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3NXU
Asym. Unit
Info
Asym.Unit (168 KB)
Biol.Unit 1 (84 KB)
Biol.Unit 2 (82 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN CYTOCHROME P4503A4 BOUND TO AN INHIBITOR RITONAVIR
Authors
:
I. F. Sevrioukova, T. L. Poulos
Date
:
14 Jul 10 (Deposition) - 20 Oct 10 (Release) - 22 Dec 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Alpha Beta Protein, Cytochrome P450 Fold, Hemoprotein, Monooxygenase, Cytochrome P450 Reductase, Endoplasmic Reticulum, Oxidoreductase- Oxidoreductase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
I. F. Sevrioukova, T. L. Poulos
Structure And Mechanism Of The Complex Between Cytochrome P4503A4 And Ritonavir.
Proc. Natl. Acad. Sci. Usa V. 107 18422 2010
[
close entry info
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Hetero Components
(3, 10)
Info
All Hetero Components
1a: DIMETHYL SULFOXIDE (DMSa)
1b: DIMETHYL SULFOXIDE (DMSb)
1c: DIMETHYL SULFOXIDE (DMSc)
1d: DIMETHYL SULFOXIDE (DMSd)
1e: DIMETHYL SULFOXIDE (DMSe)
1f: DIMETHYL SULFOXIDE (DMSf)
2a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
2b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
3a: RITONAVIR (RITa)
3b: RITONAVIR (RITb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
DMS
6
Ligand/Ion
DIMETHYL SULFOXIDE
2
HEM
2
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
3
RIT
2
Ligand/Ion
RITONAVIR
[
close Hetero Component info
]
Sites
(10, 10)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLY A:56 , PHE A:57 , CYS A:58 , MET A:371 , SER A:478 , LEU A:479 , GLY A:480
BINDING SITE FOR RESIDUE DMS A 700
02
AC2
SOFTWARE
PHE A:226 , PRO A:227 , PHE A:228 , PRO B:231 , HOH B:670
BINDING SITE FOR RESIDUE DMS A 701
03
AC3
SOFTWARE
ILE A:50 , TYR A:53 , PHE A:215 , LEU A:216
BINDING SITE FOR RESIDUE DMS A 702
04
AC4
SOFTWARE
CYS A:239 , VAL A:240 , ARG A:243 , HOH A:630
BINDING SITE FOR RESIDUE DMS A 703
05
AC5
SOFTWARE
HOH A:11 , ARG A:105 , ILE A:118 , TRP A:126 , ARG A:130 , PHE A:302 , ALA A:305 , THR A:309 , ILE A:369 , ALA A:370 , ARG A:375 , PRO A:434 , PHE A:435 , GLY A:436 , SER A:437 , ARG A:440 , ASN A:441 , CYS A:442 , ILE A:443 , GLY A:444 , MET A:452 , RIT A:600
BINDING SITE FOR RESIDUE HEM A 508
06
AC6
SOFTWARE
HOH A:1 , PHE A:108 , SER A:119 , ILE A:120 , LEU A:210 , LEU A:211 , PHE A:215 , PHE A:241 , ILE A:301 , PHE A:304 , ALA A:305 , THR A:309 , ILE A:369 , ALA A:370 , ARG A:372 , GLU A:374 , GLY A:481 , HEM A:508 , HOH A:511 , HOH A:628
BINDING SITE FOR RESIDUE RIT A 600
07
AC7
SOFTWARE
GLY B:56 , PHE B:57 , CYS B:58 , MET B:371 , LEU B:477 , SER B:478 , LEU B:479 , GLY B:480
BINDING SITE FOR RESIDUE DMS B 704
08
AC8
SOFTWARE
PHE B:219 , CYS B:239
BINDING SITE FOR RESIDUE DMS B 705
09
AC9
SOFTWARE
ARG B:105 , ILE B:118 , SER B:119 , TRP B:126 , ARG B:130 , PHE B:302 , ALA B:305 , VAL B:313 , ILE B:369 , ALA B:370 , ARG B:375 , PRO B:434 , PHE B:435 , GLY B:436 , ARG B:440 , ASN B:441 , CYS B:442 , ILE B:443 , MET B:452 , HOH B:546 , RIT B:600
BINDING SITE FOR RESIDUE HEM B 508
10
BC1
SOFTWARE
