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3QU8
Biol. Unit 4
Info
Asym.Unit (470 KB)
Biol.Unit 1 (82 KB)
Biol.Unit 2 (83 KB)
Biol.Unit 3 (83 KB)
Biol.Unit 4 (83 KB)
Biol.Unit 5 (82 KB)
Biol.Unit 6 (80 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF A HUMAN CYTOCHROME P450 2B6 (Y226H/K262R) IN COMPLEX WITH THE INHIBITOR 4-(4-NITROBENZYL)PYRIDINE.
Authors
:
M. B. Shah, J. Pascual, C. D. Stout, J. R. Halpert
Date
:
23 Feb 11 (Deposition) - 21 Sep 11 (Release) - 05 Dec 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.80
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Biol. Unit 5: E (1x)
Biol. Unit 6: F (1x)
Keywords
:
P450, Cytochrome P450 2B6, Monooxygenase, Membrane Protein, Cyp2B6, Endoplasmic Reticulum, Heme, Iron, Membrane, Metal Binding, Microsome, Phosphoprotein, Oxidoreductase-Oxidoreductase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. B. Shah, J. Pascual, Q. Zhang, C. D. Stout, J. R. Halpert
Structures Of Cytochrome P450 2B6 Bound To 4-Benzylpyridine And 4-(4-Nitrobenzyl)Pyridine: Insight Into Inhibitor Binding And Rearrangement Of Active Site Side Chains.
Mol. Pharmacol. V. 80 1047 2011
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Hetero Components
(3, 4)
Info
All Hetero Components
1a: 4-(4-NITROBENZYL)PYRIDINE (3QUa)
1b: 4-(4-NITROBENZYL)PYRIDINE (3QUb)
1c: 4-(4-NITROBENZYL)PYRIDINE (3QUc)
1d: 4-(4-NITROBENZYL)PYRIDINE (3QUd)
1e: 4-(4-NITROBENZYL)PYRIDINE (3QUe)
2a: 5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTO... (CM5a)
2b: 5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTO... (CM5b)
2c: 5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTO... (CM5c)
2d: 5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTO... (CM5d)
2e: 5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTO... (CM5e)
2f: 5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTO... (CM5f)
2g: 5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTO... (CM5g)
2h: 5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTO... (CM5h)
3a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
3b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
3c: PROTOPORPHYRIN IX CONTAINING FE (HEMc)
3d: PROTOPORPHYRIN IX CONTAINING FE (HEMd)
3e: PROTOPORPHYRIN IX CONTAINING FE (HEMe)
3f: PROTOPORPHYRIN IX CONTAINING FE (HEMf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
3QU
1
Ligand/Ion
4-(4-NITROBENZYL)PYRIDINE
2
CM5
2
Ligand/Ion
5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTOSIDE
3
HEM
1
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
[
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Sites
(8, 8)
Info
All Sites
1: AC3 (SOFTWARE)
2: AC7 (SOFTWARE)
3: BC2 (SOFTWARE)
4: BC3 (SOFTWARE)
5: BC4 (SOFTWARE)
6: BC5 (SOFTWARE)
7: BC8 (SOFTWARE)
8: CC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC3
SOFTWARE
PHE A:223 , HIS A:226 , PHE A:227 , PRO A:228 , ARG A:232 , LEU C:39 , PRO D:38
BINDING SITE FOR RESIDUE CM5 A 601
2
AC7
SOFTWARE
LEU B:39 , PHE B:220 , GLY B:222 , PHE B:223 , LYS B:225 , HOH B:517 , CM5 B:602 , CM5 D:607
BINDING SITE FOR RESIDUE CM5 B 608
3
BC2
SOFTWARE
ARG D:98 , VAL D:113 , ILE D:114 , TRP D:121 , ARG D:125 , ILE D:179 , LEU D:295 , ALA D:298 , GLY D:299 , THR D:302 , THR D:306 , GLN D:357 , LEU D:363 , HIS D:369 , LEU D:392 , PRO D:428 , PHE D:429 , SER D:430 , ARG D:434 , CYS D:436 , LEU D:437 , GLY D:438 , 3QU D:501
