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4DBV
Asym. Unit
Info
Asym.Unit (221 KB)
Biol.Unit 1 (216 KB)
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(1)
Title
:
GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE MUTANT WITH LEU 33 REPLACED BY THR, THR 34 REPLACED BY GLY, ASP 36 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
:
06 Jan 97 (Deposition) - 07 Jul 97 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
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:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
THR O:179 , ASP O:181 , ARG O:195 , ARG O:231 , NDP O:336 , HOH O:348 , HOH O:395
BINDING SITE FOR RESIDUE SO4 O 338
02
AC2
SOFTWARE
SER O:148 , THR O:208 , GLY O:209 , ALA O:210 , HOH O:346 , HOH O:378 , HOH O:417
BINDING SITE FOR RESIDUE SO4 O 339
03
AC3
SOFTWARE
THR P:179 , ARG P:195 , ARG P:231 , NDP P:336 , HOH P:352 , HOH P:404
BINDING SITE FOR RESIDUE SO4 P 338
04
AC4
SOFTWARE
SER P:148 , THR P:208 , GLY P:209 , ALA P:210 , HOH P:385
BINDING SITE FOR RESIDUE SO4 P 339
05
AC5
SOFTWARE
THR Q:179 , ASP Q:181 , ARG Q:195 , ARG Q:231 , NDP Q:336 , HOH Q:348
BINDING SITE FOR RESIDUE SO4 Q 338
06
AC6
SOFTWARE
SER Q:148 , THR Q:208 , GLY Q:209 , ALA Q:210 , HOH Q:377 , HOH Q:406
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:353 , HOH R:402 , HOH R:407
BINDING SITE FOR RESIDUE SO4 R 338
08
AC8
SOFTWARE
SER R:148 , THR R:208 , GLY R:209 , ALA R:210 , HOH R:413
BINDING SITE FOR RESIDUE SO4 R 339
09
AC9
SOFTWARE
GLY O:7 , GLY O:9 , ARG O:10 , ILE O:11 , ASN O:31 , ASP O:32 , THR O:33 , ARG O:77 , SER O:95 , THR O:96 , GLY O:97 , ARG O:98 , SER O:119 , ALA O:120 , CYS O:149 , ASN O:180 , ASN O:313 , SO4 O:338 , HOH O:348 , HOH O:349 , HOH O:351 , HOH O:358 , HOH O:367 , HOH O:371 , HOH O:391 , HOH O:418
BINDING SITE FOR RESIDUE NDP O 336
10
BC1
SOFTWARE
GLY P:7 , GLY P:9 , ARG P:10 , ILE P:11 , ASN P:31 , ASP P:32 , THR 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 , ASN P:180 , ASN P:313 , TYR P:317 , SO4 P:338 , HOH P:352 , HOH P:353 , HOH P:355 , HOH P:364 , HOH P:374 , HOH P:378 , HOH P:380 , HOH P:431 , HOH Q:341
BINDING SITE FOR RESIDUE NDP P 336
11
BC2
SOFTWARE
HOH P:438 , GLY Q:7 , GLY Q:9 , ARG Q:10 , ILE Q:11 , ASN Q:31 , ASP Q:32 , THR Q:33 , GLU Q:76 , ARG Q:77 , SER Q:95 , THR Q:96 , GLY Q:97 , ARG Q:98 , SER Q:119 , ALA Q:120 , CYS Q:149 , ASN Q:180 , ASN Q:313 , TYR Q:317 , SO4 Q:338 , HOH Q:348 , HOH Q:349 , HOH Q:351 , HOH Q:358 , HOH Q:368 , HOH Q:371 , HOH Q:372
BINDING SITE FOR RESIDUE NDP Q 336
12
BC3
SOFTWARE
HOH O:429 , HOH O:430 , GLY R:7 , GLY R:9 , ARG R:10 , ILE R:11 , ASN R:31 , ASP R:32 , THR R:33 , GLU R:76 , ARG R:77 , SER R:95 , THR R:96 , GLY R:97 , ARG R:98 , SER R:119 , ALA R:120 , ASN R:180 , ASN R:313 , TYR R:317 , SO4 R:338 , HOH R:353 , HOH R:354 , HOH R:356 , HOH R:375
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_d4dbvo2 (O:149-312)
1b: SCOP_d4dbvp2 (P:149-312)
1c: SCOP_d4dbvq2 (Q:149-312)
1d: SCOP_d4dbvr2 (R:149-312)
2a: SCOP_d4dbvo1 (O:0-148,O:313-333)
2b: SCOP_d4dbvp1 (P:0-148,P:313-333)
2c: SCOP_d4dbvq1 (Q:0-148,Q:313-333)
2d: SCOP_d4dbvr1 (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
d4dbvo2
O:149-312
1b
d4dbvp2
P:149-312
1c
d4dbvq2
Q:149-312
1d
d4dbvr2
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
d4dbvo1
O:0-148,O:313-333
2b
d4dbvp1
P:0-148,P:313-333
2c
d4dbvq1
Q:0-148,Q:313-333
2d
d4dbvr1
R:0-148,R:313-333
[
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CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_4dbvO02 (O:148-313)
1b: CATH_4dbvP02 (P:148-313)
1c: CATH_4dbvQ02 (Q:148-313)
1d: CATH_4dbvR02 (R:148-313)
2a: CATH_4dbvO01 (O:0-147,O:314-333)
2b: CATH_4dbvP01 (P:0-147,P:314-333)
2c: CATH_4dbvQ01 (Q:0-147,Q:314-333)
2d: CATH_4dbvR01 (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
4dbvO02
O:148-313
1b
4dbvP02
P:148-313
1c
4dbvQ02
Q:148-313
1d
4dbvR02
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
4dbvO01
O:0-147,O:314-333
2b
4dbvP01
P:0-147,P:314-333
2c
4dbvQ01
Q:0-147,Q:314-333
2d
4dbvR01
R:0-147,R:314-333
[
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Pfam Domains
(0, 0)
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Asym.Unit (221 KB)
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