HOH B:6 , PHE B:108 , SER B:119 , ILE B:120 , LEU B:210 , LEU B:211 , PHE B:213 , PHE B:215 , PHE B:241 , ILE B:301 , PHE B:304 , ALA B:305 , THR B:309 , ARG B:372 , GLU B:374 , GLY B:481 , HEM B:508 , HOH B:521 , HOH B:522 , HOH B:546 , HOH B:650 , HOH B:656
BINDING SITE FOR RESIDUE RIT B 600
[
close Site info
]
SAPs(SNPs)/Variants
(20, 40)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_011598 (G56D, chain A/B, )
02: VAR_037547 (K96E, chain A/B, )
03: VAR_011599 (I118V, chain A/B, )
04: VAR_011600 (R130Q, chain A/B, )
05: VAR_011601 (R162Q, chain A/B, )
06: VAR_011602 (V170I, chain A/B, )
07: VAR_011603 (D174H, chain A/B, )
08: VAR_011604 (T185S, chain A/B, )
09: VAR_014322 (F189S, chain A/B, )
10: VAR_011605 (P218R, chain A/B, )
11: VAR_008363 (S222P, chain A/B, )
12: VAR_037548 (S252A, chain A/B, )
13: VAR_014323 (L293P, chain A/B, )
14: VAR_037549 (T349N, chain A/B, )
15: VAR_011606 (T363M, chain A/B, )
16: VAR_011607 (L373F, chain A/B, )
17: VAR_011608 (P416L, chain A/B, )
18: VAR_037550 (I431T, chain A/B, )
19: VAR_008364 (M445T, chain A/B, )
20: VAR_014324 (P467S, chain A/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
A/B
G
56
D
02
UniProt
VAR_037547
K
96
E
CP3A4_HUMAN
Polymorphism
3091339
A/B
K
96
E
03
UniProt
VAR_011599
I
118
V
CP3A4_HUMAN
Polymorphism
55951658
A/B
I
118
V
04
UniProt
VAR_011600
R
130
Q
CP3A4_HUMAN
Polymorphism
---
A/B
R
130
Q
05
UniProt
VAR_011601
R
162
Q
CP3A4_HUMAN
Polymorphism
4986907
A/B
R
162
Q
06
UniProt
VAR_011602
V
170
I
CP3A4_HUMAN
Polymorphism
---
A/B
V
170
I
07
UniProt
VAR_011603
D
174
H
CP3A4_HUMAN
Polymorphism
4986908
A/B
D
174
H
08
UniProt
VAR_011604
T
185
S
CP3A4_HUMAN
Polymorphism
12721627
A/B
T
185
S
09
UniProt
VAR_014322
F
189
S
CP3A4_HUMAN
Polymorphism
4987161
A/B
F
189
S
10
UniProt
VAR_011605
P
218
R
CP3A4_HUMAN
Polymorphism
55901263
A/B
P
218
R
11
UniProt
VAR_008363
S
222
P
CP3A4_HUMAN
Polymorphism
55785340
A/B
S
222
P
12
UniProt
VAR_037548
S
252
A
CP3A4_HUMAN
Polymorphism
3208363
A/B
S
252
A
13
UniProt
VAR_014323
L
293
P
CP3A4_HUMAN
Polymorphism
28371759
A/B
L
293
P
14
UniProt
VAR_037549
T
349
N
CP3A4_HUMAN
Polymorphism
10250778
A/B
T
349
N
15
UniProt
VAR_011606
T
363
M
CP3A4_HUMAN
Polymorphism
67784355
A/B
T
363
M
16
UniProt
VAR_011607
L
373
F
CP3A4_HUMAN
Polymorphism
12721629
A/B
L
373
F
17
UniProt
VAR_011608
P
416
L
CP3A4_HUMAN
Polymorphism
4986909
A/B
P
416
L
18
UniProt
VAR_037550
I
431
T
CP3A4_HUMAN
Polymorphism
1041988
A/B
I
431
T
19
UniProt
VAR_008364
M
445
T
CP3A4_HUMAN
Polymorphism
4986910
A/B
M
445
T
20
UniProt
VAR_014324
P
467
S
CP3A4_HUMAN
Polymorphism
4986913
A/B
P
467
S
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: CYTOCHROME_P450 (A:435-444,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
2
A:435-444
B:435-444
[
close PROSITE info
]
Exons
(12, 24)
Info
All Exons
Exon 1.2b (A:29-55 | B:29-55)
Exon 1.3b (A:56-73 | B:56-73)
Exon 1.4 (A:73-106 | B:73-106)
Exon 1.5b (A:107-144 | B:107-144)
Exon 1.6a (A:145-174 | B:145-174)
Exon 1.7 (A:174-224 | B:174-224)
Exon 1.8 (A:224-264 | B:224-264)
Exon 1.9 (A:268-289 (gaps) | B:268-289 (gaps...)
