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1ZBQ
Asym. Unit
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
[
close entry info
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Hetero Components
(1, 6)
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
6
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
[
close Hetero Component info
]
Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (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
3
AC3
SOFTWARE
GLY C:16 , ALA C:19 , GLY C:20 , LEU C:21 , ASN C:39 , ASP C:40 , LEU C:41 , GLY C:43 , SER C:75 , VAL C:76 , ASN C:99 , ALA C:100 , GLY C:101 , HIS C:123 , THR C:149 , SER C:150 , SER C:151 , TYR C:164 , LYS C:168 , PRO C:194 , ASN C:195 , ALA C:196 , SER C:198 , ARG C:199 , MET C:200 , HOH C:1006 , HOH C:1007 , HOH C:1015 , HOH C:1026 , HOH C:1047
BINDING SITE FOR RESIDUE NAD C 1003
4
AC4
SOFTWARE
GLY D:16 , ALA D:19 , GLY D:20 , LEU D:21 , ASN D:39 , ASP D:40 , LEU D:41 , SER D:75 , VAL D:76 , ASN D:99 , ALA D:100 , GLY D:101 , ILE D:102 , HIS D:123 , THR D:149 , SER D:150 , SER D:151 , TYR D:164 , LYS D:168 , PRO D:194 , ASN D:195 , ALA D:196 , SER D:198 , ARG D:199 , MET D:200 , THR D:201 , HOH D:1006 , HOH D:1011 , HOH D:1025
BINDING SITE FOR RESIDUE NAD D 1004
5
AC5
SOFTWARE
GLY E:16 , ALA E:19 , GLY E:20 , LEU E:21 , ASN E:39 , ASP E:40 , LEU E:41 , SER E:75 , VAL E:76 , ASN E:99 , ALA E:100 , GLY E:101 , HIS E:123 , THR E:149 , SER E:150 , SER E:151 , TYR E:164 , LYS E:168 , PRO E:194 , ASN E:195 , ALA E:196 , SER E:198 , ARG E:199 , MET E:200 , THR E:201 , HOH E:1006 , HOH E:1017
BINDING SITE FOR RESIDUE NAD E 1005
6
AC6
SOFTWARE
GLY F:16 , ALA F:19 , GLY F:20 , LEU F:21 , ASN F:39 , ASP F:40 , LEU F:41 , SER F:75 , VAL F:76 , ASN F:99 , ALA F:100 , GLY F:101 , HIS F:123 , THR F:149 , SER F:150 , SER F:151 , TYR F:164 , LYS F:168 , PRO F:194 , ASN F:195 , ALA F:196 , SER F:198 , ARG F:199 , MET F:200 , THR F:201 , HOH F:1007 , HOH F:1012 , HOH F:1026
BINDING SITE FOR RESIDUE NAD F 1006
[
close Site info
]
SAPs(SNPs)/Variants
(7, 42)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_037576 (G16S, chain A/B/C/D/E/F, )
2: VAR_052309 (F90L, chain A/B/C/D/E/F, )
3: VAR_014872 (R106H, chain A/B/C/D/E/F, )
4: VAR_065906 (R106P, chain A/B/C/D/E/F, )
5: VAR_052310 (K140N, chain A/B/C/D/E/F, )
6: VAR_065907 (Y217C, chain A/B/C/D/E/F, )
7: VAR_024625 (T292S, chain A/B/C/D/E/F, )
View:
Select:
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/C/D/E/F
G
16
S
2
UniProt
VAR_052309
F
90
L
DHB4_HUMAN
Polymorphism
28943588
A/B/C/D/E/F
F
90
L
3
UniProt
VAR_014872
R
106
H
DHB4_HUMAN
Polymorphism
25640
A/B/C/D/E/F
R
106
H
4
UniProt
VAR_065906
R
106
P
DHB4_HUMAN
Disease (DBPD)
25640
A/B/C/D/E/F
R
106
P
5
UniProt
VAR_052310
K
140
N
DHB4_HUMAN
Polymorphism
28943589
A/B/C/D/E/F
K
140
N
6
UniProt
VAR_065907
Y
217
C
DHB4_HUMAN
Disease (PRLTS1)
---
A/B/C/D/E/F
Y
217
C
7
UniProt
VAR_024625
T
292
S
DHB4_HUMAN
Polymorphism
1143650
A/B/C/D/E/F
T
292
S
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 6)
Info
All PROSITE Patterns/Profiles
1: ADH_SHORT (A:151-179,B:151-179,C:151-179,D:15...)
