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1CF2
Asym. Unit
Info
Asym.Unit (241 KB)
Biol.Unit 1 (235 KB)
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(1)
Title
:
THREE-DIMENSIONAL STRUCTURE OF D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE FROM THE HYPERTHERMOPHILIC ARCHAEON METHANOTHERMUS FERVIDUS
Authors
:
C. Charron, F. Talfournier, M. N. Isuppov, G. Branlant, J. A. Littlechild, B. Vitoux, A. Aubry
Date
:
24 Mar 99 (Deposition) - 29 Mar 00 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : O,P,Q,R
Biol. Unit 1: O,P,Q,R (1x)
Keywords
:
Oxydoreductase, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. Charron, F. Talfournier, M. N. Isupov, G. Branlant, J. A. Littlechild, B. Vitoux, A. Aubry
Crystallization And Preliminary X-Ray Diffraction Studies Of D-Glyceraldehyde-3-Phosphate Dehydrogenase From The Hyperthermophilic Archaeon Methanothermus Fervidus.
Acta Crystallogr. , Sect. D V. 55 1353 1999
(for further references see the
PDB file header
)
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Hetero Components
(2, 8)
Info
All Hetero Components
1a: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPa)
1b: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPb)
1c: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPc)
1d: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPd)
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
NAP
4
Ligand/Ion
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2
SO4
4
Ligand/Ion
SULFATE 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:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
SER P:139 , CYS P:140 , ASN P:141 , ARG P:167 , HIS P:193 , HIS P:194 , HOH P:1216
BINDING SITE FOR RESIDUE SO4 P 1001
2
AC2
SOFTWARE
SER R:139 , CYS R:140 , ASN R:141 , ARG R:167 , HIS R:193 , HIS R:194
BINDING SITE FOR RESIDUE SO4 R 1002
3
AC3
SOFTWARE
SER O:139 , CYS O:140 , ASN O:141 , ARG O:167 , HIS O:193 , HIS O:194 , HOH O:1045 , HOH O:1126
BINDING SITE FOR RESIDUE SO4 O 1003
4
AC4
SOFTWARE
SER Q:139 , CYS Q:140 , ASN Q:141 , ARG Q:167 , HIS Q:193 , HIS Q:194 , HOH Q:1212
BINDING SITE FOR RESIDUE SO4 Q 1004
5
AC5
SOFTWARE
ASN P:7 , GLY P:8 , TYR P:9 , GLY P:10 , THR P:11 , VAL P:12 , LYS P:33 , THR P:34 , ARG P:35 , ALA P:53 , CYS P:85 , THR P:86 , PRO P:87 , GLU P:88 , ILE P:90 , GLN P:108 , GLY P:110 , ARG P:168 , ASP P:171 , GLN P:300 , HOH P:1048 , HOH P:1053 , HOH P:1061 , HOH P:1069 , HOH P:1078 , HOH P:1088 , HOH P:1096 , HOH P:1097 , HOH P:1104 , HOH P:1107 , HOH P:1109 , HOH P:1111 , HOH P:1165 , HOH P:1229 , HOH P:1232
BINDING SITE FOR RESIDUE NAP P 340
6
AC6
SOFTWARE
ASN R:7 , GLY R:8 , TYR R:9 , GLY R:10 , THR R:11 , VAL R:12 , LYS R:33 , THR R:34 , ARG R:35 , CYS R:85 , THR R:86 , PRO R:87 , GLU R:88 , GLN R:108 , GLY R:110 , ASP R:171 , GLN R:300 , HOH R:1006 , HOH R:1008 , HOH R:1012 , HOH R:1015 , HOH R:1016 , HOH R:1018 , HOH R:1104 , HOH R:1112 , HOH R:1176
