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.
3OYT
Asym. Unit
Info
Asym.Unit (266 KB)
Biol.Unit 1 (257 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
1.84 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF 3-OXOACYL-(ACYL CARRIER PROTEIN) SYNTHASE I (FABB) FROM YERSINIA PESTIS CO92
Authors
:
A. S. Halavaty, Z. Wawrzak, O. Onopriyenko, S. Peterson, A. Savchenko, W. F. Anderson, Center For Structural Genomics Of Infectious D (Csgid)
Date
:
23 Sep 10 (Deposition) - 12 Jan 11 (Release) - 12 Jan 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.84
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Condensation Reaction, Fatty Acid Synthase, Beta-Ketoacyl-Acp Synthase, Fatty Acid And Phospholipid Metabolism, 3-Oxoacyl-(Acyl Carrier Protein) Synthase I, Transferase, Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. S. Halavaty, Z. Wawrzak, O. Onopriyenko, S. Peterson, A. Savchenko W. F. Anderson
1. 84 Angstrom Resolution Crystal Structure Of 3-Oxoacyl-(Acyl Carrier Protein) Synthase I (Fabb) From Yersinia Pestis Co92
To Be Published
[
close entry info
]
Hetero Components
(7, 59)
Info
All Hetero Components
1a: 1,2-ETHANEDIOL (EDOa)
1b: 1,2-ETHANEDIOL (EDOb)
1c: 1,2-ETHANEDIOL (EDOc)
1d: 1,2-ETHANEDIOL (EDOd)
2a: POTASSIUM ION (Ka)
2b: POTASSIUM ION (Kb)
3a: SELENOMETHIONINE (MSEa)
3aa: SELENOMETHIONINE (MSEaa)
3ab: SELENOMETHIONINE (MSEab)
3ac: SELENOMETHIONINE (MSEac)
3ad: SELENOMETHIONINE (MSEad)
3ae: SELENOMETHIONINE (MSEae)
3af: SELENOMETHIONINE (MSEaf)
3ag: SELENOMETHIONINE (MSEag)
3ah: SELENOMETHIONINE (MSEah)
3ai: SELENOMETHIONINE (MSEai)
3aj: SELENOMETHIONINE (MSEaj)
3ak: SELENOMETHIONINE (MSEak)
3al: SELENOMETHIONINE (MSEal)
3am: SELENOMETHIONINE (MSEam)
3b: SELENOMETHIONINE (MSEb)
3c: SELENOMETHIONINE (MSEc)
3d: SELENOMETHIONINE (MSEd)
3e: SELENOMETHIONINE (MSEe)
3f: SELENOMETHIONINE (MSEf)
3g: SELENOMETHIONINE (MSEg)
3h: SELENOMETHIONINE (MSEh)
3i: SELENOMETHIONINE (MSEi)
3j: SELENOMETHIONINE (MSEj)
3k: SELENOMETHIONINE (MSEk)
3l: SELENOMETHIONINE (MSEl)
3m: SELENOMETHIONINE (MSEm)
3n: SELENOMETHIONINE (MSEn)
3o: SELENOMETHIONINE (MSEo)
3p: SELENOMETHIONINE (MSEp)
3q: SELENOMETHIONINE (MSEq)
3r: SELENOMETHIONINE (MSEr)
3s: SELENOMETHIONINE (MSEs)
3t: SELENOMETHIONINE (MSEt)
3u: SELENOMETHIONINE (MSEu)
3v: SELENOMETHIONINE (MSEv)
3w: SELENOMETHIONINE (MSEw)
3x: SELENOMETHIONINE (MSEx)
3y: SELENOMETHIONINE (MSEy)
3z: SELENOMETHIONINE (MSEz)
4a: DI(HYDROXYETHYL)ETHER (PEGa)
4b: DI(HYDROXYETHYL)ETHER (PEGb)
4c: DI(HYDROXYETHYL)ETHER (PEGc)
4d: DI(HYDROXYETHYL)ETHER (PEGd)
4e: DI(HYDROXYETHYL)ETHER (PEGe)
4f: DI(HYDROXYETHYL)ETHER (PEGf)
4g: DI(HYDROXYETHYL)ETHER (PEGg)
4h: DI(HYDROXYETHYL)ETHER (PEGh)
5a: TETRAETHYLENE GLYCOL (PG4a)
5b: TETRAETHYLENE GLYCOL (PG4b)
6a: TRIETHYLENE GLYCOL (PGEa)
7a: PHOSPHATE ION (PO4a)
7b: PHOSPHATE ION (PO4b)
7c: PHOSPHATE ION (PO4c)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EDO
4
Ligand/Ion
1,2-ETHANEDIOL
2
K
2
Ligand/Ion
POTASSIUM ION
3
MSE
39
Mod. Amino Acid
SELENOMETHIONINE
4
PEG
8
Ligand/Ion
DI(HYDROXYETHYL)ETHER
5
PG4
2
Ligand/Ion
TETRAETHYLENE GLYCOL
6
PGE
1
Ligand/Ion
TRIETHYLENE GLYCOL
7
PO4
3
Ligand/Ion
PHOSPHATE ION
[
close Hetero Component info
]
Sites
(19, 19)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:297 , VAL A:298 , GLU A:343 , SER A:388 , ASN A:389
