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1Z82
Asym. Unit
Info
Asym.Unit (116 KB)
Biol.Unit 1 (108 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF GLYCEROL-3-PHOSPHATE DEHYDROGENASE (TM0378) FROM THERMOTOGA MARITIMA AT 2.00 A RESOLUTION
Authors
:
Joint Center For Structural Genomics (Jcsg)
Date
:
29 Mar 05 (Deposition) - 12 Apr 05 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Tm0378, Glycerol-3-Phosphate Dehydrogenase, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Glycerol-3-Phosphate Dehydrogenase (Tm0378) From Thermotoga Maritima At 2. 00 A Resolution
To Be Published
[
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Hetero Components
(6, 32)
Info
All Hetero Components
1a: GLYCERALDEHYDE-3-PHOSPHATE (G3Ha)
2a: SN-GLYCEROL-3-PHOSPHATE (G3Pa)
3a: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDa)
3b: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDb)
3c: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDc)
4a: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDa)
4b: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDb)
4c: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDc)
4d: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDd)
4e: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDe)
5a: SELENOMETHIONINE (MSEa)
5b: SELENOMETHIONINE (MSEb)
5c: SELENOMETHIONINE (MSEc)
5d: SELENOMETHIONINE (MSEd)
5e: SELENOMETHIONINE (MSEe)
5f: SELENOMETHIONINE (MSEf)
5g: SELENOMETHIONINE (MSEg)
5h: SELENOMETHIONINE (MSEh)
5i: SELENOMETHIONINE (MSEi)
5j: SELENOMETHIONINE (MSEj)
5k: SELENOMETHIONINE (MSEk)
5l: SELENOMETHIONINE (MSEl)
5m: SELENOMETHIONINE (MSEm)
5n: SELENOMETHIONINE (MSEn)
5o: SELENOMETHIONINE (MSEo)
5p: SELENOMETHIONINE (MSEp)
5q: SELENOMETHIONINE (MSEq)
5r: SELENOMETHIONINE (MSEr)
5s: SELENOMETHIONINE (MSEs)
5t: SELENOMETHIONINE (MSEt)
6a: NADPH DIHYDRO-NICOTINAMIDE-ADENINE... (NDPa)
6b: NADPH DIHYDRO-NICOTINAMIDE-ADENINE... (NDPb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
G3H
1
Ligand/Ion
GLYCERALDEHYDE-3-PHOSPHATE
2
G3P
1
Ligand/Ion
SN-GLYCEROL-3-PHOSPHATE
3
MPD
3
Ligand/Ion
(4S)-2-METHYL-2,4-PENTANEDIOL
4
MRD
5
Ligand/Ion
(4R)-2-METHYLPENTANE-2,4-DIOL
5
MSE
20
Mod. Amino Acid
SELENOMETHIONINE
6
NDP
2
Ligand/Ion
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
[
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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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No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ALA A:10 , GLY A:11 , SER A:12 , TRP A:13 , ARG A:33 , ARG A:34 , TYR A:49 , ALA A:75 , PRO A:77 , TYR A:80 , HIS A:84 , SER A:99 , LYS A:100 , SER A:129 , HIS A:130 , ALA A:131 , ARG A:243 , ASN A:265 , GLN A:266 , VAL A:267 , GLU A:269 , HOH A:621 , HOH A:626 , HOH A:629 , HOH A:634 , HOH A:641 , HOH A:648 , HOH A:651 , HOH A:663 , HOH A:664 , HOH A:687 , G3P B:600
BINDING SITE FOR RESIDUE NDP A 500
02
AC2
SOFTWARE
HOH A:613 , LYS B:100 , GLY B:127 , PRO B:128 , SER B:129 , HIS B:130 , LYS B:179 , ASN B:180 , ASP B:232 , THR B:236 , TYR B:241 , SER B:242 , ARG B:243 , ASN B:244 , NDP B:500 , HOH B:618 , HOH B:635
BINDING SITE FOR RESIDUE G3H A 600
03
AC3
SOFTWARE