BINDING SITE FOR RESIDUE HEM D 500
4
BC3
SOFTWARE
PHE D:297 , ALA D:298 , THR D:302 , LEU D:363 , HEM D:500
BINDING SITE FOR RESIDUE 3QU D 501
5
BC4
SOFTWARE
PHE D:223 , HIS D:226 , PHE D:227 , PRO D:228 , ARG D:232 , CM5 E:605
BINDING SITE FOR RESIDUE CM5 D 604
6
BC5
SOFTWARE
CM5 B:608 , LEU D:40 , PHE D:220 , GLY D:222 , HIS D:226
BINDING SITE FOR RESIDUE CM5 D 607
7
BC8
SOFTWARE
LEU B:37 , CM5 D:604 , HIS E:226 , PHE E:227 , ARG E:232 , ARG F:35
BINDING SITE FOR RESIDUE CM5 E 605
8
CC1
SOFTWARE
PRO D:38 , LEU D:39 , HIS F:226 , PHE F:227 , PRO F:228 , ARG F:232
BINDING SITE FOR RESIDUE CM5 F 606
[
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SAPs(SNPs)/Variants
(14, 14)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
01: VAR_025207 (G28G, chain D, )
02: VAR_033819 (K29P, chain D, )
03: VAR_025208 (K29S, chain D, )
04: VAR_023564 (M46V, chain D, )
05: VAR_023565 (G99E, chain D, )
06: VAR_016924 (P167A, chain D, )
07: VAR_016925 (Q172H, chain D, )
08: VAR_016928 (S259R, chain D, )
09: VAR_016926 (R262R, chain D, )
10: VAR_025209 (N289K, chain D, )
11: VAR_025210 (T306S, chain D, )
12: VAR_024716 (I328T, chain D, )
13: VAR_023567 (I391N, chain D, )
14: VAR_016929 (R487C, chain D, )
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
D
G
28
G
02
UniProt
VAR_033819
R
29
P
CP2B6_HUMAN
Polymorphism
34284776
D
K
29
P
03
UniProt
VAR_025208
R
29
S
CP2B6_HUMAN
Polymorphism
33926104
D
K
29
S
04
UniProt
VAR_023564
M
46
V
CP2B6_HUMAN
Polymorphism
35303484
D
M
46
V
05
UniProt
VAR_023565
G
99
E
CP2B6_HUMAN
Polymorphism
36060847
D
G
99
E
08
UniProt
VAR_016924
P
167
A
CP2B6_HUMAN
Polymorphism
3826711
D
P
167
A
09
UniProt
VAR_016925
Q
172
H
CP2B6_HUMAN
Polymorphism
3745274
D
Q
172
H
10
UniProt
VAR_016928
S
259
R
CP2B6_HUMAN
Polymorphism
45482602
D
S
259
R
11
UniProt
VAR_016926
K
262
R
CP2B6_HUMAN
Polymorphism
2279343
D
R
262
R
12
UniProt
VAR_025209
N
289
K
CP2B6_HUMAN
Polymorphism
34277950
D
N
289
K
13
UniProt
VAR_025210
T
306
S
CP2B6_HUMAN
Polymorphism
34698757
D
T
306
S
14
UniProt
VAR_024716
I
328
T
CP2B6_HUMAN
Polymorphism
28399499
D
I
328
T
15
UniProt
VAR_023567
I
391
N
CP2B6_HUMAN
Polymorphism
35979566
D
I
391
N
16
UniProt
VAR_016929
R
487
C
CP2B6_HUMAN
Polymorphism
3211371
D
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 (D: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
-
-
-
D: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.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 6)
Info
All SCOP Domains
1a: SCOP_d3qu8a_ (A:)
1b: SCOP_d3qu8b_ (B:)
1c: SCOP_d3qu8c_ (C:)
1d: SCOP_d3qu8d_ (D:)
1e: SCOP_d3qu8e_ (E:)
1f: SCOP_d3qu8f_ (F:)
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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
d3qu8a_
A:
1b
d3qu8b_
B:
1c
d3qu8c_
C:
1d
d3qu8d_
D:
1e
d3qu8e_
E:
1f
d3qu8f_
F:
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CATH Domains
(0, 0)
Info
all CATH domains
View:
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Label:
Sorry, no Info available
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Label:
Sorry, no Info available
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Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain D
Asymmetric Unit 1
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