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...
No precomputed SNP/Variant structure found.
Calculating the structure may take several minutes.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
3ZBY
Asym. Unit
Info
Asym.Unit (940 KB)
Biol.Unit 1 (313 KB)
Biol.Unit 2 (313 KB)
Biol.Unit 3 (311 KB)
Biol.Unit 4 (314 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
LIGAND-FREE STRUCTURE OF CYP142 FROM MYCOBACTERIUM SMEGMATIS
Authors
:
E. Garcia-Fernandez, D. J. Frank, B. Galan, P. M. Kells, L. M. Podust, J. P. R. Ortiz De Montellano
Date
:
13 Nov 12 (Deposition) - 27 Feb 13 (Release) - 14 Aug 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.93
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: C,F (1x)
Biol. Unit 2: B,E (1x)
Biol. Unit 3: A (2x)
Biol. Unit 4: D (2x)
Keywords
:
Oxidoreductase, Cyp142, Cholesterol Metabolism
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. Garcia-Fernandez, D. J. Frank, B. Galan, P. M. Kells, L. M. Podust, J. L. Garcia, P. R. Ortiz De Montellano
A Highly Conserved Mycobacterial Cholesterol Catabolic Pathway.
Environ. Microbiol. V. 15 2342 2013
[
close entry info
]
Hetero Components
(4, 35)
Info
All Hetero Components
1a: BETA-CYCLODEXTRIN (BCDa)
1b: BETA-CYCLODEXTRIN (BCDb)
1c: BETA-CYCLODEXTRIN (BCDc)
1d: BETA-CYCLODEXTRIN (BCDd)
1e: BETA-CYCLODEXTRIN (BCDe)
1f: BETA-CYCLODEXTRIN (BCDf)
2a: 1,2-ETHANEDIOL (EDOa)
2b: 1,2-ETHANEDIOL (EDOb)
2c: 1,2-ETHANEDIOL (EDOc)
2d: 1,2-ETHANEDIOL (EDOd)
2e: 1,2-ETHANEDIOL (EDOe)
2f: 1,2-ETHANEDIOL (EDOf)
3a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
3b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
3c: PROTOPORPHYRIN IX CONTAINING FE (HEMc)
3d: PROTOPORPHYRIN IX CONTAINING FE (HEMd)
3e: PROTOPORPHYRIN IX CONTAINING FE (HEMe)
3f: PROTOPORPHYRIN IX CONTAINING FE (HEMf)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
4c: SULFATE ION (SO4c)
4d: SULFATE ION (SO4d)
4e: SULFATE ION (SO4e)
4f: SULFATE ION (SO4f)
4g: SULFATE ION (SO4g)
4h: SULFATE ION (SO4h)
4i: SULFATE ION (SO4i)
4j: SULFATE ION (SO4j)
4k: SULFATE ION (SO4k)
4l: SULFATE ION (SO4l)
4m: SULFATE ION (SO4m)
4n: SULFATE ION (SO4n)
4o: SULFATE ION (SO4o)
4p: SULFATE ION (SO4p)
4q: SULFATE ION (SO4q)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BCD
6
Ligand/Ion
BETA-CYCLODEXTRIN
2
EDO
6
Ligand/Ion
1,2-ETHANEDIOL
3
HEM
6
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
4
SO4
17
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(35, 35)
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)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU A:56 , MET A:78 , ILE A:79 , HIS A:86 , ARG A:90 , ILE A:230 , GLY A:233 , GLY A:234 , THR A:237 , THR A:238 , THR A:241 , VAL A:280 , MET A:283 , ARG A:285 , ALA A:335 , PHE A:336 , GLY A:337 , PHE A:338 , HIS A:341 , CYS A:343 , GLY A:345 , ALA A:349 , EDO A:1406 , HOH A:2348
BINDING SITE FOR RESIDUE HEM A1402
02
AC2
SOFTWARE
