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2NVB
Biol. Unit 1
Info
Asym.Unit (225 KB)
Biol.Unit 1 (218 KB)
Biol.Unit 2 (111 KB)
Biol.Unit 3 (112 KB)
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(1)
Title
:
CONTRIBUTION OF PRO275 TO THE THERMOSTABILITY OF THE ALCOHOL DEHYDROGENASES (ADHS)
Authors
:
E. Goihberg, S. Tel-Or, M. Peretz, F. Frolow, O. Dym, Y. Burstein, Israel Structural Proteomics Center (Ispc)
Date
:
12 Nov 06 (Deposition) - 13 Nov 07 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.80
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)
Keywords
:
Rossmann Fold, Structural Genomics, Israel Structural Proteomics Center, Ispc, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
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)
Reference
:
E. Goihberg, O. Dym, S. Tel-Or, L. Shimon, F. Frolow, M. Peretz, Y. Burstein
Thermal Stabilization Of The Protozoan Entamoeba Histolytica Alcohol Dehydrogenase By A Single Proline Substitution
Proteins V. 72 711 2008
(for further references see the
PDB file header
)
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Hetero Components
(1, 4)
Info
All Hetero Components
1a: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPa)
1b: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPb)
1c: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPc)
1d: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPd)
2a: ZINC ION (ZNa)
2b: ZINC ION (ZNb)
2c: ZINC ION (ZNc)
2d: ZINC ION (ZNd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NAP
4
Ligand/Ion
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2
ZN
-1
Ligand/Ion
ZINC 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
CYS A:37 , SER A:39 , HIS A:59 , ASP A:150 , NAP A:353
BINDING SITE FOR RESIDUE ZN A 354
2
AC2
SOFTWARE
CYS B:37 , SER B:39 , HIS B:59 , ASP B:150 , NAP B:1353
BINDING SITE FOR RESIDUE ZN B 1354
3
AC3
SOFTWARE
CYS C:37 , SER C:39 , HIS C:59 , ASP C:150 , NAP C:2353
BINDING SITE FOR RESIDUE ZN C 2354
4
AC4
SOFTWARE
CYS D:37 , SER D:39 , ASP D:150 , NAP D:3353
BINDING SITE FOR RESIDUE ZN D 3354
5
AC5
SOFTWARE
THR A:38 , SER A:39 , TRP A:110 , ASP A:150 , THR A:154 , GLY A:174 , ILE A:175 , GLY A:176 , PRO A:177 , VAL A:178 , VAL A:197 , GLY A:198 , SER A:199 , ARG A:200 , TYR A:218 , ALA A:242 , VAL A:265 , ASN A:266 , TYR A:267 , LYS A:340 , ZN A:354 , MET B:285
BINDING SITE FOR RESIDUE NAP A 353
6
AC6
SOFTWARE
MET A:285 , THR B:38 , SER B:39 , TRP B:110 , ASP B:150 , THR B:154 , GLY B:174 , ILE B:175 , GLY B:176 , PRO B:177 , VAL B:178 , VAL B:197 , GLY B:198 , SER B:199 , ARG B:200 , TYR B:218 , ALA B:242 , GLY B:244 , ASN B:245 , ASN B:266 , TYR B:267 , LYS B:340 , ZN B:1354
BINDING SITE FOR RESIDUE NAP B 1353
7
AC7
SOFTWARE
THR C:38 , SER C:39 , HIS C:42 , TRP C:110 , ASP C:150 , THR C:154 , GLY C:174 , ILE C:175 , GLY C:176 , PRO C:177 , VAL C:178 , VAL C:197 , SER C:199 , ARG C:200 , TYR C:218 , TYR C:267 , LYS C:340 , ZN C:2354 , MET D:285
BINDING SITE FOR RESIDUE NAP C 2353
8
AC8
SOFTWARE
MET C:285 , THR D:38 , SER D:39 , ASP D:150 , THR D:154 , GLY D:174 , ILE D:175 , GLY D:176 , PRO D:177 , VAL D:178 , SER D:199 , ARG D:200 , TYR D:218 , GLY D:244 , VAL D:265 , ASN D:266 , TYR D:267 , ZN D:3354
BINDING SITE FOR RESIDUE NAP D 3353
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
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: ADH_ZINC (A:58-72,B:58-72,C:58-72,D:58-72)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ADH_ZINC
PS00059
Zinc-containing alcohol dehydrogenases signature.