BINDING SITE FOR RESIDUE NAP R 340
7
AC7
SOFTWARE
ASN O:7 , GLY O:8 , TYR O:9 , GLY O:10 , THR O:11 , VAL O:12 , LYS O:33 , THR O:34 , ARG O:35 , CYS O:85 , THR O:86 , PRO O:87 , GLU O:88 , GLN O:108 , GLY O:110 , ASP O:171 , GLN O:300 , ILE O:304 , HOH O:1029 , HOH O:1039 , HOH O:1048 , HOH O:1061 , HOH O:1066 , HOH O:1071 , HOH O:1078 , HOH O:1085 , HOH O:1103 , HOH O:1106 , HOH O:1161 , HOH O:1172 , HOH O:1192
BINDING SITE FOR RESIDUE NAP O 340
8
AC8
SOFTWARE
ASN Q:7 , GLY Q:8 , TYR Q:9 , GLY Q:10 , THR Q:11 , VAL Q:12 , LYS Q:33 , THR Q:34 , ARG Q:35 , CYS Q:85 , THR Q:86 , PRO Q:87 , GLU Q:88 , ILE Q:90 , GLN Q:108 , GLY Q:110 , ARG Q:168 , ASP Q:171 , GLN Q:300 , ILE Q:304 , HOH Q:1051 , HOH Q:1064 , HOH Q:1079 , HOH Q:1087 , HOH Q:1088 , HOH Q:1099 , HOH Q:1104 , HOH Q:1109 , HOH Q:1112 , HOH Q:1124 , HOH Q:1202 , HOH Q:1213
BINDING SITE FOR RESIDUE NAP Q 340
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: GAPDH (O:138-145,P:138-145,Q:138-145,R:13...)
;
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.
G3P_METFE
138-145
4
O:138-145
P:138-145
Q:138-145
R:138-145
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Exons
(0, 0)
Info
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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, 8)
Info
All SCOP Domains
1a: SCOP_d1cf2o2 (O:139-303)
1b: SCOP_d1cf2p2 (P:139-303)
1c: SCOP_d1cf2q2 (Q:139-303)
1d: SCOP_d1cf2r2 (R:139-303)
2a: SCOP_d1cf2o1 (O:1-138,O:304-336)
2b: SCOP_d1cf2p1 (P:1-138,P:304-336)
2c: SCOP_d1cf2q1 (Q:1-138,Q:304-336)
2d: SCOP_d1cf2r1 (R:1-138,R:304-336)
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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)
Methanothermus fervidus [TaxId: 2180]
(1)
1a
d1cf2o2
O:139-303
1b
d1cf2p2
P:139-303
1c
d1cf2q2
Q:139-303
1d
d1cf2r2
R:139-303
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)
Methanothermus fervidus [TaxId: 2180]
(1)
2a
d1cf2o1
O:1-138,O:304-336
2b
d1cf2p1
P:1-138,P:304-336
2c
d1cf2q1
Q:1-138,Q:304-336
2d
d1cf2r1
R:1-138,R:304-336
[
close SCOP info
]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1cf2O02 (O:139-303)
1b: CATH_1cf2P02 (P:139-303)
1c: CATH_1cf2Q02 (Q:139-303)
1d: CATH_1cf2R02 (R:139-303)
2a: CATH_1cf2O01 (O:1-138,O:304-336)
2b: CATH_1cf2P01 (P:1-138,P:304-336)
2c: CATH_1cf2Q01 (Q:1-138,Q:304-336)
2d: CATH_1cf2R01 (R:1-138,R:304-336)
View:
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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)
Methanothermus fervidus. Organism_taxid: 2180.
(1)
1a
1cf2O02
O:139-303
1b
1cf2P02
P:139-303
1c
1cf2Q02
Q:139-303
1d
1cf2R02
R:139-303
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Methanothermus fervidus. Organism_taxid: 2180.
(1)
2a
1cf2O01
O:1-138,O:304-336
2b
1cf2P01
P:1-138,P:304-336
2c
1cf2Q01
Q:1-138,Q:304-336
2d
1cf2R01
R:1-138,R:304-336
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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