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2V0M
Biol. Unit 2
Info
Asym.Unit (310 KB)
Biol.Unit 1 (80 KB)
Biol.Unit 2 (78 KB)
Biol.Unit 3 (80 KB)
Biol.Unit 4 (79 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN P450 3A4 IN COMPLEX WITH KETOCONAZOLE
Authors
:
T. Sjogren, M. Ekroos
Date
:
15 May 07 (Deposition) - 26 Jun 07 (Release) - 03 Aug 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.80
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Keywords
:
Metal-Binding, Transmembrane, Oxidoreductase, Endoplasmic Reticulum, Drug Metabolizing Enzyme, Ketoconazol, Polymorphism, Monooxygenase, P450, Nadp, Iron, Heme, Cyp3A4, Membrane, Microsome
(Keyword Search:
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Reference
:
M. Ekroos, T. Sjogren
Structural Basis For Ligand Promiscuity In Cytochrome P450 3A4
Proc. Natl. Acad. Sci. Usa V. 103 13682 2006
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Hetero Components
(2, 3)
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-ACETYL-4-(4-{[(2S,4R)-2-(2,4-DIC... (KLNa)
2b: 1-ACETYL-4-(4-{[(2S,4R)-2-(2,4-DIC... (KLNb)
2c: 1-ACETYL-4-(4-{[(2S,4R)-2-(2,4-DIC... (KLNc)
2d: 1-ACETYL-4-(4-{[(2S,4R)-2-(2,4-DIC... (KLNd)
2e: 1-ACETYL-4-(4-{[(2S,4R)-2-(2,4-DIC... (KLNe)
2f: 1-ACETYL-4-(4-{[(2S,4R)-2-(2,4-DIC... (KLNf)
2g: 1-ACETYL-4-(4-{[(2S,4R)-2-(2,4-DIC... (KLNg)
2h: 1-ACETYL-4-(4-{[(2S,4R)-2-(2,4-DIC... (KLNh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
HEM
1
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
2
KLN
2
Ligand/Ion
1-ACETYL-4-(4-{[(2S,4R)-2-(2,4-DICHLOROPHENYL)-2-(1H-IMIDAZOL-1-YLMETHYL)-1,3-DIOXOLAYL]METHOXY}PHENYL)PIPERAZINE
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Sites
(3, 3)
Info
All Sites
1: AC4 (SOFTWARE)
2: AC5 (SOFTWARE)
3: AC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC4
SOFTWARE
ARG B:105 , ILE B:118 , TRP B:126 , ARG B:130 , PHE B:302 , ALA B:305 , THR B:309 , VAL B:313 , ALA B:370 , ARG B:375 , PRO B:434 , PHE B:435 , GLY B:436 , SER B:437 , ARG B:440 , ASN B:441 , CYS B:442 , ILE B:443 , PHE B:447 , MET B:452 , KLN B:1498
BINDING SITE FOR RESIDUE HEM B1497
2
AC5
SOFTWARE
ARG B:105 , SER B:119 , LEU B:210 , PHE B:241 , ILE B:301 , PHE B:304 , ALA B:370 , ARG B:372 , GLY B:481 , LEU B:482 , HEM B:1497 , KLN B:1499
BINDING SITE FOR RESIDUE KLN B1498
3
AC6
SOFTWARE
PHE B:57 , PHE B:108 , SER B:119 , THR B:224 , KLN B:1498
BINDING SITE FOR RESIDUE KLN B1499
[
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SAPs(SNPs)/Variants
(20, 20)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
01: VAR_011598 (G56D, chain B, )
02: VAR_037547 (K96E, chain B, )
03: VAR_011599 (I118V, chain B, )
04: VAR_011600 (R130Q, chain B, )
05: VAR_011601 (R162Q, chain B, )
06: VAR_011602 (V170I, chain B, )
07: VAR_011603 (D174H, chain B, )
08: VAR_011604 (T185S, chain B, )
09: VAR_014322 (F189S, chain B, )
10: VAR_011605 (P218R, chain B, )
11: VAR_008363 (S222P, chain B, )
12: VAR_037548 (S252A, chain B, )
13: VAR_014323 (L293P, chain B, )
14: VAR_037549 (T349N, chain B, )
15: VAR_011606 (T363M, chain B, )
16: VAR_011607 (L373F, chain B, )
17: VAR_011608 (P416L, chain B, )
18: VAR_037550 (I431T, chain B, )
19: VAR_008364 (M445T, chain B, )
20: VAR_014324 (P467S, chain B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_011598
G
56
D
CP3A4_HUMAN
Polymorphism
56324128
B
G
56
D
02
UniProt
VAR_037547
K
96
E
CP3A4_HUMAN
Polymorphism
3091339
B