MET A:179 , LYS A:190 , ASP A:221 , PHE A:225 , HOH A:2446 , PRO F:76 , PHE F:182 , ASP F:221 , PHE F:225 , BCD F:1403 , HOH F:2415
BINDING SITE FOR RESIDUE BCD A1403
03
AC3
SOFTWARE
GLU B:56 , MET B:78 , ILE B:79 , HIS B:86 , ARG B:90 , PHE B:97 , GLY B:233 , GLY B:234 , THR B:237 , THR B:238 , THR B:241 , VAL B:280 , ARG B:285 , ALA B:335 , PHE B:336 , GLY B:337 , PHE B:338 , HIS B:341 , CYS B:343 , GLY B:345 , ALA B:349 , EDO B:1409 , HOH B:2342
BINDING SITE FOR RESIDUE HEM B1402
04
AC4
SOFTWARE
MET B:179 , PHE B:182 , LYS B:190 , ASP B:221 , PHE B:225 , HOH B:2144
BINDING SITE FOR RESIDUE BCD B1403
05
AC5
SOFTWARE
GLU C:56 , MET C:78 , ILE C:79 , HIS C:86 , ARG C:90 , PHE C:97 , ILE C:230 , GLY C:233 , GLY C:234 , THR C:237 , THR C:238 , LEU C:274 , VAL C:280 , ARG C:285 , ALA C:335 , PHE C:336 , GLY C:337 , PHE C:338 , HIS C:341 , CYS C:343 , GLY C:345 , ALA C:349 , EDO C:1407 , HOH C:2356
BINDING SITE FOR RESIDUE HEM C1402
06
AC6
SOFTWARE
MET C:179 , PHE C:182 , ASP C:221 , PHE C:225
BINDING SITE FOR RESIDUE BCD C1403
07
AC7
SOFTWARE
GLU D:56 , MET D:78 , ILE D:79 , HIS D:86 , ARG D:90 , ILE D:230 , GLY D:233 , GLY D:234 , THR D:237 , THR D:238 , VAL D:280 , ARG D:285 , ALA D:335 , PHE D:336 , GLY D:337 , PHE D:338 , HIS D:341 , CYS D:343 , GLY D:345 , ALA D:349 , EDO D:1407 , HOH D:2330
BINDING SITE FOR RESIDUE HEM D1402
08
AC8
SOFTWARE
MET D:179 , LYS D:190 , ASP D:221 , MET E:179 , PHE E:182 , ASP E:221 , PHE E:225 , BCD E:1403 , HOH E:2443
BINDING SITE FOR RESIDUE BCD D1403
09
AC9
SOFTWARE
GLU E:56 , MET E:78 , ILE E:79 , HIS E:86 , ARG E:90 , PHE E:97 , GLY E:233 , GLY E:234 , THR E:237 , THR E:238 , THR E:241 , VAL E:280 , ARG E:285 , ALA E:335 , PHE E:336 , GLY E:337 , PHE E:338 , HIS E:341 , CYS E:343 , GLY E:345 , ALA E:349 , EDO E:1407 , HOH E:2343
BINDING SITE FOR RESIDUE HEM E1402
10
BC1
SOFTWARE
PRO D:76 , ALA D:183 , ASP D:221 , PHE D:225 , BCD D:1403 , LYS E:190 , ASP E:221 , HOH E:2442 , HOH E:2443
BINDING SITE FOR RESIDUE BCD E1403
11
BC2
SOFTWARE
GLU F:56 , MET F:78 , ILE F:79 , HIS F:86 , ARG F:90 , ILE F:230 , GLY F:233 , GLY F:234 , THR F:237 , THR F:238 , THR F:241 , VAL F:280 , ARG F:285 , ALA F:335 , PHE F:336 , GLY F:337 , PHE F:338 , HIS F:341 , CYS F:343 , GLY F:345 , ALA F:349 , EDO F:1407 , HOH F:2323
BINDING SITE FOR RESIDUE HEM F1402
12
BC3
SOFTWARE
MET A:179 , PHE A:182 , ASP A:221 , PHE A:225 , BCD A:1403 , HOH A:2446 , ASP F:221 , HOH F:2415
BINDING SITE FOR RESIDUE BCD F1403
13
BC4
SOFTWARE
ARG B:239 , ARG B:378
BINDING SITE FOR RESIDUE SO4 B1406
14
BC5
SOFTWARE
ARG E:24 , ARG E:28 , HOH E:2049 , HOH E:2051 , HOH E:2061
BINDING SITE FOR RESIDUE SO4 E1404
15
BC6
SOFTWARE
ARG B:28 , HOH B:2044 , HOH B:2053 , HOH B:2060
BINDING SITE FOR RESIDUE SO4 B1407
16
BC7
SOFTWARE
ARG C:28 , HOH C:2055 , HOH C:2056 , HOH C:2063 , HOH C:2457
BINDING SITE FOR RESIDUE SO4 C1404
17
BC8
SOFTWARE
ARG F:28 , HOH F:2039 , HOH F:2041 , HOH F:2049
BINDING SITE FOR RESIDUE SO4 F1404
18
BC9
SOFTWARE
ARG C:239 , ARG C:378 , HOH C:2316
BINDING SITE FOR RESIDUE SO4 C1405
