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1GPD
Asym. Unit
Info
Asym.Unit (93 KB)
Biol.Unit 1 (90 KB)
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(1)
Title
:
STUDIES OF ASYMMETRY IN THE THREE-DIMENSIONAL STRUCTURE OF LOBSTER D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
Authors
:
D. Moras, K. W. Olsen, M. N. Sabesan, M. Buehner, G. C. Ford, M. G. Rossman
Date
:
01 Jul 75 (Deposition) - 17 Feb 77 (Release) - 29 Oct 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.90
Chains
:
Asym. Unit : G,R
Biol. Unit 1: G,R (1x)
Keywords
:
Oxido-Reductase(Aldehyde/Donr, Nad/Accpt), Oxido-Reductase(Aldehyde- Donr, Nad-Accpt) Complex, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. Moras, K. W. Olsen, M. N. Sabesan, M. Buehner, G. C. Ford, M. G. Rossmann
Studies Of Asymmetry In The Three-Dimensional Structure Of Lobster D-Glyceraldehyde-3-Phosphate Dehydrogenase.
J. Biol. Chem. V. 250 9137 1975
(for further references see the
PDB file header
)
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Hetero Components
(3, 8)
Info
All Hetero Components
1a: ACETYL GROUP (ACEa)
1b: ACETYL GROUP (ACEb)
2a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
2b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
3a: PHOSPHATE ION (PO4a)
3b: PHOSPHATE ION (PO4b)
3c: PHOSPHATE ION (PO4c)
3d: PHOSPHATE ION (PO4d)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACE
2
Mod. Amino Acid
ACETYL GROUP
2
NAD
2
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
3
PO4
4
Ligand/Ion
PHOSPHATE ION
[
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Sites
(16, 16)
Info
All Sites
01: ABG (AUTHOR)
02: ABR (AUTHOR)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC7 (SOFTWARE)
06: AC8 (SOFTWARE)
07: APG (AUTHOR)
08: APR (AUTHOR)
09: ARG (AUTHOR)
10: ARR (AUTHOR)
11: NBG (AUTHOR)
12: NBR (AUTHOR)
13: NPG (AUTHOR)
14: NPR (AUTHOR)
15: NRG (AUTHOR)
16: NRR (AUTHOR)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
ABG
AUTHOR
ASN G:6 , ASN G:31 , ASP G:32 , PHE G:34 , THR G:96 , PHE G:99
RESIDUES INTERACTING WITH THE ADENINE BASE OF THE COFACTOR
02
ABR
AUTHOR
ASN R:6 , ASN R:31 , ASP R:32 , PHE R:34 , THR R:96 , PHE R:99
RESIDUES INTERACTING WITH THE ADENINE BASE OF THE COFACTOR
03
AC3
SOFTWARE
GLY G:7 , PHE G:8 , GLY G:9 , ARG G:10 , ILE G:11 , ASP G:32 , PHE G:34 , ILE G:35 , PHE G:99 , SER G:119 , GLU G:314
BINDING SITE FOR RESIDUE NAD G 335
04
AC4
SOFTWARE
PHE R:8 , ARG R:10 , ASP R:32 , THR R:96 , PHE R:99 , SER R:119 , ALA R:120 , CYS R:149 , ASN R:313 , TYR R:317
BINDING SITE FOR RESIDUE NAD R 339
05
AC7
SOFTWARE
THR R:179
BINDING SITE FOR RESIDUE PO4 R 337
06
AC8
SOFTWARE
THR R:150 , THR R:208 , GLY R:209
BINDING SITE FOR RESIDUE PO4 R 338
07
APG
AUTHOR
ARG G:10 , ALA G:180
RESIDUES INTERACTING WITH THE PHOSPHATE OF THE ADENOSINE NUCLEOTIDE OF THE NAD COFACTOR
08
APR
AUTHOR
ARG R:10 , ALA R:180
RESIDUES INTERACTING WITH THE PHOSPHATE OF THE ADENOSINE NUCLEOTIDE OF THE NAD COFACTOR
09
ARG
AUTHOR
GLY G:7 , ASP G:32 , PRO R:188
RESIDUES INTERACTING WITH THE ADENOSINE RIBOSE OF THE NAD COFACTOR
10
ARR
AUTHOR
GLY R:7 , PHE R:8 , ASP R:32 , PRO G:188
RESIDUES INTERACTING WITH THE ADENOSINE RIBOSE OF THE NAD COFACTOR
11
NBG
AUTHOR
ILE G:11 , CYS G:149 , ASN G:313 , TYR G:317
RESIDUES INTERACTING WITH THE NICOTINAMIDE BASE OF THE NAD COFACTOR
12
NBR
AUTHOR
ILE R:11 , CYS R:149 , ASN R:313 , TYR R:317
RESIDUES INTERACTING WITH THE NICOTINAMIDE BASE OF THE NAD COFACTOR
13
NPG
AUTHOR
ILE G:11
RESIDUES INTERACTING WITH THE PHOSPHATE OF THE NICOTINAMIDE NUCLEOTIDE OF THE NAD COFACTOR
14
NPR
AUTHOR
ILE R:11
RESIDUES INTERACTING WITH THE PHOSPHATE OF THE NICOTINAMIDE NUCLEOTIDE OF THE NAD COFACTOR
15
NRG
AUTHOR
THR G:96 , GLY G:97 , SER G:119 , ALA G:120
RESIDUES INTERACTING WITH THE RIBOSE OF THE NICOTINAMIDE NUCLEOTIDE OF THE NAD COFACTOR
16
NRR
AUTHOR
THR R:96 , GLY R:97 , SER R:119 , ALA R:120
RESIDUES INTERACTING WITH THE RIBOSE OF THE NICOTINAMIDE NUCLEOTIDE OF THE NAD COFACTOR
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: GAPDH (G:147-154,R:147-154)
;
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_HOMAM
146-153
2
G:147-154
R:147-154
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d1gpdg2 (G:149-312)
1b: SCOP_d1gpdr2 (R:149-312)
2a: SCOP_d1gpdg1 (G:1-148,G:313-334)
2b: SCOP_d1gpdr1 (R:1-148,R:313-334)
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Classes
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)
(
)
Folds
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(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
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)
American lobster (Homarus americanus) [TaxId: 6706]
(2)
1a
d1gpdg2
G:149-312
1b
d1gpdr2
R:149-312
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)
American lobster (Homarus americanus) [TaxId: 6706]
(2)
2a
d1gpdg1
G:1-148,G:313-334
2b
d1gpdr1
R:1-148,R:313-334
[
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CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1gpdG02 (G:148-313)
1b: CATH_1gpdR02 (R:148-313)
2a: CATH_1gpdG01 (G:1-147,G:314-333)
2b: CATH_1gpdR01 (R:1-147,R:314-333)
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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)
American lobster (Homarus americanus)
(2)
1a
1gpdG02
G:148-313
1b
1gpdR02
R:148-313
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
American lobster (Homarus americanus)
(2)
2a
1gpdG01
G:1-147,G:314-333
2b
1gpdR01
R:1-147,R:314-333
[
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Pfam Domains
(0, 0)
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all PFAM domains
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Chain G
Chain R
Asymmetric Unit 1
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select residue range 5 to 10 in chain 'A'
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Asym.Unit (93 KB)
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