCOP_d3gpdr2 (R:151-314)
2a: SCOP_d3gpdg1 (G:1-150,G:315-334)
2b: SCOP_d3gpdr1 (R:1-150,R:315-334)
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)
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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)
Human (Homo sapiens) [TaxId: 9606]
(1)
1a
d3gpdg2
G:151-314
1b
d3gpdr2
R:151-314
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)
Human (Homo sapiens) [TaxId: 9606]
(1)
2a
d3gpdg1
G:1-150,G:315-334
2b
d3gpdr1
R:1-150,R:315-334
[
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]
CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_3gpdG02 (G:150-313)
1b: CATH_3gpdR02 (R:150-313)
2a: CATH_3gpdG01 (G:1-149,G:314-334)
2b: CATH_3gpdR01 (R:1-149,R:314-334)
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(
)
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)
Human (Homo sapiens)
(8)
1a
3gpdG02
G:150-313
1b
3gpdR02
R:150-313
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Human (Homo sapiens)
(188)
2a
3gpdG01
G:1-149,G:314-334
2b
3gpdR01
R:1-149,R:314-334
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Asymmetric Unit 1
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