19
CC1
SOFTWARE
ARG D:24 , ARG D:28 , HOH D:2048 , HOH D:2055 , HOH D:2059
BINDING SITE FOR RESIDUE SO4 D1404
20
CC2
SOFTWARE
GLU D:236 , ARG D:239 , ARG D:378 , HOH D:2242
BINDING SITE FOR RESIDUE SO4 D1405
21
CC3
SOFTWARE
ARG E:239 , ARG E:378 , HOH E:2257
BINDING SITE FOR RESIDUE SO4 E1405
22
CC4
SOFTWARE
GLU F:236 , ARG F:239 , ARG F:378 , HOH F:2215
BINDING SITE FOR RESIDUE SO4 F1405
23
CC5
SOFTWARE
THR A:2 , GLN A:3 , MET A:4 , ARG A:7 , TRP A:29 , HOH A:2447
BINDING SITE FOR RESIDUE SO4 A1404
24
CC6
SOFTWARE
ARG A:24 , ARG A:28 , HOH A:2051 , HOH A:2059 , HOH A:2448
BINDING SITE FOR RESIDUE SO4 A1405
25
CC7
SOFTWARE
GLN B:3 , MET B:4 , ARG B:7 , TRP B:29 , GLU B:34
BINDING SITE FOR RESIDUE SO4 B1408
26
CC8
SOFTWARE
THR C:2 , GLN C:3 , MET C:4 , ARG C:7 , TRP C:29 , HOH C:2009
BINDING SITE FOR RESIDUE SO4 C1406
27
CC9
SOFTWARE
GLN D:3 , MET D:4 , ARG D:7 , TRP D:29 , HOH D:2431
BINDING SITE FOR RESIDUE SO4 D1406
28
DC1
SOFTWARE
GLN E:3 , MET E:4 , ARG E:7 , TRP E:29 , HOH E:2444
BINDING SITE FOR RESIDUE SO4 E1406
29
DC2
SOFTWARE
THR F:2 , GLN F:3 , MET F:4 , ARG F:7 , TRP F:29 , HOH F:2416
BINDING SITE FOR RESIDUE SO4 F1406
30
DC3
SOFTWARE
GLY B:233 , HEM B:1402
BINDING SITE FOR RESIDUE EDO B1409
31
DC4
SOFTWARE
GLY F:233 , HEM F:1402
BINDING SITE FOR RESIDUE EDO F1407
32
DC5
SOFTWARE
GLY A:233 , HEM A:1402
BINDING SITE FOR RESIDUE EDO A1406
33
DC6
SOFTWARE
GLY C:233 , MET C:283 , HEM C:1402
BINDING SITE FOR RESIDUE EDO C1407
34
DC7
SOFTWARE
GLY D:233 , HEM D:1402
BINDING SITE FOR RESIDUE EDO D1407
35
DC8
SOFTWARE
GLY E:233 , HEM E:1402 , HOH E:2445
BINDING SITE FOR RESIDUE EDO E1407
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 6)
Info
All PROSITE Patterns/Profiles
1: CYTOCHROME_P450 (A:336-345,B:336-345,C:336-345,D:33...)
;
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.
CP142_MYCS2
336-345
6
A:336-345
B:336-345
C:336-345
D:336-345
E:336-345
F:336-345
[
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.
SCOP Domains
(1, 6)
Info
All SCOP Domains
1a: SCOP_d3zbya_ (A:)
1b: SCOP_d3zbyb_ (B:)
1c: SCOP_d3zbyc_ (C:)
1d: SCOP_d3zbyd_ (D:)
1e: SCOP_d3zbye_ (E:)
1f: SCOP_d3zbyf_ (F:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Cytochrome P450
(480)
Superfamily
:
Cytochrome P450
(480)
Family
:
automated matches
(157)
Protein domain
:
automated matches
(157)
Mycobacterium smegmatis [TaxId: 246196]
(2)
1a
d3zbya_
A:
1b
d3zbyb_
B:
1c
d3zbyc_
C:
1d
d3zbyd_
D:
1e
d3zbye_
E:
1f
d3zbyf_
F:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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 A
Chain B
Chain C
Chain D
Chain E
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 (940 KB)
Header - Asym.Unit
Biol.Unit 1 (313 KB)
Header - Biol.Unit 1
Biol.Unit 2 (313 KB)
Header - Biol.Unit 2
Biol.Unit 3 (311 KB)
Header - Biol.Unit 3
Biol.Unit 4 (314 KB)
Header - Biol.Unit 4
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
3ZBY
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help