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3G93
Asym. Unit
Info
Asym.Unit (290 KB)
Biol.Unit 1 (279 KB)
Biol.Unit 2 (76 KB)
Biol.Unit 3 (73 KB)
Biol.Unit 4 (74 KB)
Biol.Unit 5 (73 KB)
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(1)
Title
:
SINGLE LIGAND OCCUPANCY CRYSTAL STRUCTURE OF CYTOCHROME P450 2B4 IN COMPLEX WITH THE INHIBITOR 1-BIPHENYL-4-METHYL-1H-IMIDAZOLE
Authors
:
S. C. Gay, L. Sun, K. Maekawa, J. R. Halpert, C. D. Stout
Date
:
12 Feb 09 (Deposition) - 12 May 09 (Release) - 09 Jun 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.20
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: A (1x)
Biol. Unit 3: B (1x)
Biol. Unit 4: C (1x)
Biol. Unit 5: D (1x)
Keywords
:
P450, Cytochrome P450 2B4, Monooxygenase, Oxidoreductase, Membrane Protein, Cyp 2B4, Cyp Lm2, Endoplasmic Reticulum, Heme, Iron, Membrane, Metal-Binding, Microsome, Phosphoprotein, Polymorphism
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. C. Gay, L. Sun, K. Maekawa, J. R. Halpert, C. D. Stout
Crystal Structures Of Cytochrome P450 2B4 In Complex With The Inhibitor 1-Biphenyl-4-Methyl-1H-Imidazole: Ligand-Induced Structural Response Through Alpha-Helical Repositioning.
Biochemistry V. 48 4762 2009
(for further references see the
PDB file header
)
[
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Hetero Components
(2, 8)
Info
All Hetero Components
1a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
1b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
1c: PROTOPORPHYRIN IX CONTAINING FE (HEMc)
1d: PROTOPORPHYRIN IX CONTAINING FE (HEMd)
2a: 1-(BIPHENYL-4-YLMETHYL)-1H-IMIDAZO... (PB2a)
2b: 1-(BIPHENYL-4-YLMETHYL)-1H-IMIDAZO... (PB2b)
2c: 1-(BIPHENYL-4-YLMETHYL)-1H-IMIDAZO... (PB2c)
2d: 1-(BIPHENYL-4-YLMETHYL)-1H-IMIDAZO... (PB2d)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
HEM
4
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
2
PB2
4
Ligand/Ion
1-(BIPHENYL-4-YLMETHYL)-1H-IMIDAZOLE
[
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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
ARG A:98 , TRP A:121 , ARG A:125 , PHE A:296 , GLY A:299 , THR A:302 , THR A:303 , ILE A:363 , VAL A:367 , HIS A:369 , PRO A:428 , PHE A:429 , SER A:430 , ARG A:434 , CYS A:436 , LEU A:437 , GLY A:438 , PB2 A:501
BINDING SITE FOR RESIDUE HEM A 500
2
AC2
SOFTWARE
ALA A:298 , GLY A:299 , THR A:302 , HEM A:500 , PHE B:217 , PHE B:223
BINDING SITE FOR RESIDUE PB2 A 501
3
AC3
SOFTWARE
PHE A:217 , PHE A:223 , LEU A:224 , ALA B:298 , GLY B:299 , THR B:302 , PRO B:368 , HEM B:500
BINDING SITE FOR RESIDUE PB2 A 496
4
AC4
SOFTWARE
PHE A:217 , PB2 A:496 , ARG B:98 , TRP B:121 , ARG B:125 , PHE B:296 , GLY B:299 , THR B:302 , THR B:303 , GLN B:357 , ILE B:363 , VAL B:367 , HIS B:369 , PRO B:428 , PHE B:429 , SER B:430 , ARG B:434 , CYS B:436 , GLY B:438
BINDING SITE FOR RESIDUE HEM B 500
5
AC5
SOFTWARE
ARG C:98 , ARG C:125 , PHE C:296 , GLY C:299 , THR C:300 , THR C:302 , THR C:303 , ILE C:363 , VAL C:367 , HIS C:369 , PRO C:428 , PHE C:429 , SER C:430 , ARG C:434 , CYS C:436 , GLY C:438 , ALA C:442 , PB2 C:501
BINDING SITE FOR RESIDUE HEM C 500
6
AC6
SOFTWARE
ALA C:298 , GLY C:299 , THR C:302 , ILE C:363 , HEM C:500 , PHE D:217 , PHE D:223 , LEU D:224
BINDING SITE FOR RESIDUE PB2 C 501
7
AC7
SOFTWARE
ARG D:98 , TRP D:121 , ARG D:125 , PHE D:296 , GLY D:299 , THR D:300 , THR D:302 , THR D:303 , THR D:306 , GLN D:357 , ILE D:363 , VAL D:367 , 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 , PB2 D:501
BINDING SITE FOR RESIDUE HEM D 500
8
AC8
SOFTWARE
PHE C:217 , PHE C:223 , LEU C:224 , ALA D:298 , GLY D:299 , THR D:302 , ILE D:363 , HEM D:500
BINDING SITE FOR RESIDUE PB2 D 501
[
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SAPs(SNPs)/Variants
(5, 20)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_CP2B4_RABIT_001 (V39I, chain A/B/C/D, )
2: VAR_CP2B4_RABIT_002 (I174V, chain A/B/C/D, )
3: VAR_CP2B4_RABIT_003 (L290I, chain A/B/C/D, )
4: VAR_CP2B4_RABIT_004 (M314L, chain A/B/C/D, )
5: VAR_CP2B4_RABIT_005 (L420M, chain A/B/C/D, )
View:
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Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_CP2B4_RABIT_001
*
V
39
I
CP2B4_RABIT
---
---
A/B/C/D
V
39
I
2
UniProt
VAR_CP2B4_RABIT_002
*
I
174
V
CP2B4_RABIT
---
---
A/B/C/D
I
174
V
3
UniProt
VAR_CP2B4_RABIT_003
*
L
290
I
CP2B4_RABIT
---
---
A/B/C/D
L
290
I
4
UniProt
VAR_CP2B4_RABIT_004
*
M
314
L
CP2B4_RABIT
---
---
A/B/C/D
M
314
L
5
UniProt
VAR_CP2B4_RABIT_005
*
L
420
M
CP2B4_RABIT
---
---
A/B/C/D
L
420
M
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: CYTOCHROME_P450 (A:429-438,B:429-438,C:429-438,D:42...)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
CYTOCHROME_P450
PS00086
Cytochrome P450 cysteine heme-iron ligand signature.
CP2B4_RABIT
429-438
4
A:429-438
B:429-438
C:429-438
D:429-438
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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.
SCOP Domains
(0, 0)
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CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_3g93D00 (D:28-491)
1b: CATH_3g93B00 (B:28-492)
1c: CATH_3g93C00 (C:28-491)
1d: CATH_3g93A00 (A:27-492)
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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)
European rabbit,japanese white rabbit,domesticrabbit,rabbits (Oryctolagus cuniculus)
(2)
1a
3g93D00
D:28-491
1b
3g93B00
B:28-492
1c
3g93C00
C:28-491
1d
3g93A00
A:27-492
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Pfam Domains
(0, 0)
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Asym.Unit (290 KB)
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