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.
3OIB
Asym. Unit
Info
Asym.Unit (273 KB)
Biol.Unit 1 (266 KB)
Biol.Unit 2 (528 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CRYSTAL STRUCTURE OF A PUTATIVE ACYL-COA DEHYDROGENASE FROM MYCOBACTERIUM SMEGMATIS, IODIDE SOAK
Authors
:
Seattle Structural Genomics Center For Infectious Disease (S
Date
:
18 Aug 10 (Deposition) - 01 Sep 10 (Release) - 22 Apr 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B,I
#
Biol. Unit 1: A,B (1x)
Biol. Unit 2: A,B (2x)
(
#
: chains that contain no standard or modified protein/DNA/RNA residue)
Keywords
:
Ssgcid, Acyl-Coa Dehydrogenase, Mycobacerium Smegmatis, Seattle Structural Genomics Center For Infectious Disease, Deydrogenase, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Abendroth, A. S. Gardberg, J. I. Robinson, J. S. Christensen, B. L. Staker, P. J. Myler, L. J. Stewart, T. E. Edwards
Sad Phasing Using Iodide Ions In A High-Throughput Structural Genomics Environment.
J Struct Funct Genomics 2011
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(4, 36)
Info
All Hetero Components
1a: 1,2-ETHANEDIOL (EDOa)
1b: 1,2-ETHANEDIOL (EDOb)
2a: DIHYDROFLAVINE-ADENINE DINUCLEOTID... (FDAa)
2b: DIHYDROFLAVINE-ADENINE DINUCLEOTID... (FDAb)
3a: IODIDE ION (IODa)
3aa: IODIDE ION (IODaa)
3ab: IODIDE ION (IODab)
3ac: IODIDE ION (IODac)
3ad: IODIDE ION (IODad)
3b: IODIDE ION (IODb)
3c: IODIDE ION (IODc)
3d: IODIDE ION (IODd)
3e: IODIDE ION (IODe)
3f: IODIDE ION (IODf)
3g: IODIDE ION (IODg)
3h: IODIDE ION (IODh)
3i: IODIDE ION (IODi)
3j: IODIDE ION (IODj)
3k: IODIDE ION (IODk)
3l: IODIDE ION (IODl)
3m: IODIDE ION (IODm)
3n: IODIDE ION (IODn)
3o: IODIDE ION (IODo)
3p: IODIDE ION (IODp)
3q: IODIDE ION (IODq)
3r: IODIDE ION (IODr)
3s: IODIDE ION (IODs)
3t: IODIDE ION (IODt)
3u: IODIDE ION (IODu)
3v: IODIDE ION (IODv)
3w: IODIDE ION (IODw)
3x: IODIDE ION (IODx)
3y: IODIDE ION (IODy)
3z: IODIDE ION (IODz)
4a: SODIUM ION (NAa)
4b: SODIUM ION (NAb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EDO
2
Ligand/Ion
1,2-ETHANEDIOL
2
FDA
2
Ligand/Ion
DIHYDROFLAVINE-ADENINE DINUCLEOTIDE
3
IOD
30
Ligand/Ion
IODIDE ION
4
NA
2
Ligand/Ion
SODIUM ION
[
close Hetero Component info
]
Sites
(27, 27)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:321 , HOH A:636 , HOH A:661
BINDING SITE FOR RESIDUE NA A 502
02
AC2
SOFTWARE
HIS A:322 , HOH A:643 , ARG B:321
BINDING SITE FOR RESIDUE NA B 502
03
AC3
SOFTWARE
LYS A:65
BINDING SITE FOR RESIDUE IOD A 404
04
AC4
SOFTWARE
ASN A:343 , THR A:392
BINDING SITE FOR RESIDUE IOD B 404
05
AC5
SOFTWARE
ASN B:343 , THR B:392
BINDING SITE FOR RESIDUE IOD A 405
06
AC6
SOFTWARE
HIS A:50 , ARG A:373
BINDING SITE FOR RESIDUE IOD A 406
07
AC7
SOFTWARE
HIS B:50 , ARG B:373
BINDING SITE FOR RESIDUE IOD B 405
08
AC8
SOFTWARE
LYS B:65
BINDING SITE FOR RESIDUE IOD B 406
09
AC9
SOFTWARE
ASP A:79
BINDING SITE FOR RESIDUE IOD A 407
10
BC1
SOFTWARE
GLU A:368 , ARG B:218 , ASP B:221 , HOH B:637
BINDING SITE FOR RESIDUE IOD A 408
11
BC2
SOFTWARE
LYS A:141 , HOH A:772
BINDING SITE FOR RESIDUE IOD A 409
12
BC3
SOFTWARE
HIS B:169 , IOD I:28
BINDING SITE FOR RESIDUE IOD B 410
13
