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3IBD
Asym. Unit
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Asym.Unit (87 KB)
Biol.Unit 1 (82 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF A CYTOCHROME P450 2B6 GENETIC VARIANT IN COMPLEX WITH THE INHIBITOR 4-(4-CHLOROPHENYL)IMIDAZOLE
Authors
:
S. C. Gay, L. Sun, J. C. Talakad, M. B. Shah, D. C. Stout, J. R. Halpert
Date
:
15 Jul 09 (Deposition) - 19 Jan 10 (Release) - 26 Oct 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
P450, Cytochrome P450 2B6, Monooxygenase, Oxidoreductase, Membrane Protein, Cyp 2B6, Endoplasmic Reticulum, Heme, Iron, Membrane, Metal-Binding, Microsome, Phosphoprotein, Oxidoreductase- Oxidoreductase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. C. Gay, M. B. Shah, J. C. Talakad, K. Maekawa, A. G. Roberts, P. R. Wilderman, L. Sun, J. Y. Yang, S. C. Huelga, W. X. Hong, Q. Zhang, C. D. Stout, J. R. Halpert
Crystal Structure Of A Cytochrome P450 2B6 Genetic Variant In Complex With The Inhibitor 4-(4-Chlorophenyl)Imidazole A 2. 0-A Resolution.
Mol. Pharmacol. V. 77 529 2010
[
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Hetero Components
(4, 8)
Info
All Hetero Components
1a: 5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTO... (CM5a)
1b: 5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTO... (CM5b)
2a: 4-(4-CHLOROPHENYL)IMIDAZOLE (CPZa)
3a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
4a: THIOCYANATE ION (SCNa)
4b: THIOCYANATE ION (SCNb)
4c: THIOCYANATE ION (SCNc)
4d: THIOCYANATE ION (SCNd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CM5
2
Ligand/Ion
5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTOSIDE
2
CPZ
1
Ligand/Ion
4-(4-CHLOROPHENYL)IMIDAZOLE
3
HEM
1
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
4
SCN
4
Ligand/Ion
THIOCYANATE 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:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HOH A:14 , ARG A:98 , VAL A:113 , ILE A:114 , TRP A:121 , ARG A:125 , ALA A:298 , GLY A:299 , THR A:302 , THR A:303 , THR A:306 , GLN A:357 , LEU A:363 , VAL A:367 , HIS A:369 , LEU A:392 , PRO A:428 , PHE A:429 , SER A:430 , ARG A:434 , CYS A:436 , LEU A:437 , GLY A:438 , CPZ A:501
BINDING SITE FOR RESIDUE HEM A 500
2
AC2
SOFTWARE
PHE A:297 , ALA A:298 , THR A:302 , VAL A:367 , HOH A:497 , HEM A:500
BINDING SITE FOR RESIDUE CPZ A 501
3
AC3
SOFTWARE
PHE A:188 , GLU A:194 , MET A:198 , PHE A:202 , TYR A:244 , PHE A:296
BINDING SITE FOR RESIDUE CM5 A 1001
4
AC4
SOFTWARE
ASP A:47 , LEU A:51
BINDING SITE FOR RESIDUE CM5 A 1002
5
AC5
SOFTWARE
LYS A:91 , ALA A:92 , GLU A:93 , ALA A:94 , SER A:461 , PRO A:462
BINDING SITE FOR RESIDUE SCN A 1003
6
AC6
SOFTWARE
ALA A:321 , GLU A:322 , MET A:459 , ARG A:491 , HOH A:607
BINDING SITE FOR RESIDUE SCN A 1004
7
AC7
SOFTWARE
TYR A:317 , PRO A:318 , HIS A:319
BINDING SITE FOR RESIDUE SCN A 1005
8
AC8
SOFTWARE
ARG A:57 , PHE A:58 , LYS A:61
BINDING SITE FOR RESIDUE SCN A 1006
[
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]
SAPs(SNPs)/Variants
(16, 16)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_025207 (G28G, chain A, )
02: VAR_033819 (K29P, chain A, )
03: VAR_025208 (K29S, chain A, )
04: VAR_023564 (M46V, chain A, )
05: VAR_023565 (G99E, chain A, )
06: VAR_016948 (K139E, chain A, )
07: VAR_023566 (R140Q, chain A, )
08: VAR_016924 (P167A, chain A, )
09: VAR_016925 (Q172H, chain A, )
10: VAR_016928 (S259R, chain A, )
11: VAR_016926 (R262R, chain A, )
12: VAR_025209 (N289K, chain A, )
13: VAR_025210 (T306S, chain A, )
14: VAR_024716 (I328T, chain A, )
15: VAR_023567 (I391N, chain A, )
16: VAR_016929 (R487C, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_025207
D
28
G
CP2B6_HUMAN
Polymorphism
33980385
A
G
28
G
02
UniProt
VAR_033819
R
29
P
CP2B6_HUMAN
Polymorphism
34284776
A
K
29
P
03
UniProt
VAR_025208
R
29
S
CP2B6_HUMAN
Polymorphism
33926104
A
K
29
S
04
UniProt
VAR_023564
M
46
V
CP2B6_HUMAN
Polymorphism
35303484
A
M
46
V
05
UniProt
VAR_023565
G
99
E
CP2B6_HUMAN
Polymorphism
36060847
A
G
99
E
06
UniProt
VAR_016948
K
139
E
CP2B6_HUMAN
Polymorphism
12721655
A
K
139
E
07
UniProt
VAR_023566
R
140
Q
CP2B6_HUMAN
Polymorphism
35773040
A
R
140
Q
08
UniProt
VAR_016924
P
167
A
CP2B6_HUMAN
Polymorphism
3826711
A
P
167
A
09
UniProt
VAR_016925
Q
172
H
CP2B6_HUMAN
Polymorphism
3745274
A
Q
172
H
10
UniProt
VAR_016928
S
259
R
CP2B6_HUMAN
Polymorphism
45482602
A
S
259
R
11
UniProt
VAR_016926
K
262
R
CP2B6_HUMAN
Polymorphism
2279343
A
R
262
R
12
UniProt
VAR_025209
N
289
K
CP2B6_HUMAN
Polymorphism
34277950
A
N
289
K
13
UniProt
VAR_025210
T
306
S
CP2B6_HUMAN
Polymorphism
34698757
A
T
306
S
14
UniProt
VAR_024716
I
328
T
CP2B6_HUMAN
Polymorphism
28399499
A
I
328
T
15
UniProt
VAR_023567
I
391
N
CP2B6_HUMAN
Polymorphism
35979566
A
I
391
N
16
UniProt
VAR_016929
R
487
C
CP2B6_HUMAN
Polymorphism
3211371
A
R
487
C
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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]
PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: CYTOCHROME_P450 (A:429-438)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
CYTOCHROME_P450
PS00086
Cytochrome P450 cysteine heme-iron ligand signature.
CP2B6_HUMAN
429-438
1
A:429-438
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d3ibda_ (A:)
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)
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Protein Domains
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)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Cytochrome P450
(480)
Superfamily
:
Cytochrome P450
(480)
Family
:
Cytochrome P450
(323)
Protein domain
:
automated matches
(44)
Human (Homo sapiens) [TaxId: 9606]
(17)
1a
d3ibda_
A:
[
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CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_3ibdA00 (A:28-492)
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Organisms
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)
(
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Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Cytochrome p450
(271)
Homologous Superfamily
:
Cytochrome p450
(271)
Human (Homo sapiens)
(32)
1a
3ibdA00
A:28-492
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Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Label:
Sorry, no Info available
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Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Asymmetric Unit 1
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