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2O23
Biol. Unit 1
Info
Asym.Unit (187 KB)
Biol.Unit 1 (359 KB)
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(1)
Title
:
THE STRUCTURE OF WILD-TYPE HUMAN HADH2 (17BETA-HYDROXYSTEROID DEHYDROGENASE TYPE 10) BOUND TO NAD+ AT 1.2 A
Authors
:
K. L. Kavanagh, N. Shafqat, K. Scholer, J. Debreczeni, J. Zschocke, F. V J. Weigelt, C. Arrowsmith, M. Sundstrom, A. Edwards, U. Oppermann, St Genomics Consortium (Sgc)
Date
:
29 Nov 06 (Deposition) - 12 Dec 06 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.20
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (2x)
Keywords
:
Hsd17B10, Schad, Erab, Type Ii Hadh, 2-Methyl-3-Hydroxybutyryl-Coa Dehydrogenase, Mhbd, Structural Genomics, Structural Genomics Consortium, Sgc, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. L. Kavanagh, N. Shafqat, K. Scholer, J. Debreczeni, J. Zschocke, F. Von Delft, J. Weigelt, C. Arrowsmith, M. Sundstrom, A. Edwards, U. Oppermann
The Structure Of Wild-Type Human Hadh2 (17Beta-Hydroxysteroid Dehydrogenase Type 10) Bound To Nad+ At 1. 2 A
To Be Published
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Hetero Components
(2, 6)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
2a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
2b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
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Label:
No.
Name
Count
Type
Full Name
1
GOL
2
Ligand/Ion
GLYCEROL
2
NAD
4
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
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Sites
(3, 3)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLY A:17 , SER A:20 , GLY A:21 , LEU A:22 , ASP A:41 , LEU A:42 , ALA A:63 , ASP A:64 , VAL A:65 , CYS A:91 , ALA A:92 , VAL A:120 , THR A:153 , ALA A:154 , TYR A:168 , LYS A:172 , PRO A:198 , GLY A:199 , PHE A:201 , THR A:203 , PRO A:204 , HOH A:806 , HOH A:844 , HOH A:851 , HOH A:859 , HOH A:928 , HOH A:939 , HOH A:964 , HOH A:995
BINDING SITE FOR RESIDUE NAD A 802
2
AC2
SOFTWARE
GLY B:17 , SER B:20 , GLY B:21 , LEU B:22 , ASP B:41 , LEU B:42 , ALA B:63 , ASP B:64 , VAL B:65 , CYS B:91 , ALA B:92 , GLY B:93 , VAL B:120 , THR B:153 , ALA B:154 , TYR B:168 , LYS B:172 , PRO B:198 , GLY B:199 , LEU B:200 , PHE B:201 , THR B:203 , PRO B:204 , LEU B:205 , HOH B:806 , HOH B:845 , HOH B:848 , HOH B:867 , HOH B:886 , HOH B:913 , HOH B:1035
BINDING SITE FOR RESIDUE NAD B 803
3
AC3
SOFTWARE
GLU A:249 , VAL A:250 , ARG A:252 , GLU B:249 , VAL B:250 , ARG B:252 , HOH B:884 , HOH B:900 , HOH B:1090
BINDING SITE FOR RESIDUE GOL B 801
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SAPs(SNPs)/Variants
(3, 12)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_015987 (L122V, chain A/B, )
2: VAR_015988 (R130C, chain A/B, )
3: VAR_032093 (N247S, chain A/B, )
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dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_015987
L
122
V
HCD2_HUMAN
Disease (MHBD deficiency)
28935476
A/B
L
122
V
2
UniProt
VAR_015988
R
130
C
HCD2_HUMAN
Disease (MHBD deficiency)
28935475
A/B
R
130
C
3
UniProt
VAR_032093
N
247
S
HCD2_HUMAN
Disease (MHBD deficiency)
---
A/B
N
247
S
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: ADH_SHORT (A:155-183,B:155-183)
;
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ADH_SHORT
PS00061
Short-chain dehydrogenases/reductases family signature.
HCD2_HUMAN
155-183
4
A:155-183
B:155-183
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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, 2)
Info
All SCOP Domains
1a: SCOP_d2o23a_ (A:)
1b: SCOP_d2o23b_ (B:)
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Protein Domains
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Organisms
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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
:
Tyrosine-dependent oxidoreductases
(503)
Protein domain
:
automated matches
(114)
Human (Homo sapiens) [TaxId: 9606]
(8)
1a
d2o23a_
A:
1b
d2o23b_
B:
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CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_2o23A00 (A:6-263)
1b: CATH_2o23B00 (B:1-263)
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Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Human (Homo sapiens)
(188)
1a
2o23A00
A:6-263
1b
2o23B00
B:1-263
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Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_adh_short_2o23B01 (B:11-187)
1b: PFAM_adh_short_2o23B02 (B:11-187)
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Clan
:
NADP_Rossmann
(1239)
Family
:
adh_short
(92)
Homo sapiens (Human)
(21)
1a
adh_short-2o23B01
B:11-187
1b
adh_short-2o23B02
B:11-187
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