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1ZBQ
Biol. Unit 1
Info
Asym.Unit (293 KB)
Biol.Unit 1 (98 KB)
Biol.Unit 2 (99 KB)
Biol.Unit 3 (96 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN 17-BETA-HYDROXYSTEROID DEHYDROGENASE TYPE 4 IN COMPLEX WITH NAD
Authors
:
P. Lukacik, N. Shafqat, K. Kavanagh, J. Bray, F. Von Delft, A. Edwards, C. Arrowsmith, M. Sundstrom, U. Oppermann, Structural Genomics Co (Sgc)
Date
:
08 Apr 05 (Deposition) - 26 Apr 05 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.71
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: E,F (1x)
Keywords
:
Short-Chain Dehydrogenase, Hydroxysteroid Dehydrogenase, Peroxisomal Beta-Oxidation, Human, Structural Genomics, Structural Genomics Consortium, Sgc, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. Lukacik, N. Shafqat, K. Kavanagh, J. Bray, F. Von Delft, A. Edwards C. Arrowsmith, M. Sundstrom, U. Oppermann
Crystal Structure Of Human 17-Beta-Hydroxysteroid Dehydrogenase Type 4 In Complex With Nad
To Be Published
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Hetero Components
(1, 2)
Info
All Hetero Components
1a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
1b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
1c: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADc)
1d: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADd)
1e: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADe)
1f: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NAD
2
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
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Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLY A:16 , ALA A:19 , GLY A:20 , LEU A:21 , ASN A:39 , ASP A:40 , LEU A:41 , SER A:75 , VAL A:76 , ASN A:99 , ALA A:100 , GLY A:101 , ILE A:102 , HIS A:123 , THR A:149 , SER A:150 , SER A:151 , TYR A:164 , LYS A:168 , PRO A:194 , ASN A:195 , ALA A:196 , SER A:198 , ARG A:199 , MET A:200 , HOH A:1002 , HOH A:1011 , HOH A:1012
BINDING SITE FOR RESIDUE NAD A 1001
2
AC2
SOFTWARE
GLY B:16 , ALA B:19 , GLY B:20 , LEU B:21 , ASN B:39 , ASP B:40 , LEU B:41 , SER B:75 , VAL B:76 , ASN B:99 , ALA B:100 , GLY B:101 , ILE B:102 , VAL B:122 , HIS B:123 , THR B:149 , SER B:150 , SER B:151 , TYR B:164 , LYS B:168 , PRO B:194 , ASN B:195 , ALA B:196 , SER B:198 , ARG B:199 , MET B:200 , THR B:201 , HOH B:1003 , HOH B:1004 , HOH B:1024 , HOH B:1031 , HOH B:1039 , HOH B:1056
BINDING SITE FOR RESIDUE NAD B 1002
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SAPs(SNPs)/Variants
(7, 14)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_037576 (G16S, chain A/B, )
2: VAR_052309 (F90L, chain A/B, )
3: VAR_014872 (R106H, chain A/B, )
4: VAR_065906 (R106P, chain A/B, )
5: VAR_052310 (K140N, chain A/B, )
6: VAR_065907 (Y217C, chain A/B, )
7: VAR_024625 (T292S, chain A/B, )
View:
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Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_037576
G
16
S
DHB4_HUMAN
Disease (DBPD)
---
A/B
G
16
S
2
UniProt
VAR_052309
F
90
L
DHB4_HUMAN
Polymorphism
28943588
A/B
F
90
L
3
UniProt
VAR_014872
R
106
H
DHB4_HUMAN
Polymorphism
25640
A/B
R
106
H
4
UniProt
VAR_065906
R
106
P
DHB4_HUMAN
Disease (DBPD)
25640
A/B
R
106
P
5
UniProt
VAR_052310
K
140
N
DHB4_HUMAN
Polymorphism
28943589
A/B
K
140
N
6
UniProt
VAR_065907
Y
217
C
DHB4_HUMAN
Disease (PRLTS1)
---
A/B
Y
217
C
7
UniProt
VAR_024625
T
292
S
DHB4_HUMAN
Polymorphism
1143650
A/B
T
292
S
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: ADH_SHORT (A:151-179,B:151-179)
;
View:
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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.
DHB4_HUMAN
151-179
2
A:151-179
B:151-179
-
-
-
-
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 6)
Info
All SCOP Domains
1a: SCOP_d1zbqa1 (A:3-304)
1b: SCOP_d1zbqb_ (B:)
1c: SCOP_d1zbqc_ (C:)
1d: SCOP_d1zbqd_ (D:)
1e: SCOP_d1zbqe_ (E:)
1f: SCOP_d1zbqf_ (F:)
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Protein Domains
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(
)
Organisms
(
)
(
)
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
:
Peroxisomal multifunctional enzyme type 2
(1)
Human (Homo sapiens) [TaxId: 9606]
(1)
1a
d1zbqa1
A:3-304
1b
d1zbqb_
B:
1c
d1zbqc_
C:
1d
d1zbqd_
D:
1e
d1zbqe_
E:
1f
d1zbqf_
F:
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CATH Domains
(1, 6)
Info
all CATH domains
1a: CATH_1zbqA01 (A:3-246)
1b: CATH_1zbqB01 (B:3-246)
1c: CATH_1zbqC01 (C:3-246)
1d: CATH_1zbqD01 (D:3-246)
1e: CATH_1zbqE01 (E:3-246)
1f: CATH_1zbqF01 (F:3-246)
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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)
Human (Homo sapiens)
(188)
1a
1zbqA01
A:3-246
1b
1zbqB01
B:3-246
1c
1zbqC01
C:3-246
1d
1zbqD01
D:3-246
1e
1zbqE01
E:3-246
1f
1zbqF01
F:3-246
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Pfam Domains
(1, 6)
Info
all PFAM domains
1a: PFAM_adh_short_1zbqF01 (F:10-183)
1b: PFAM_adh_short_1zbqF02 (F:10-183)
1c: PFAM_adh_short_1zbqF03 (F:10-183)
1d: PFAM_adh_short_1zbqF04 (F:10-183)
1e: PFAM_adh_short_1zbqF05 (F:10-183)
1f: PFAM_adh_short_1zbqF06 (F:10-183)
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)
Clan
:
NADP_Rossmann
(1239)
Family
:
adh_short
(92)
Homo sapiens (Human)
(21)
1a
adh_short-1zbqF01
F:10-183
1b
adh_short-1zbqF02
F:10-183
1c
adh_short-1zbqF03
F:10-183
1d
adh_short-1zbqF04
F:10-183
1e
adh_short-1zbqF05
F:10-183
1f
adh_short-1zbqF06
F:10-183
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Asymmetric Unit 1
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Asym.Unit (293 KB)
Header - Asym.Unit
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