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3G5N
Asym. Unit
Info
Asym.Unit (312 KB)
Biol.Unit 1 (301 KB)
Biol.Unit 2 (81 KB)
Biol.Unit 3 (80 KB)
Biol.Unit 4 (80 KB)
Biol.Unit 5 (81 KB)
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(1)
Title
:
TRIPLE 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
:
05 Feb 09 (Deposition) - 12 May 09 (Release) - 09 Jun 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
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
)
[
close entry info
]
Hetero Components
(3, 20)
Info
All Hetero Components
1a: 5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTO... (CM5a)
1b: 5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTO... (CM5b)
1c: 5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTO... (CM5c)
1d: 5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTO... (CM5d)
2a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
2b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
2c: PROTOPORPHYRIN IX CONTAINING FE (HEMc)
2d: PROTOPORPHYRIN IX CONTAINING FE (HEMd)
3a: 1-(BIPHENYL-4-YLMETHYL)-1H-IMIDAZO... (PB2a)
3b: 1-(BIPHENYL-4-YLMETHYL)-1H-IMIDAZO... (PB2b)
3c: 1-(BIPHENYL-4-YLMETHYL)-1H-IMIDAZO... (PB2c)
3d: 1-(BIPHENYL-4-YLMETHYL)-1H-IMIDAZO... (PB2d)
3e: 1-(BIPHENYL-4-YLMETHYL)-1H-IMIDAZO... (PB2e)
3f: 1-(BIPHENYL-4-YLMETHYL)-1H-IMIDAZO... (PB2f)
3g: 1-(BIPHENYL-4-YLMETHYL)-1H-IMIDAZO... (PB2g)
3h: 1-(BIPHENYL-4-YLMETHYL)-1H-IMIDAZO... (PB2h)
3i: 1-(BIPHENYL-4-YLMETHYL)-1H-IMIDAZO... (PB2i)
3j: 1-(BIPHENYL-4-YLMETHYL)-1H-IMIDAZO... (PB2j)
3k: 1-(BIPHENYL-4-YLMETHYL)-1H-IMIDAZO... (PB2k)
3l: 1-(BIPHENYL-4-YLMETHYL)-1H-IMIDAZO... (PB2l)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CM5
4
Ligand/Ion
5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTOSIDE
2
HEM
4
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
3
PB2
12
Ligand/Ion
1-(BIPHENYL-4-YLMETHYL)-1H-IMIDAZOLE
[
close Hetero Component info
]
Sites
(20, 20)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:98 , TRP A:121 , ARG A:125 , PHE A:296 , GLY A:299 , THR A:300 , THR A:302 , THR A:303 , GLN A:357 , 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 , HOH A:525
BINDING SITE FOR RESIDUE HEM A 500
02
AC2
SOFTWARE
ALA A:298 , GLY A:299 , THR A:302 , VAL A:367 , HEM A:500 , PHE B:217 , PHE B:223 , LYS B:225
BINDING SITE FOR RESIDUE PB2 A 501
03
AC3
SOFTWARE
LEU A:70 , ARG A:73 , GLU A:387 , ILE B:101 , PHE B:223 , LEU B:224 , PB2 B:502 , HOH B:525
BINDING SITE FOR RESIDUE PB2 A 503
04
AC4
SOFTWARE
ARG A:98 , ILE A:114 , ASN A:117 , TRP A:121 , LEU A:288
BINDING SITE FOR RESIDUE CM5 A 504
05
AC5
SOFTWARE
TYR A:69 , LEU A:70 , VAL A:477 , PB2 A:503 , LEU B:224 , LYS B:225 , PRO B:228 , THR B:230
BINDING SITE FOR RESIDUE PB2 B 502
06
AC6
SOFTWARE
ARG B:98 , TRP B:121 , ARG B:125 , PHE B:296 , GLY B:299 , THR B:300 , THR B:302 , THR B:303 , THR B:306 , 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 , LEU B:437 , GLY B:438 , HOH B:499 , PB2 B:501 , HOH B:520
BINDING SITE FOR RESIDUE HEM B 500
07
AC7
SOFTWARE
PHE A:217 , PHE A:223 , ALA B:298 , GLY B:299 , THR B:302 , VAL B:367 , PRO B:368 , HEM B:500
BINDING SITE FOR RESIDUE PB2 B 501
08
AC8
SOFTWARE
LYS A:225 , PHE A:227 , PRO A:228 , LEU B:43 , LEU B:51 , TYR B:69 , LEU B:70 , PRO B:368 , PHE B:389 , VAL B:477 , PB2 B:503 , HOH B:535
BINDING SITE FOR RESIDUE PB2 B 496