Exon 1.10 (A:289-342 | B:289-342)
Exon 1.11 (A:343-418 | B:343-418)
Exon 1.12 (A:418-472 | B:418-472)
Exon 1.13a (A:473-496 | B:473-496)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.1a/1.2b
02: Boundary 1.2b/1.3b
03: Boundary 1.3b/1.4
04: Boundary 1.4/1.5b
05: Boundary 1.5b/1.6a
06: Boundary 1.6a/1.7
07: Boundary 1.7/1.8
08: Boundary 1.8/1.9
09: Boundary 1.9/1.10
10: Boundary 1.10/1.11
11: Boundary 1.11/1.12
12: Boundary 1.12/1.13a
13: Boundary 1.13a/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1a
ENST00000336411
1a
ENSE00001957287
chr7:
99381888-99381634
255
CP3A4_HUMAN
1-24
24
0
-
-
1.2b
ENST00000336411
2b
ENSE00001696932
chr7:
99377708-99377615
94
CP3A4_HUMAN
24-55
32
2
A:29-55
B:29-55
27
27
1.3b
ENST00000336411
3b
ENSE00001786394
chr7:
99375703-99375651
53
CP3A4_HUMAN
56-73
18
2
A:56-73
B:56-73
18
18
1.4
ENST00000336411
4
ENSE00001055096
chr7:
99370312-99370213
100
CP3A4_HUMAN
73-106
34
2
A:73-106
B:73-106
34
34
1.5b
ENST00000336411
5b
ENSE00001630478
chr7:
99367858-99367745
114
CP3A4_HUMAN
107-144
38
2
A:107-144
B:107-144
38
38
1.6a
ENST00000336411
6a
ENSE00001766439
chr7:
99367479-99367391
89
CP3A4_HUMAN
145-174
30
2
A:145-174
B:145-174
30
30
1.7
ENST00000336411
7
ENSE00001717945
chr7:
99366125-99365977
149
CP3A4_HUMAN
174-224
51
2
A:174-224
B:174-224
51
51
1.8
ENST00000336411
8
ENSE00001055106
chr7:
99364881-99364754
128
CP3A4_HUMAN
224-266
43
2
A:224-264
B:224-264
41
41
1.9
ENST00000336411
9
ENSE00001784871
chr7:
99364066-99364000
67
CP3A4_HUMAN
267-289
23
2
A:268-289 (gaps)
B:268-289 (gaps)
22
22
1.10
ENST00000336411
10
ENSE00001643301
chr7:
99361638-99361478
161
CP3A4_HUMAN
289-342
54
2
A:289-342
B:289-342
54
54
1.11
ENST00000336411
11
ENSE00001651983
chr7:
99359890-99359664
227
CP3A4_HUMAN
343-418
76
2
A:343-418
B:343-418
76
76
1.12
ENST00000336411
12
ENSE00001055100
chr7:
99358604-99358442
163
CP3A4_HUMAN
418-472
55
2
A:418-472
B:418-472
55
55
1.13a
ENST00000336411
13a
ENSE00001910683
chr7:
99355851-99355299
553
CP3A4_HUMAN
473-503
31
2
A:473-496
B:473-496
24
24
[
close EXON info
]
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d3nxua_ (A:)
1b: SCOP_d3nxub_ (B:)
View:
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Classes
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)
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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
:
automated matches
(44)
Human (Homo sapiens) [TaxId: 9606]
(17)
1a
d3nxua_
A:
1b
d3nxub_
B:
[
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]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_p450_3nxuB01 (B:38-493)
1b: PFAM_p450_3nxuB02 (B:38-493)
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Families
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(
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(
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(
)
Clan
:
no clan defined [family: p450]
(161)
Family
:
p450
(161)
Homo sapiens (Human)
(33)
1a
p450-3nxuB01
B:38-493
1b
p450-3nxuB02
B:38-493
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