BINDING SITE FOR RESIDUE K A 408
02
AC2
SOFTWARE
PHE A:35 , LYS A:40 , HIS A:47 , ASN A:213 , ASP A:214 , HOH A:715
BINDING SITE FOR RESIDUE PO4 A 409
03
AC3
SOFTWARE
LYS A:59 , ILE A:62 , ASP A:63
BINDING SITE FOR RESIDUE EDO A 410
04
AC4
SOFTWARE
ARG A:45 , GLY A:206 , LYS B:128
BINDING SITE FOR RESIDUE PEG A 411
05
AC5
SOFTWARE
LYS A:65 , LYS A:211 , TYR A:212 , ASP A:226
BINDING SITE FOR RESIDUE PEG A 412
06
AC6
SOFTWARE
ALA A:42 , TRP A:196 , HOH A:600 , MSE B:121
BINDING SITE FOR RESIDUE PEG A 413
07
AC7
SOFTWARE
THR A:378 , GLN A:380
BINDING SITE FOR RESIDUE PEG A 414
08
AC8
SOFTWARE
ALA A:287 , GLY A:288 , VAL A:289 , ARG A:315 , HOH A:594 , HOH A:597
BINDING SITE FOR RESIDUE PEG A 415
09
AC9
SOFTWARE
ASP A:363 , ASN A:364 , LEU A:365 , HOH A:566
BINDING SITE FOR RESIDUE PEG A 416
10
BC1
SOFTWARE
ASN B:297 , VAL B:298 , GLU B:343 , SER B:388 , ASN B:389
BINDING SITE FOR RESIDUE K B 408
11
BC2
SOFTWARE
HIS A:253 , LYS A:407 , HOH A:657 , HIS B:253 , HOH B:595
BINDING SITE FOR RESIDUE PO4 B 409
12
BC3
SOFTWARE
PHE B:35 , LYS B:40 , HIS B:47 , ASN B:213 , ASP B:214 , HOH B:455 , HOH B:570
BINDING SITE FOR RESIDUE PO4 B 410
13
BC4
SOFTWARE
GLU A:28 , ASP B:63 , PEG B:414
BINDING SITE FOR RESIDUE EDO B 412
14
BC5
SOFTWARE
ASP B:294 , HOH B:584 , HOH B:648
BINDING SITE FOR RESIDUE EDO B 413
15
BC6
SOFTWARE
ASP B:63 , TYR B:78 , PRO B:150 , PHE B:151 , EDO B:412 , HOH B:612
BINDING SITE FOR RESIDUE PEG B 414
16
BC7
SOFTWARE
LYS B:65 , LYS B:211 , ASP B:226 , ARG B:227 , ASP B:228
BINDING SITE FOR RESIDUE PEG B 415
17
BC8
SOFTWARE
ASP B:41 , ALA B:249 , ARG B:250 , PG4 B:417 , HOH B:589 , HOH B:606
BINDING SITE FOR RESIDUE PGE B 416
18
BC9
SOFTWARE
ARG A:122 , ASP B:41 , GLU B:245 , LEU B:248 , PGE B:416 , HOH B:509 , HOH B:510 , HOH B:515 , HOH B:657 , HOH B:663
BINDING SITE FOR RESIDUE PG4 B 417
19
CC1
SOFTWARE
LEU A:127 , LYS A:128 , ARG B:45 , ALA B:204 , GLY B:206 , THR B:210
BINDING SITE FOR RESIDUE PG4 B 418
[
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
(1, 4)
Info
All SCOP Domains
1a: SCOP_d3oyta1 (A:1-252)
1b: SCOP_d3oyta2 (A:253-407)
1c: SCOP_d3oytb1 (B:1-252)
1d: SCOP_d3oytb2 (B:253-406)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Thiolase-like
(231)
Superfamily
:
Thiolase-like
(231)
Family
:
automated matches
(108)
Protein domain
:
automated matches
(108)
Yersinia pestis [TaxId: 632]
(1)
1a
d3oyta1
A:1-252
1b
d3oyta2
A:253-407
1c
d3oytb1
B:1-252
1d
d3oytb2
B:253-406
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_Ketoacyl_synt_C_3oytB01 (B:255-363)
1b: PFAM_Ketoacyl_synt_C_3oytB02 (B:255-363)
2a: PFAM_ketoacyl_synt_3oytB03 (B:1-247)
2b: PFAM_ketoacyl_synt_3oytB04 (B:1-247)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Thiolase
(72)
Family
:
Ketoacyl-synt_C
(19)
Yersinia pestis
(1)
1a
Ketoacyl-synt_C-3oytB01
B:255-363
1b
Ketoacyl-synt_C-3oytB02
B:255-363
Family
:
ketoacyl-synt
(19)
Yersinia pestis
(1)
2a
ketoacyl-synt-3oytB03
B:1-247
2b
ketoacyl-synt-3oytB04
B:1-247
[
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 (266 KB)
Header - Asym.Unit
Biol.Unit 1 (257 KB)
Header - Biol.Unit 1
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
3OYT
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help