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.
5K8F
Asym. Unit
Info
Asym.Unit (657 KB)
Biol.Unit 1 (223 KB)
Biol.Unit 2 (218 KB)
Biol.Unit 3 (219 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 ACETYL-COA SYNTHETASE IN COMPLEX WITH ATP AND ACETYL-AMP FROM CRYPTOCOCCUS NEOFORMANS H99
Authors
:
Seattle Structural Genomics Center For Infectious Disease (S D. Fox Iii, S. L. Delker, K. T. Potts, D. D. Lorimer, T. E. Edwards, M. W. Ssgcid
Date
:
30 May 16 (Deposition) - 13 Jul 16 (Release) - 13 Jul 16 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.45
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Keywords
:
Ssgcid, Nih, Niaid, Synthetase, Acs1, Acetyl-Amp, Atp, Adenosine Triphosphate, Acetyl Adenylate, Structural Genomics, Seattle Structural Genomics Center For Infectious Disease, Ligase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Seattle Structural Genomics Center For Infectious Disease (Ssgcid), Ssgcid, D. Fox Iii, S. L. Delker, K. T. Potts, M. M. Numa, T. E. Edwards, D. D. Lorimer, M. W. Mutz, D. J. Krysan
Crystal Structure Of Acetyl-Coa Synthetase In Complex With Atp And Acetyl-Amp From Cryptococcus Neoformans H99
To Be Published
[
close entry info
]
Hetero Components
(5, 23)
Info
All Hetero Components
1a: [[(2~{R},3~{S},4~{R},5~{R})-5-(6-A... (6R9a)
1b: [[(2~{R},3~{S},4~{R},5~{R})-5-(6-A... (6R9b)
1c: [[(2~{R},3~{S},4~{R},5~{R})-5-(6-A... (6R9c)
2a: ADENOSINE-5'-TRIPHOSPHATE (ATPa)
2b: ADENOSINE-5'-TRIPHOSPHATE (ATPb)
2c: ADENOSINE-5'-TRIPHOSPHATE (ATPc)
3a: 1,2-ETHANEDIOL (EDOa)
3b: 1,2-ETHANEDIOL (EDOb)
3c: 1,2-ETHANEDIOL (EDOc)
3d: 1,2-ETHANEDIOL (EDOd)
3e: 1,2-ETHANEDIOL (EDOe)
3f: 1,2-ETHANEDIOL (EDOf)
3g: 1,2-ETHANEDIOL (EDOg)
3h: 1,2-ETHANEDIOL (EDOh)
3i: 1,2-ETHANEDIOL (EDOi)
4a: MAGNESIUM ION (MGa)
4b: MAGNESIUM ION (MGb)
4c: MAGNESIUM ION (MGc)
4d: MAGNESIUM ION (MGd)
4e: MAGNESIUM ION (MGe)
4f: MAGNESIUM ION (MGf)
4g: MAGNESIUM ION (MGg)
5a: PHOSPHATE ION (PO4a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
6R9
3
Ligand/Ion
[[(2~{R},3~{S},4~{R},5~{R})-5-(6-AMINOPURIN-9-YL)-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL]ETHANOATE
2
ATP
3
Ligand/Ion
ADENOSINE-5'-TRIPHOSPHATE
3
EDO
9
Ligand/Ion
1,2-ETHANEDIOL
4
MG
7
Ligand/Ion
MAGNESIUM ION
5
PO4
1
Ligand/Ion
PHOSPHATE ION
[
close Hetero Component info
]
Sites
(23, 23)
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: AD1 (SOFTWARE)
11: AD2 (SOFTWARE)
12: AD3 (SOFTWARE)
13: AD4 (SOFTWARE)
14: AD5 (SOFTWARE)
15: AD6 (SOFTWARE)
16: AD7 (SOFTWARE)
17: AD8 (SOFTWARE)
18: AD9 (SOFTWARE)
19: AE1 (SOFTWARE)
20: AE2 (SOFTWARE)
21: AE3 (SOFTWARE)
22: AE4 (SOFTWARE)
23: AE5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU A:442 , MG A:702 , ATP A:703 , 6R9 A:704 , HOH A:802
binding site for residue MG A 701
02
AC2
SOFTWARE
ARG A:542 , MG A:701 , ATP A:703 , HOH A:802
binding site for residue MG A 702
03
AC3
SOFTWARE
THR A:289 , SER A:290 , SER A:292 , THR A:293 , LYS A:297 , TRP A:334 , GLY A:412 , GLU A:413 , PRO A:414 , ASP A:436 , THR A:437 , TYR A:438 , TRP A:439 , MET A:440 , THR A:441 , ASP A:527 , ILE A:539 , ARG A:542 , LYS A:640 , MG A:701 , MG A:702 , 6R9 A:704 , EDO A:708 , HOH A:802
binding site for residue ATP A 703