09
AC9
SOFTWARE
LEU A:224 , ARG B:73 , GLU B:387 , PB2 B:496
BINDING SITE FOR RESIDUE PB2 B 503
10
BC1
SOFTWARE
PHE A:220 , ARG B:98 , ILE B:114 , ASN B:117 , ARG B:120 , LEU B:288
BINDING SITE FOR RESIDUE CM5 B 504
11
BC2
SOFTWARE
ARG C:98 , TRP C:121 , ARG C:125 , PHE C:296 , GLY C:299 , 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 , LEU C:437 , GLY C:438 , PB2 C:501 , HOH C:510 , PHE D:220
BINDING SITE FOR RESIDUE HEM C 500
12
BC3
SOFTWARE
ALA C:298 , GLY C:299 , THR C:302 , VAL C:367 , PRO C:368 , HEM C:500 , PHE D:217 , PHE D:223
BINDING SITE FOR RESIDUE PB2 C 501
13
BC4
SOFTWARE
LEU C:43 , LEU C:51 , TYR C:69 , LEU C:70 , VAL C:477 , PB2 C:503 , LEU D:224 , LYS D:225 , PHE D:227 , PRO D:228 , THR D:230
BINDING SITE FOR RESIDUE PB2 C 502
14
BC5
SOFTWARE
ARG C:73 , GLU C:387 , PB2 C:502 , PHE D:223 , LEU D:224
BINDING SITE FOR RESIDUE PB2 C 503
15
BC6
SOFTWARE
VAL C:39 , ARG D:98 , ASN D:117 , TRP D:121 , LEU D:288 , HOH D:513
BINDING SITE FOR RESIDUE CM5 D 504
16
BC7
SOFTWARE
ARG C:98 , ILE C:114 , ASN C:117 , LEU C:288 , PHE D:220
BINDING SITE FOR RESIDUE CM5 C 504
17
BC8
SOFTWARE
ARG D:98 , TRP D:121 , ARG D:125 , PHE D:296 , GLY D:299 , THR D:302 , THR D:303 , ILE D:363 , VAL D:367 , HIS D:369 , 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
18
BC9
SOFTWARE
PHE C:217 , PHE C:223 , ALA D:298 , GLY D:299 , THR D:302 , VAL D:367 , PRO D:368 , HEM D:500
BINDING SITE FOR RESIDUE PB2 D 501
19
CC1
SOFTWARE
PRO C:228 , THR C:230 , LEU D:43 , TYR D:69 , LEU D:70 , PHE D:365 , VAL D:477 , PB2 D:503
BINDING SITE FOR RESIDUE PB2 D 502
20
CC2
SOFTWARE
LEU C:224 , LEU D:70 , ARG D:73 , GLU D:387 , PHE D:389 , PB2 D:502
BINDING SITE FOR RESIDUE PB2 D 503
[
close Site info
]
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:
Select:
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)
[
close SNP/Variant info
]
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:
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.
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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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, 4)
Info
All SCOP Domains
1a: SCOP_d3g5na_ (A:)
1b: SCOP_d3g5nd_ (D:)
1c: SCOP_d3g5nb_ (B:)
1d: SCOP_d3g5nc_ (C:)
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Protein Domains
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(
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Organisms
(
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(
)
Class
:
All alpha proteins
(14657)
Fold
:
Cytochrome P450
(480)
Superfamily
:
Cytochrome P450
(480)
Family
:
Cytochrome P450
(323)
Protein domain
:
Mammalian cytochrome p450 2b4
(10)
Rabbit (Oryctolagus cuniculus) [TaxId: 9986]
(10)
1a
d3g5na_
A:
1b
d3g5nd_
D:
1c
d3g5nb_
B:
1d
d3g5nc_
C:
[
close SCOP info
]
CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_3g5nB00 (B:28-492)
1b: CATH_3g5nD00 (D:28-492)
1c: CATH_3g5nC00 (C:26-492)
1d: CATH_3g5nA00 (A:27-493)
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Organisms
(
)
(
)
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
3g5nB00
B:28-492
1b
3g5nD00
D:28-492
1c
3g5nC00
C:26-492
1d
3g5nA00
A:27-493
[
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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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