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2DBV
Asym. Unit
Info
Asym.Unit (223 KB)
Biol.Unit 1 (217 KB)
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(1)
Title
:
GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE MUTANT WITH ASP 32 REPLACED BY GLY, LEU 187 REPLACED BY ALA, AND PRO 188 REPLACED BY SER COMPLEXED WITH NADP+
Authors
:
C. Didierjean, S. Rahuel-Clermont, B. Vitoux, O. Dideberg, G. Branlant, A. Aubry
Date
:
19 Dec 96 (Deposition) - 07 Jul 97 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : O,P,Q,R
Biol. Unit 1: O,P,Q,R (1x)
Keywords
:
Oxidoreductase, Nad(P) Selectivity
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. Didierjean, S. Rahuel-Clermont, B. Vitoux, O. Dideberg, G. Branlant, A. Aubry
A Crystallographic Comparison Between Mutated Glyceraldehyde-3-Phosphate Dehydrogenases From Bacillus Stearothermophilus Complexed With Either Nad+ Or Nadp+.
J. Mol. Biol. V. 268 739 1997
(for further references see the
PDB file header
)
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Hetero Components
(2, 12)
Info
All Hetero Components
1a: NADPH DIHYDRO-NICOTINAMIDE-ADENINE... (NDPa)
1b: NADPH DIHYDRO-NICOTINAMIDE-ADENINE... (NDPb)
1c: NADPH DIHYDRO-NICOTINAMIDE-ADENINE... (NDPc)
1d: NADPH DIHYDRO-NICOTINAMIDE-ADENINE... (NDPd)
2a: SULFATE ION (SO4a)
2b: SULFATE ION (SO4b)
2c: SULFATE ION (SO4c)
2d: SULFATE ION (SO4d)
2e: SULFATE ION (SO4e)
2f: SULFATE ION (SO4f)
2g: SULFATE ION (SO4g)
2h: SULFATE ION (SO4h)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NDP
4
Ligand/Ion
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
2
SO4
8
Ligand/Ion
SULFATE ION
[
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Sites
(12, 12)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
THR O:179 , ARG O:195 , ARG O:231 , NDP O:336 , HOH O:400
BINDING SITE FOR RESIDUE SO4 O 338
02
AC2
SOFTWARE
SER O:148 , THR O:208 , GLY O:209 , ALA O:210 , HOH O:399
BINDING SITE FOR RESIDUE SO4 O 339
03
AC3
SOFTWARE
THR P:179 , ASP P:181 , ARG P:195 , ARG P:231 , NDP P:336 , HOH P:351 , HOH P:400 , HOH P:408 , HOH P:411
BINDING SITE FOR RESIDUE SO4 P 338
04
AC4
SOFTWARE
SER P:148 , THR P:208 , GLY P:209 , ALA P:210 , HOH P:349 , HOH P:387 , HOH P:424 , HOH P:427
BINDING SITE FOR RESIDUE SO4 P 339
05
AC5
SOFTWARE
THR Q:179 , ASP Q:181 , ARG Q:231 , NDP Q:336 , HOH Q:349 , HOH Q:396
BINDING SITE FOR RESIDUE SO4 Q 338
06
AC6
SOFTWARE
SER Q:148 , THR Q:208 , GLY Q:209 , ALA Q:210 , HOH Q:418
BINDING SITE FOR RESIDUE SO4 Q 339
07
AC7
SOFTWARE
THR R:179 , ASP R:181 , ARG R:195 , ARG R:231 , NDP R:336 , HOH R:356 , HOH R:405
BINDING SITE FOR RESIDUE SO4 R 338
08
AC8
SOFTWARE
SER R:148 , THR R:208 , GLY R:209 , ALA R:210 , HOH R:354 , HOH R:387 , HOH R:427
BINDING SITE FOR RESIDUE SO4 R 339
09
AC9
SOFTWARE
ASN O:6 , GLY O:7 , GLY O:9 , ARG O:10 , ILE O:11 , ASN O:31 , GLY O:32 , LEU O:33 , ARG O:77 , SER O:95 , THR O:96 , GLY O:97 , SER O:119 , ALA O:120 , CYS O:149 , ASN O:180 , ASN O:313 , TYR O:317 , SO4 O:338 , HOH O:347 , HOH O:355 , HOH O:356 , HOH O:362 , HOH O:368 , HOH O:370 , HOH O:371 , HOH O:422 , HOH O:423 , HOH O:424 , SER R:188
BINDING SITE FOR RESIDUE NDP O 336
10
BC1
SOFTWARE