BC4
SOFTWARE
ASN A:288
BINDING SITE FOR RESIDUE IOD A 411
14
BC5
SOFTWARE
ARG A:218 , ASP A:221
BINDING SITE FOR RESIDUE IOD B 411
15
BC6
SOFTWARE
VAL B:338
BINDING SITE FOR RESIDUE IOD B 412
16
BC7
SOFTWARE
ARG A:160 , ALA A:175
BINDING SITE FOR RESIDUE IOD A 412
17
BC8
SOFTWARE
GLN B:327
BINDING SITE FOR RESIDUE IOD B 414
18
BC9
SOFTWARE
GLY B:151
BINDING SITE FOR RESIDUE IOD B 415
19
CC1
SOFTWARE
ARG A:264
BINDING SITE FOR RESIDUE IOD A 414
20
CC2
SOFTWARE
ALA A:258
BINDING SITE FOR RESIDUE IOD A 415
21
CC3
SOFTWARE
GLY A:151 , ARG A:160
BINDING SITE FOR RESIDUE IOD A 416
22
CC4
SOFTWARE
ALA B:175
BINDING SITE FOR RESIDUE IOD B 416
23
CC5
SOFTWARE
HIS B:169 , ARG B:239
BINDING SITE FOR RESIDUE IOD I 28
24
CC6
SOFTWARE
ARG A:289 , THR A:291 , LEU A:296 , ARG A:299 , GLN A:300 , GLN A:358 , LEU A:359 , GLY A:361 , GLY A:362 , HOH A:677 , LEU B:145 , ILE B:147 , THR B:148 , GLY B:153 , SER B:154 , TYR B:178 , ILE B:179 , THR B:180 , LYS B:222 , ILE B:383 , THR B:387 , GLU B:389 , HOH B:650 , HOH B:729
BINDING SITE FOR RESIDUE FDA B 500
25
CC7
SOFTWARE
GLN A:276 , ALA A:310 , ARG A:317 , HOH A:759 , LEU B:399
BINDING SITE FOR RESIDUE EDO A 501
26
CC8
SOFTWARE
LEU A:145 , ILE A:147 , THR A:148 , GLY A:152 , GLY A:153 , SER A:154 , TYR A:178 , ILE A:179 , THR A:180 , LYS A:222 , ILE A:380 , ILE A:383 , THR A:387 , GLU A:389 , HOH A:649 , HOH A:655 , HOH A:733 , HOH A:766 , ARG B:289 , THR B:291 , LEU B:296 , ARG B:299 , GLN B:300 , GLN B:358 , LEU B:359 , GLY B:361 , GLY B:362
BINDING SITE FOR RESIDUE FDA A 500
27
CC9
SOFTWARE
HOH A:699 , GLN B:276 , ALA B:310 , ARG B:317 , HOH B:641
BINDING SITE FOR RESIDUE EDO B 501
[
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
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
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
(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
(3, 6)
Info
all PFAM domains
1a: PFAM_Acyl_CoA_dh_1_3oibB01 (B:250-400)
1b: PFAM_Acyl_CoA_dh_1_3oibB02 (B:250-400)
2a: PFAM_Acyl_CoA_dh_M_3oibB03 (B:144-196)
2b: PFAM_Acyl_CoA_dh_M_3oibB04 (B:144-196)
3a: PFAM_Acyl_CoA_dh_N_3oibB05 (B:27-140)
3b: PFAM_Acyl_CoA_dh_N_3oibB06 (B:27-140)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Acyl-CoA_dh
(32)
Family
:
Acyl-CoA_dh_1
(24)
Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
(3)
1a
Acyl-CoA_dh_1-3oibB01
B:250-400
1b
Acyl-CoA_dh_1-3oibB02
B:250-400
Clan
:
no clan defined [family: Acyl-CoA_dh_M]
(24)
Family
:
Acyl-CoA_dh_M
(24)
Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
(3)
2a
Acyl-CoA_dh_M-3oibB03
B:144-196
2b
Acyl-CoA_dh_M-3oibB04
B:144-196
Clan
:
no clan defined [family: Acyl-CoA_dh_N]
(23)
Family
:
Acyl-CoA_dh_N
(23)
Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
(3)
3a
Acyl-CoA_dh_N-3oibB05
B:27-140
3b
Acyl-CoA_dh_N-3oibB06
B:27-140
[
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
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 (273 KB)
Header - Asym.Unit
Biol.Unit 1 (266 KB)
Header - Biol.Unit 1
Biol.Unit 2 (528 KB)
Header - Biol.Unit 2
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
3OIB
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help