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.
4MVJ
Biol. Unit 6
Info
Asym.Unit (1.7 MB)
Biol.Unit 1 (121 KB)
Biol.Unit 10 (122 KB)
Biol.Unit 11 (121 KB)
Biol.Unit 12 (123 KB)
Biol.Unit 13 (120 KB)
Biol.Unit 14 (123 KB)
Biol.Unit 15 (121 KB)
Biol.Unit 16 (123 KB)
Biol.Unit 2 (122 KB)
Biol.Unit 3 (121 KB)
Biol.Unit 4 (123 KB)
Biol.Unit 5 (122 KB)
Biol.Unit 6 (124 KB)
Biol.Unit 7 (121 KB)
Biol.Unit 8 (121 KB)
Biol.Unit 9 (123 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
2.85 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE A (GAPA) FROM ESCHERICHIA COLI MODIFIED BY ACETYL PHOSPHATE.
Authors
:
G. Minasov, M. Kuhn, I. Dubrovska, J. Winsor, L. Shuvalova, S. Grimshaw W. F. Anderson, Center For Structural Genomics Of Infectious D (Csgid)
Date
:
24 Sep 13 (Deposition) - 23 Apr 14 (Release) - 07 May 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.85
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P
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)
Biol. Unit 9: I (1x)
Biol. Unit 10: J (1x)
Biol. Unit 11: K (1x)
Biol. Unit 12: L (1x)
Biol. Unit 13: M (1x)
Biol. Unit 14: N (1x)
Biol. Unit 15: O (1x)
Biol. Unit 16: P (1x)
Keywords
:
Structural Genomics, Niaid, National Institute Of Allergy And Infectious Diseases, Center For Structural Genomics Of Infectious Diseases, Csgid, N-Terminal Nad Binding Domain, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. L. Kuhn, B. Zemaitaitis, L. I. Hu, A. Sahu, D. Sorensen, G. Minasov, B. P. Lima, M. Scholle, M. Mrksich, W. F. Anderson, B. W. Gibson, B. