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2EKQ
Biol. Unit 5
Info
Asym.Unit (170 KB)
Biol.Unit 1 (165 KB)
Biol.Unit 2 (86 KB)
Biol.Unit 3 (82 KB)
Biol.Unit 4 (85 KB)
Biol.Unit 5 (83 KB)
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(1)
Title
:
STRUCTURE OF TT0495 PROTEIN FROM THERMUS THERMOPHILUS
Authors
:
N. K. Lokanath, K. J. Pampa, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date
:
23 Mar 07 (Deposition) - 01 Apr 08 (Release) - 16 Apr 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: A,B (1x)
Biol. Unit 3: C,D (1x)
Biol. Unit 4: A,C (1x)
Biol. Unit 5: B,D (1x)
Keywords
:
Gluconate Dehydrogenase, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. J. Pampa, N. K. Lokanath, N. Kunishima, R. V. Rai
The First Crystal Structure Of Nad-Dependent 3-Dehydro-2-Deoxy-D-Gluconate Dehydrogenase From Thermus Thermophilus Hb8
Acta Crystallogr. , Sect. D V. 70 994 2014
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Hetero Components
(2, 6)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1b: GLYCEROL (GOLb)
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)
2i: SULFATE ION (SO4i)
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Label:
No.
Name
Count
Type
Full Name
1
GOL
1
Ligand/Ion
GLYCEROL
2
SO4
5
Ligand/Ion
SULFATE ION
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Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC4 (SOFTWARE)
3: AC5 (SOFTWARE)
4: AC6 (SOFTWARE)
5: AC7 (SOFTWARE)
6: AC8 (SOFTWARE)
7: AC9 (SOFTWARE)
8: BC1 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ARG B:12 , GLY B:13 , THR B:179 , GLU B:180 , HOH B:2089 , HOH B:2187 , HOH B:2188 , HOH B:2189 , HOH C:2022 , HOH C:2053
BINDING SITE FOR RESIDUE SO4 B 2001
2
AC4
SOFTWARE
GLY B:128 , SER B:129 , TYR B:144 , LYS B:148 , PRO B:174 , HOH B:2085 , HOH B:2220 , HOH B:2259
BINDING SITE FOR RESIDUE SO4 B 2004
3
AC5
SOFTWARE
SER A:90 , TYR A:91 , HOH A:2241 , GLN B:110 , HOH B:2263 , HOH B:2264
BINDING SITE FOR RESIDUE SO4 B 2005
4
AC6
SOFTWARE
GLN A:110 , SER B:90 , TYR B:91 , HOH B:2177 , HOH B:2229
BINDING SITE FOR RESIDUE SO4 B 2006
5
AC7
SOFTWARE
LEU C:89 , SER C:90 , TYR C:91 , HOH C:2224 , HOH C:2276 , HOH C:2280 , GLN D:110
BINDING SITE FOR RESIDUE SO4 C 2007
6
AC8
SOFTWARE
LEU C:107 , GLN C:110 , HOH C:2211 , HOH C:2212 , SER D:90 , TYR D:91
BINDING SITE FOR RESIDUE SO4 C 2008
7
AC9
SOFTWARE
SER B:11 , SER B:33 , ARG B:34 , HOH B:2121 , HOH B:2266 , HOH B:2267 , HOH B:2268 , GLU C:92
BINDING SITE FOR RESIDUE SO4 B 2009
8
BC1
SOFTWARE
SER B:129 , ILE B:141 , LEU B:185 , HOH B:2019 , HOH B:2085
BINDING SITE FOR RESIDUE GOL B 1287
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
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Exons
(0, 0)
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d2ekqa_ (A:)
1b: SCOP_d2ekqb_ (B:)
1c: SCOP_d2ekqc_ (C:)
1d: SCOP_d2ekqd_ (D:)
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Protein Domains
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(
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Organisms
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(
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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)
Thermus thermophilus HB8 [TaxId: 300852]
(16)
1a
d2ekqa_
A:
1b
d2ekqb_
B:
1c
d2ekqc_
C:
1d
d2ekqd_
D:
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CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_2ekqD00 (D:2-239)
1b: CATH_2ekqA00 (A:2-239)
1c: CATH_2ekqB00 (B:2-239)
1d: CATH_2ekqC00 (C:2-239)
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(
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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)
Thermus thermophilus hb8. Organism_taxid: 300852. Strain: hb8.
(8)
1a
2ekqD00
D:2-239
1b
2ekqA00
A:2-239
1c
2ekqB00
B:2-239
1d
2ekqC00
C:2-239
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Pfam Domains
(0, 0)
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Asymmetric Unit 1
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Asym.Unit (170 KB)
Header - Asym.Unit
Biol.Unit 1 (165 KB)
Header - Biol.Unit 1
Biol.Unit 2 (86 KB)
Header - Biol.Unit 2
Biol.Unit 3 (82 KB)
Header - Biol.Unit 3
Biol.Unit 4 (85 KB)
Header - Biol.Unit 4
Biol.Unit 5 (83 KB)
Header - Biol.Unit 5
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