04
AC4
SOFTWARE
TRP A:334 , VAL A:411 , GLY A:412 , GLU A:413 , PRO A:414 , ASP A:436 , THR A:437 , TYR A:438 , TRP A:439 , MET A:440 , THR A:441 , ASP A:527 , ILE A:539 , ARG A:542 , LYS A:640 , MG A:701 , ATP A:703 , EDO A:708
binding site for residue 6R9 A 704
05
AC5
SOFTWARE
ALA A:320 , HIS A:321 , PRO A:322 , ASN A:348
binding site for residue EDO A 705
06
AC6
SOFTWARE
THR A:74 , ARG A:111 , HIS A:112 , ALA A:347 , HOH A:948
binding site for residue EDO A 706
07
AC7
SOFTWARE
ASP A:76 , TRP A:77 , TYR A:78
binding site for residue EDO A 707
08
AC8
SOFTWARE
PRO A:414 , GLY A:541 , ARG A:542 , ASP A:545 , THR A:556 , ARG A:643 , ATP A:703 , 6R9 A:704
binding site for residue EDO A 708
09
AC9
SOFTWARE
MET B:440 , GLU B:442 , MG B:702 , ATP B:703 , 6R9 B:704
binding site for residue MG B 701
10
AD1
SOFTWARE
MG B:701 , ATP B:703
binding site for residue MG B 702
11
AD2
SOFTWARE
THR B:289 , GLY B:291 , SER B:292 , THR B:293 , TRP B:334 , GLY B:412 , GLU B:413 , PRO B:414 , ASP B:436 , THR B:437 , TYR B:438 , TRP B:439 , MET B:440 , THR B:441 , ASP B:527 , ILE B:539 , ARG B:542 , LYS B:640 , MG B:701 , MG B:702 , 6R9 B:704
binding site for residue ATP B 703
12
AD3
SOFTWARE
TRP B:334 , ILE B:335 , GLY B:412 , GLU B:413 , PRO B:414 , ASP B:436 , THR B:437 , TRP B:439 , MET B:440 , THR B:441 , ASP B:527 , ILE B:539 , LYS B:640 , MG B:701 , ATP B:703
binding site for residue 6R9 B 704
13
AD4
SOFTWARE
ASP B:76 , TRP B:77 , TYR B:106
binding site for residue EDO B 705
14
AD5
SOFTWARE
ALA A:86 , GLY A:87 , TYR B:113 , PRO B:117
binding site for residue EDO B 706
15
AD6
SOFTWARE
HIS B:43 , LYS B:315 , TYR B:316
binding site for residue EDO B 707
16
AD7
SOFTWARE
GLU C:442 , MG C:702 , ATP C:703 , 6R9 C:704
binding site for residue MG C 701
17
AD8
SOFTWARE
ARG C:542 , MG C:701 , ATP C:703
binding site for residue MG C 702
18
AD9
SOFTWARE
THR C:289 , SER C:290 , TRP C:334 , GLY C:412 , GLU C:413 , PRO C:414 , ASP C:436 , THR C:437 , TYR C:438 , TRP C:439 , MET C:440 , THR C:441 , ASP C:527 , ILE C:539 , ARG C:542 , LYS C:640 , MG C:701 , MG C:702 , 6R9 C:704
binding site for residue ATP C 703
19
AE1
SOFTWARE
TRP C:334 , ILE C:335 , GLY C:412 , GLU C:413 , PRO C:414 , ASP C:436 , THR C:437 , TYR C:438 , TRP C:439 , MET C:440 , THR C:441 , ASP C:527 , ILE C:539 , ARG C:542 , LYS C:640 , MG C:701 , ATP C:703
binding site for residue 6R9 C 704
20
AE2
SOFTWARE
GLU A:138 , GLU C:90 , HIS C:91 , HOH C:813
binding site for residue MG C 705
21
AE3
SOFTWARE
HIS C:43 , LYS C:315 , TYR C:316
binding site for residue PO4 C 706
22
AE4
SOFTWARE
ASP C:160 , ALA C:161 , CYS C:205 , GLU C:206 , TYR C:505
binding site for residue EDO C 707
23
AE5
SOFTWARE
VAL C:13 , HIS C:14 , LEU C:16 , LYS C:540
binding site for residue EDO C 708
[
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
(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
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 (657 KB)
Header - Asym.Unit
Biol.Unit 1 (223 KB)
Header - Biol.Unit 1
Biol.Unit 2 (218 KB)
Header - Biol.Unit 2
Biol.Unit 3 (219 KB)
Header - Biol.Unit 3
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
5K8F
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