ARG A:87 , G3H A:600 , ALA B:10 , GLY B:11 , SER B:12 , TRP B:13 , ARG B:33 , ARG B:34 , TYR B:49 , ALA B:75 , PRO B:77 , TYR B:80 , GLU B:83 , HIS B:84 , SER B:99 , LYS B:100 , SER B:129 , HIS B:130 , ALA B:131 , ARG B:243 , ASN B:265 , GLN B:266 , VAL B:267 , GLU B:269 , HOH B:618 , HOH B:620 , HOH B:621 , HOH B:633 , HOH B:635 , HOH B:636 , HOH B:638 , HOH B:652 , HOH B:653
BINDING SITE FOR RESIDUE NDP B 500
04
AC4
SOFTWARE
LYS A:100 , GLY A:127 , SER A:129 , HIS A:130 , LYS A:179 , ASP A:232 , THR A:236 , TYR A:241 , SER A:242 , ARG A:243 , ASN A:244 , NDP A:500 , HOH A:621 , HOH A:626 , HOH B:630
BINDING SITE FOR RESIDUE G3P B 600
05
AC5
SOFTWARE
ALA B:185 , ILE B:188 , GLU B:293 , SER B:307 , MSE B:308 , LEU B:311 , MRD B:602 , HOH B:684
BINDING SITE FOR RESIDUE MRD B 601
06
AC6
SOFTWARE
ALA A:185 , ILE A:188 , LEU A:189 , GLU A:293 , VAL A:294 , SER A:307 , MSE A:308 , LEU A:311 , HOH A:735
BINDING SITE FOR RESIDUE MRD A 601
07
AC7
SOFTWARE
THR A:140 , MSE B:312 , MRD B:601 , HOH B:684
BINDING SITE FOR RESIDUE MRD B 602
08
AC8
SOFTWARE
ARG B:243 , ARG B:246 , LEU B:260 , SER B:263 , SER B:264 , GLN B:266 , VAL B:268
BINDING SITE FOR RESIDUE MRD B 603
09
AC9
SOFTWARE
VAL A:43 , SER A:44 , MSE B:3 , GLU B:151
BINDING SITE FOR RESIDUE MRD B 604
10
BC1
SOFTWARE
ARG A:205 , LEU A:311 , HOH A:735
BINDING SITE FOR RESIDUE MPD A 602
11
BC2
SOFTWARE
ARG A:243 , ARG A:246 , LEU A:260 , SER A:263 , SER A:264 , GLN A:266
BINDING SITE FOR RESIDUE MPD A 603
12
BC3
SOFTWARE
GLY A:254 , PHE A:255
BINDING SITE FOR RESIDUE MPD A 604
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
Info
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Sorry, no Info available
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Exons
(0, 0)
Info
All Exons
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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, 4)
Info
All SCOP Domains
1a: SCOP_d1z82a2 (A:167-313)
1b: SCOP_d1z82b2 (B:167-314)
2a: SCOP_d1z82a1 (A:2-166)
2b: SCOP_d1z82b1 (B:3-166)
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Organisms
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(
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Class
:
All alpha proteins
(14657)
Fold
:
6-phosphogluconate dehydrogenase C-terminal domain-like
(119)
Superfamily
:
6-phosphogluconate dehydrogenase C-terminal domain-like
(119)
Family
:
automated matches
(50)
Protein domain
:
automated matches
(50)
Thermotoga maritima [TaxId: 243274]
(1)
1a
d1z82a2
A:167-313
1b
d1z82b2
B:167-314
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
:
automated matches
(447)
Protein domain
:
automated matches
(447)
Thermotoga maritima [TaxId: 243274]
(1)
2a
d1z82a1
A:2-166
2b
d1z82b1
B:3-166
[
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CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_1z82B02 (B:177-314)
1b: CATH_1z82A02 (A:177-313)
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Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2
(60)
Homologous Superfamily
:
N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2
(59)
Thermotoga maritima msb8. Organism_taxid: 243274. Strain: msb8.
(1)
1a
1z82B02
B:177-314
1b
1z82A02
A:177-313
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Pfam Domains
(0, 0)
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Asymmetric Unit 1
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