;
View:
Select:
Label:
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
6
A:151-179
B:151-179
C:151-179
D:151-179
E:151-179
F:151-179
[
close PROSITE info
]
Exons
(12, 72)
Info
All Exons
Exon 1.1a (A:3-20 | B:3-20 | C:3-20 | D:3-20 ...)
Exon 1.2b (A:20-38 | B:20-38 | C:20-38 | D:20...)
Exon 1.4c (A:38-74 | B:38-74 | C:38-74 | D:38...)
Exon 1.5b (A:74-94 | B:74-94 | C:74-94 | D:74...)
Exon 1.6b (A:94-101 | B:94-101 | C:94-101 | D...)
Exon 1.7a (A:101-117 | B:101-117 | C:101-117 ...)
Exon 1.10c (A:117-145 | B:117-145 | C:117-145 ...)
Exon 1.12f (A:145-208 | B:145-208 | C:145-208 ...)
Exon 1.13 (A:208-238 | B:208-238 | C:208-238 ...)
Exon 1.14 (A:239-247 | B:239-247 | C:239-247 ...)
Exon 1.15c (A:247-290 | B:247-290 | C:247-290 ...)
Exon 1.17c (A:290-304 | B:290-304 | C:290-304 ...)
View:
Select:
Label:
All Exon Boundaries
01: Boundary -/1.1a
02: Boundary 1.1a/1.2b
03: Boundary 1.2b/1.4c
04: Boundary 1.4c/1.5b
05: Boundary 1.5b/1.6b
06: Boundary 1.6b/1.7a
07: Boundary 1.7a/1.10c
08: Boundary 1.10c/1.12f
09: Boundary 1.12f/1.13
10: Boundary 1.13/1.14
11: Boundary 1.14/1.15c
12: Boundary 1.15c/1.17c
13: Boundary 1.17c/1.18a
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1a
ENST00000256216
1a
ENSE00002062781
chr5:
118788138-118788328
191
DHB4_HUMAN
1-20
20
6
A:3-20
B:3-20
C:3-20
D:3-20
E:3-20
F:3-20
18
18
18
18
18
18
1.2b
ENST00000256216
2b
ENSE00001715680
chr5:
118792010-118792063
54
DHB4_HUMAN
20-38
19
6
A:20-38
B:20-38
C:20-38
D:20-38
E:20-38
F:20-38
19
19
19
19
19
19
1.4c
ENST00000256216
4c
ENSE00001645814
chr5:
118809603-118809710
108
DHB4_HUMAN
38-74
37
6
A:38-74
B:38-74
C:38-74
D:38-74
E:38-74
F:38-74
37
37
37
37
37
37
1.5b
ENST00000256216
5b
ENSE00001703065
chr5:
118810096-118810155
60
DHB4_HUMAN
74-94
21
6
A:74-94
B:74-94
C:74-94
D:74-94
E:74-94
F:74-94
21
21
21
21
21
21
1.6b
ENST00000256216
6b
ENSE00001607423
chr5:
118811401-118811422
22
DHB4_HUMAN
94-101
8
6
A:94-101
B:94-101
C:94-101
D:94-101
E:94-101
F:94-101
8
8
8
8
8
8
1.7a
ENST00000256216
7a
ENSE00001705604
chr5:
118811519-118811565
47
DHB4_HUMAN
101-117
17
6
A:101-117
B:101-117
C:101-117
D:101-117
E:101-117
F:101-117
17
17
17
17
17
17
1.10c
ENST00000256216
10c
ENSE00001647277
chr5:
118813112-118813196
85
DHB4_HUMAN
117-145
29
6
A:117-145
B:117-145
C:117-145
D:117-145
E:117-145
F:117-145
29
29
29
29
29
29
1.12f
ENST00000256216
12f
ENSE00001790487
chr5:
118814529-118814716
188
DHB4_HUMAN
145-208
64
6
A:145-208
B:145-208
C:145-208
D:145-208
E:145-208
F:145-208
64
64
64
64
64
64
1.13
ENST00000256216
13
ENSE00000972272
chr5:
118824887-118824978
92
