PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
Getting 'PROSITE' information from database.
3R1A
Biol. Unit 6
Info
Asym.Unit (595 KB)
Biol.Unit 1 (83 KB)
Biol.Unit 2 (82 KB)
Biol.Unit 3 (83 KB)
Biol.Unit 4 (83 KB)
Biol.Unit 5 (82 KB)
Biol.Unit 6 (81 KB)
Biol.Unit 7 (82 KB)
Biol.Unit 8 (75 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CLOSED CRYSTAL STRUCTURE OF CYTOCHROME P450 2B4 COVALENTLY BOUND TO THE MECHANISM-BASED INACTIVATOR TERT-BUTYLPHENYLACETYLENE
Authors
:
S. C. Gay, H. Zhang, C. D. Stout, P. F. Hollenberg, J. R. Halpert
Date
:
09 Mar 11 (Deposition) - 11 May 11 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.50
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
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)
Biol. Unit 7: G (1x)
Biol. Unit 8: H (1x)
Keywords
:
Cytochrome P450 2B4, Monooxygenase, Oxidoreductase, Membrane Protein, T302 Covalently Linked To Tert-Butylphenylacetylene, Oxidoreductase- Oxidoreductase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. C. Gay, H. Zhang, P. R. Wilderman, A. G. Roberts, T. Liu, S. Li, H. L. Lin, Q. Zhang, V. L. Woods, C. D. Stout, P. F. Hollenberg, J. R. Halpert
Structural Analysis Of Mammalian Cytochrome P450 2B4 Covalently Bound To The Mechanism-Based Inactivator Tert-Butylphenylacetylene: Insight Into Partial Enzymatic Activity.
Biochemistry V. 50 4903 2011
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 2)
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)
1e: PROTOPORPHYRIN IX CONTAINING FE (HEMe)
1f: PROTOPORPHYRIN IX CONTAINING FE (HEMf)
1g: PROTOPORPHYRIN IX CONTAINING FE (HEMg)
1h: PROTOPORPHYRIN IX CONTAINING FE (HEMh)
2a: (4-TERT-BUTYLPHENYL)ACETALDEHYDE (TB2a)
2b: (4-TERT-BUTYLPHENYL)ACETALDEHYDE (TB2b)
2c: (4-TERT-BUTYLPHENYL)ACETALDEHYDE (TB2c)
2d: (4-TERT-BUTYLPHENYL)ACETALDEHYDE (TB2d)
2e: (4-TERT-BUTYLPHENYL)ACETALDEHYDE (TB2e)
2f: (4-TERT-BUTYLPHENYL)ACETALDEHYDE (TB2f)
2g: (4-TERT-BUTYLPHENYL)ACETALDEHYDE (TB2g)
2h: (4-TERT-BUTYLPHENYL)ACETALDEHYDE (TB2h)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
HEM
1
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
2
TB2
1
Ligand/Ion
(4-TERT-BUTYLPHENYL)ACETALDEHYDE
[
close Hetero Component info
]
Sites
(2, 2)
Info
All Sites
1: BC2 (SOFTWARE)
2: BC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
BC2
SOFTWARE
ARG F:98 , VAL F:113 , ILE F:114 , TRP F:121 , ARG F:125 , ILE F:179 , LEU F:295 , GLY F:299 , THR F:302 , THR F:303 , GLN F:357 , VAL F:367 , HIS F:369 , LEU F:392 , PRO F:428 , PHE F:429 , SER F:430 , ARG F:434 , CYS F:436 , LEU F:437 , GLY F:438 , ALA F:442
BINDING SITE FOR RESIDUE HEM F 500
2
BC3
SOFTWARE
PHE F:115 , PHE F:206 , ALA F:298 , THR F:302
BINDING SITE FOR RESIDUE TB2 F 501
[
close Site info
]
SAPs(SNPs)/Variants
(5, 5)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_CP2B4_RABIT_001 (V39I, chain F, )
2: VAR_CP2B4_RABIT_002 (I174V, chain F, )
3: VAR_CP2B4_RABIT_003 (L290I, chain F, )
4: VAR_CP2B4_RABIT_004 (M314L, chain F, )
5: VAR_CP2B4_RABIT_005 (L420M, chain F, )
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
---
---
F
V
39
I
2
UniProt
VAR_CP2B4_RABIT_002
*
I
174
V
CP2B4_RABIT
---
---
F
I
174
V
3
UniProt
VAR_CP2B4_RABIT_003
*
L
290
I
CP2B4_RABIT
---
---
F
L
290
I
4
UniProt
VAR_CP2B4_RABIT_004
*
M
314
L
CP2B4_RABIT
---
---
F
M
314
L
5
UniProt
VAR_CP2B4_RABIT_005
*
L
420
M
CP2B4_RABIT
---
---
F
L
420
M
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: CYTOCHROME_P450 (F: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.
CP2B4_RABIT
429-438
1
-
-
-
-
-
F:429-438
-
-
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
All Exon Boundaries
View:
Label:
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
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(1, 8)
Info
all PFAM domains
1a: PFAM_p450_3r1aH01 (H:31-488)
1b: PFAM_p450_3r1aH02 (H:31-488)
1c: PFAM_p450_3r1aH03 (H:31-488)
1d: PFAM_p450_3r1aH04 (H:31-488)
1e: PFAM_p450_3r1aH05 (H:31-488)
1f: PFAM_p450_3r1aH06 (H:31-488)
1g: PFAM_p450_3r1aH07 (H:31-488)
1h: PFAM_p450_3r1aH08 (H:31-488)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: p450]
(161)
Family
:
p450
(161)
Oryctolagus cuniculus (Rabbit)
(10)
1a
p450-3r1aH01
H:31-488
1b
p450-3r1aH02
H:31-488
1c
p450-3r1aH03
H:31-488
1d
p450-3r1aH04
H:31-488
1e
p450-3r1aH05
H:31-488
1f
p450-3r1aH06
H:31-488
1g
p450-3r1aH07
H:31-488
1h
p450-3r1aH08
H:31-488
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain F
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
close Script example commands
]
Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (595 KB)
Header - Asym.Unit
Biol.Unit 1 (83 KB)
Header - Biol.Unit 1
Biol.Unit 2 (82 KB)
Header - Biol.Unit 2
Biol.Unit 3 (83 KB)
Header - Biol.Unit 3
Biol.Unit 4 (83 KB)
Header - Biol.Unit 4
Biol.Unit 5 (82 KB)
Header - Biol.Unit 5
Biol.Unit 6 (81 KB)
Header - Biol.Unit 6
Biol.Unit 7 (82 KB)
Header - Biol.Unit 7
Biol.Unit 8 (75 KB)
Header - Biol.Unit 8
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
3R1A
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help