GLY P:9 , ARG P:10 , ILE P:11 , ASN P:31 , LEU P:33 , GLU P:76 , ARG P:77 , SER P:95 , THR P:96 , GLY P:97 , ARG P:98 , PHE P:99 , SER P:119 , ALA P:120 , CYS P:149 , ASN P:180 , ASN P:313 , GLU P:314 , SO4 P:338 , HOH P:351 , HOH P:352 , HOH P:353 , HOH P:360 , HOH P:365 , HOH P:371 , HOH P:376 , HOH P:390 , HOH P:435 , SER Q:188 , HOH Q:343
BINDING SITE FOR RESIDUE NDP P 336
11
BC2
SOFTWARE
SER P:188 , PHE Q:8 , GLY Q:9 , ARG Q:10 , ILE Q:11 , ASN Q:31 , LEU Q:33 , ARG Q:77 , SER Q:95 , THR Q:96 , GLY Q:97 , SER Q:119 , ALA Q:120 , ASN Q:180 , ASN Q:313 , TYR Q:317 , SO4 Q:338 , HOH Q:350 , HOH Q:361 , HOH Q:362 , HOH Q:365 , HOH Q:371 , HOH Q:375 , HOH Q:421 , HOH Q:422 , HOH Q:423
BINDING SITE FOR RESIDUE NDP Q 336
12
BC3
SOFTWARE
SER O:188 , GLY R:7 , PHE R:8 , GLY R:9 , ARG R:10 , ILE R:11 , ASN R:31 , GLY R:32 , LEU R:33 , ARG R:77 , SER R:95 , THR R:96 , GLY R:97 , SER R:119 , ALA R:120 , CYS R:149 , ASN R:180 , ASN R:313 , TYR R:317 , SO4 R:338 , HOH R:356 , HOH R:357 , HOH R:366 , HOH R:367 , HOH R:375 , HOH R:381 , HOH R:432 , HOH R:433 , HOH R:434
BINDING SITE FOR RESIDUE NDP R 336
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: GAPDH (O:147-154,P:147-154,Q:147-154,R:14...)
;
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_GEOSE
150-157
4
O:147-154
P:147-154
Q:147-154
R:147-154
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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_d2dbvo2 (O:149-312)
1b: SCOP_d2dbvp2 (P:149-312)
1c: SCOP_d2dbvq2 (Q:149-312)
1d: SCOP_d2dbvr2 (R:149-312)
2a: SCOP_d2dbvo1 (O:0-148,O:313-333)
2b: SCOP_d2dbvp1 (P:0-148,P:313-333)
2c: SCOP_d2dbvq1 (Q:0-148,Q:313-333)
2d: SCOP_d2dbvr1 (R:0-148,R:313-333)
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Protein Domains
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)
(
)
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)
Bacillus stearothermophilus, nca 1503 [TaxId: 1422]
(11)
1a
d2dbvo2
O:149-312
1b
d2dbvp2
P:149-312
1c
d2dbvq2
Q:149-312
1d
d2dbvr2
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)
Bacillus stearothermophilus, nca 1503 [TaxId: 1422]
(11)
2a
d2dbvo1
O:0-148,O:313-333
2b
d2dbvp1
P:0-148,P:313-333
2c
d2dbvq1
Q:0-148,Q:313-333
2d
d2dbvr1
R:0-148,R:313-333
[
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]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_2dbvO02 (O:148-313)
1b: CATH_2dbvP02 (P:148-313)
1c: CATH_2dbvQ02 (Q:148-313)
1d: CATH_2dbvR02 (R:148-313)
2a: CATH_2dbvO01 (O:0-147,O:314-333)
2b: CATH_2dbvP01 (P:0-147,P:314-333)
2c: CATH_2dbvQ01 (Q:0-147,Q:314-333)
2d: CATH_2dbvR01 (R:0-147,R:314-333)
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)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Dihydrodipicolinate Reductase; domain 2
(182)
Homologous Superfamily
:
Dihydrodipicolinate Reductase; domain 2
(178)
Geobacillus stearothermophilus. Organism_taxid: 1422.
(8)
1a
2dbvO02
O:148-313
1b
2dbvP02
P:148-313
1c
2dbvQ02
Q:148-313
1d
2dbvR02
R:148-313
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Geobacillus stearothermophilus. Organism_taxid: 1422.
(10)
2a
2dbvO01
O:0-147,O:314-333
2b
2dbvP01
P:0-147,P:314-333
2c
2dbvQ01
Q:0-147,Q:314-333
2d
2dbvR01
R:0-147,R:314-333
[
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Pfam Domains
(0, 0)
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