K
96
E
03
UniProt
VAR_011599
I
118
V
CP3A4_HUMAN
Polymorphism
55951658
B
I
118
V
04
UniProt
VAR_011600
R
130
Q
CP3A4_HUMAN
Polymorphism
---
B
R
130
Q
05
UniProt
VAR_011601
R
162
Q
CP3A4_HUMAN
Polymorphism
4986907
B
R
162
Q
06
UniProt
VAR_011602
V
170
I
CP3A4_HUMAN
Polymorphism
---
B
V
170
I
07
UniProt
VAR_011603
D
174
H
CP3A4_HUMAN
Polymorphism
4986908
B
D
174
H
08
UniProt
VAR_011604
T
185
S
CP3A4_HUMAN
Polymorphism
12721627
B
T
185
S
09
UniProt
VAR_014322
F
189
S
CP3A4_HUMAN
Polymorphism
4987161
B
F
189
S
10
UniProt
VAR_011605
P
218
R
CP3A4_HUMAN
Polymorphism
55901263
B
P
218
R
11
UniProt
VAR_008363
S
222
P
CP3A4_HUMAN
Polymorphism
55785340
B
S
222
P
12
UniProt
VAR_037548
S
252
A
CP3A4_HUMAN
Polymorphism
3208363
B
S
252
A
13
UniProt
VAR_014323
L
293
P
CP3A4_HUMAN
Polymorphism
28371759
B
L
293
P
14
UniProt
VAR_037549
T
349
N
CP3A4_HUMAN
Polymorphism
10250778
B
T
349
N
15
UniProt
VAR_011606
T
363
M
CP3A4_HUMAN
Polymorphism
67784355
B
T
363
M
16
UniProt
VAR_011607
L
373
F
CP3A4_HUMAN
Polymorphism
12721629
B
L
373
F
17
UniProt
VAR_011608
P
416
L
CP3A4_HUMAN
Polymorphism
4986909
B
P
416
L
18
UniProt
VAR_037550
I
431
T
CP3A4_HUMAN
Polymorphism
1041988
B
I
431
T
19
UniProt
VAR_008364
M
445
T
CP3A4_HUMAN
Polymorphism
4986910
B
M
445
T
20
UniProt
VAR_014324
P
467
S
CP3A4_HUMAN
Polymorphism
4986913
B
P
467
S
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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]
PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: CYTOCHROME_P450 (B:435-444)
;
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.
CP3A4_HUMAN
435-444
1
-
B:435-444
-
-
[
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d2v0ma1 (A:30-498)
1b: SCOP_d2v0mb1 (B:30-496)
1c: SCOP_d2v0mc1 (C:30-496)
1d: SCOP_d2v0md1 (D:30-496)
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(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Cytochrome P450
(480)
Superfamily
:
Cytochrome P450
(480)
Family
:
Cytochrome P450
(323)
Protein domain
:
Mammalian cytochrome P450 3a4
(6)
Human (Homo sapiens) [TaxId: 9606]
(6)
1a
d2v0ma1
A:30-498
1b
d2v0mb1
B:30-496
1c
d2v0mc1
C:30-496
1d
d2v0md1
D:30-496
[
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CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_2v0mB00 (B:30-496)
1b: CATH_2v0mD00 (D:30-496)
1c: CATH_2v0mA00 (A:30-498)
1d: CATH_2v0mC00 (C:30-496)
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(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Cytochrome p450
(271)
Homologous Superfamily
:
Cytochrome p450
(271)
Human (Homo sapiens)
(32)
1a
2v0mB00
B:30-496
1b
2v0mD00
D:30-496
1c
2v0mA00
A:30-498
1d
2v0mC00
C:30-496
[
close CATH info
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Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_p450_2v0mD01 (D:38-493)
1b: PFAM_p450_2v0mD02 (D:38-493)
1c: PFAM_p450_2v0mD03 (D:38-493)
1d: PFAM_p450_2v0mD04 (D:38-493)
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Clans
(
)
(
)
Families
(
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(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: p450]
(161)
Family
:
p450
(161)
Homo sapiens (Human)
(33)
1a
p450-2v0mD01
D:38-493
1b
p450-2v0mD02
D:38-493
1c
p450-2v0mD03
D:38-493
1d
p450-2v0mD04
D:38-493
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]
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Protein & NOT Variant
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