DHB4_HUMAN
208-238
31
6
A:208-238
B:208-238
C:208-238
D:208-238
E:208-238
F:208-238
31
31
31
31
31
31
1.14
ENST00000256216
14
ENSE00000998891
chr5:
118827795-118827819
25
DHB4_HUMAN
239-247
9
6
A:239-247
B:239-247
C:239-247
D:239-247
E:239-247
F:239-247
9
9
9
9
9
9
1.15c
ENST00000256216
15c
ENSE00001143969
chr5:
118829513-118829641
129
DHB4_HUMAN
247-290
44
6
A:247-290
B:247-290
C:247-290
D:247-290
E:247-290
F:247-290
44
44
44
44
44
44
1.17c
ENST00000256216
17c
ENSE00001143964
chr5:
118832238-118832341
104
DHB4_HUMAN
290-324
35
6
A:290-304
B:290-304
C:290-304
D:290-304
E:290-304
F:290-304
15
15
15
15
15
15
1.18a
ENST00000256216
18a
ENSE00001143958
chr5:
118835012-118835248
237
DHB4_HUMAN
325-403
79
0
-
-
1.19b
ENST00000256216
19b
ENSE00001143950
chr5:
118837736-118837787
52
DHB4_HUMAN
404-421
18
0
-
-
1.20
ENST00000256216
20
ENSE00001143943
chr5:
118842513-118842584
72
DHB4_HUMAN
421-445
25
0
-
-
1.21
ENST00000256216
21
ENSE00001143936
chr5:
118844836-118844939
104
DHB4_HUMAN
445-479
35
0
-
-
1.23
ENST00000256216
23
ENSE00001143927
chr5:
118850676-118850741
66
DHB4_HUMAN
480-501
22
0
-
-
1.24a
ENST00000256216
24a
ENSE00000972280
chr5:
118860911-118860980
70
DHB4_HUMAN
502-525
24
0
-
-
1.25c
ENST00000256216
25c
ENSE00000972281
chr5:
118861612-118861718
107
DHB4_HUMAN
525-560
36
0
-
-
1.26a
ENST00000256216
26a
ENSE00000972282
chr5:
118862828-118862914
87
DHB4_HUMAN
561-589
29
0
-
-
1.27a
ENST00000256216
27a
ENSE00000972283
chr5:
118865589-118865675
87
DHB4_HUMAN
590-618
29
0
-
-
1.28
ENST00000256216
28
ENSE00000972284
chr5:
118866961-118867099
139
DHB4_HUMAN
619-665
47
0
-
-
1.29b
ENST00000256216
29b
ENSE00000972285
chr5:
118872118-118872245
128
DHB4_HUMAN
665-707
43
0
-
-
1.30i
ENST00000256216
30i
ENSE00001833743
chr5:
118877600-118878028
429
DHB4_HUMAN
708-736
29
0
-
-
[
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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
(
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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
:
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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Homologous Superfamilies
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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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Organisms
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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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Asym.Unit (293 KB)
Header - Asym.Unit
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