ADH_THEBR
58-72
4
A:58-72
B:58-72
C:58-72
D:58-72
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(2, 8)
Info
All SCOP Domains
1a: SCOP_d2nvba1 (A:1-139,A:314-352)
1b: SCOP_d2nvbb1 (B:1-139,B:314-352)
1c: SCOP_d2nvbc1 (C:1-139,C:314-352)
1d: SCOP_d2nvbd1 (D:1-139,D:314-352)
2a: SCOP_d2nvba2 (A:140-313)
2b: SCOP_d2nvbb2 (B:140-313)
2c: SCOP_d2nvbc2 (C:140-313)
2d: SCOP_d2nvbd2 (D:140-313)
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Classes
(
)
(
)
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(
)
(
)
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)
(
)
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(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
GroES-like
(132)
Superfamily
:
GroES-like
(130)
Family
:
Alcohol dehydrogenase-like, N-terminal domain
(114)
Protein domain
:
Bacterial secondary alcohol dehydrogenase
(7)
Thermoanaerobacter brockii [TaxId: 29323]
(3)
1a
d2nvba1
A:1-139,A:314-352
1b
d2nvbb1
B:1-139,B:314-352
1c
d2nvbc1
C:1-139,C:314-352
1d
d2nvbd1
D:1-139,D:314-352
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
:
Alcohol dehydrogenase-like, C-terminal domain
(115)
Protein domain
:
Bacterial secondary alcohol dehydrogenase
(7)
Thermoanaerobacter brockii [TaxId: 29323]
(3)
2a
d2nvba2
A:140-313
2b
d2nvbb2
B:140-313
2c
d2nvbc2
C:140-313
2d
d2nvbd2
D:140-313
[
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]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_2nvbA02 (A:162-292)
1b: CATH_2nvbB02 (B:162-292)
1c: CATH_2nvbC02 (C:162-292)
1d: CATH_2nvbD02 (D:162-292)
2a: CATH_2nvbA01 (A:1-161,A:293-352)
2b: CATH_2nvbB01 (B:1-161,B:293-352)
2c: CATH_2nvbC01 (C:1-161,C:293-352)
2d: CATH_2nvbD01 (D:1-161,D:293-352)
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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)
Thermoanaerobacter brockii. Organism_taxid: 29323.
(1)
1a
2nvbA02
A:162-292
1b
2nvbB02
B:162-292
1c
2nvbC02
C:162-292
1d
2nvbD02
D:162-292
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Quinone Oxidoreductase; Chain A, domain 1
(131)
Homologous Superfamily
:
Medium-chain alcohol dehydrogenases, catalytic domain
(131)
Thermoanaerobacter brockii. Organism_taxid: 29323.
(1)
2a
2nvbA01
A:1-161,A:293-352
2b
2nvbB01
B:1-161,B:293-352
2c
2nvbC01
C:1-161,C:293-352
2d
2nvbD01
D:1-161,D:293-352
[
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Pfam Domains
(2, 8)
Info
all PFAM domains
1a: PFAM_ADH_N_2nvbD01 (D:24-135)
1b: PFAM_ADH_N_2nvbD02 (D:24-135)
1c: PFAM_ADH_N_2nvbD03 (D:24-135)
1d: PFAM_ADH_N_2nvbD04 (D:24-135)
2a: PFAM_ADH_zinc_N_2nvbD05 (D:177-310)
2b: PFAM_ADH_zinc_N_2nvbD06 (D:177-310)
2c: PFAM_ADH_zinc_N_2nvbD07 (D:177-310)
2d: PFAM_ADH_zinc_N_2nvbD08 (D:177-310)
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Clans
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)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
GroES
(70)
Family
:
ADH_N
(62)
Thermoanaerobacter brockii (Thermoanaerobium brockii)
(2)
1a
ADH_N-2nvbD01
D:24-135
1b
ADH_N-2nvbD02
D:24-135
1c
ADH_N-2nvbD03
D:24-135
1d
ADH_N-2nvbD04
D:24-135
Clan
:
NADP_Rossmann
(1239)
Family
:
ADH_zinc_N
(75)
Thermoanaerobacter brockii (Thermoanaerobium brockii)
(2)
2a
ADH_zinc_N-2nvbD05
D:177-310
2b
ADH_zinc_N-2nvbD06
D:177-310
2c
ADH_zinc_N-2nvbD07
D:177-310
2d
ADH_zinc_N-2nvbD08
D:177-310
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