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2J5Q
Asym. Unit
Info
Asym.Unit (208 KB)
Biol.Unit 1 (203 KB)
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(1)
Title
:
2.15 A RESOLUTION STRUCTURE OF THE WILD TYPE MALATE DEHYDROGENASE FROM HALOARCULA MARISMORTUI AFTER FIRST RADIATION BURN (RADIATION DAMAGE SERIES)
Authors
:
E. Fioravanti, F. M. D. Vellieux, P. Amara, D. Madern, M. Weik
Date
:
19 Sep 06 (Deposition) - 21 Sep 06 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.15
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Nad, Halophile, Oxidoreductase, Radiation Damage, Malate Dehydrogenase, Tricarboxylic Acid Cycle
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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Reference
:
E. Fioravanti, F. M. D. Vellieux, P. Amara, D. Madern, M. Weik
Specific Radiation Damage To Acidic Residues And Its Relation To Their Chemical And Structural Environment.
J. Synchrotron Radiat. V. 14 84 2007
(for further references see the
PDB file header
)
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Hetero Components
(1, 8)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
1c: CHLORIDE ION (CLc)
1d: CHLORIDE ION (CLd)
1e: CHLORIDE ION (CLe)
1f: CHLORIDE ION (CLf)
1g: CHLORIDE ION (CLg)
1h: CHLORIDE ION (CLh)
View:
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No.
Name
Count
Type
Full Name
1
CL
8
Ligand/Ion
CHLORIDE 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:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
LYS A:205 , ASP A:306 , THR D:210B , ASP D:211
BINDING SITE FOR RESIDUE CL A1331
2
AC2
SOFTWARE
THR A:210B , ASP A:211 , HOH A:2181 , LYS D:205 , ASP D:306
BINDING SITE FOR RESIDUE CL A1332
3
AC3
SOFTWARE
ARG A:166 , ARG A:252 , HIS A:256 , ASP B:73 , HOH B:2037
BINDING SITE FOR RESIDUE CL A1333
4
AC4
SOFTWARE
LYS B:205 , ASP B:306 , THR C:210B , ASP C:211
BINDING SITE FOR RESIDUE CL B1331
5
AC5
SOFTWARE
TYR A:72 , ASP A:73 , HOH A:2046 , ARG B:166 , ARG B:252 , HIS B:256
BINDING SITE FOR RESIDUE CL B1332
6
AC6
SOFTWARE
THR B:210B , ASP B:211 , LYS C:205 , ASP C:306
BINDING SITE FOR RESIDUE CL C1331
7
AC7
SOFTWARE
ARG C:166 , ARG C:252 , HIS C:256 , TYR D:72 , ASP D:73 , HOH D:2057
BINDING SITE FOR RESIDUE CL C1332
8
AC8
SOFTWARE
TYR C:72 , ASP C:73 , ARG D:166 , ARG D:252 , HIS D:256 , HOH D:2210
BINDING SITE FOR RESIDUE CL D1331
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are not available)
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PROSITE Patterns/Profiles
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Exons
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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_d2j5qa2 (A:163-330)
1b: SCOP_d2j5qc2 (C:163-330)
1c: SCOP_d2j5qd2 (D:163-330)
1d: SCOP_d2j5qb2 (B:163-330)
2a: SCOP_d2j5qa1 (A:22-162)
2b: SCOP_d2j5qc1 (C:22-162)
2c: SCOP_d2j5qd1 (D:22-162)
2d: SCOP_d2j5qb1 (B:22-162)
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)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
LDH C-terminal domain-like
(172)
Superfamily
:
LDH C-terminal domain-like
(172)
Family
:
Lactate & malate dehydrogenases, C-terminal domain
(125)
Protein domain
:
automated matches
(30)
Haloarcula marismortui [TaxId: 2238]
(4)
1a
d2j5qa2
A:163-330
1b
d2j5qc2
C:163-330
1c
d2j5qd2
D:163-330
1d
d2j5qb2
B:163-330
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
:
LDH N-terminal domain-like
(117)
Protein domain
:
automated matches
(15)
Haloarcula marismortui [TaxId: 2238]
(4)
2a
d2j5qa1
A:22-162
2b
d2j5qc1
C:22-162
2c
d2j5qd1
D:22-162
2d
d2j5qb1
B:22-162
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CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_2j5qA01 (A:22-162)
1b: CATH_2j5qC01 (C:22-162)
1c: CATH_2j5qB01 (B:22-162)
1d: CATH_2j5qD01 (D:22-162)
2a: CATH_2j5qA02 (A:163-330)
2b: CATH_2j5qB02 (B:163-330)
2c: CATH_2j5qC02 (C:163-330)
2d: CATH_2j5qD02 (D:163-330)
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)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Haloarcula marismortui. Organism_taxid: 2238. Strain: hms174.
(3)
1a
2j5qA01
A:22-162
1b
2j5qC01
C:22-162
1c
2j5qB01
B:22-162
1d
2j5qD01
D:22-162
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2
(116)
Homologous Superfamily
:
L-2-Hydroxyisocaproate Dehydrogenase, subunit A, domain 2
(116)
Haloarcula marismortui. Organism_taxid: 2238. Strain: hms174.
(3)
2a
2j5qA02
A:163-330
2b
2j5qB02
B:163-330
2c
2j5qC02
C:163-330
2d
2j5qD02
D:163-330
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Pfam Domains
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Asymmetric Unit 1
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Asym.Unit (208 KB)
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Header - Biol.Unit 1
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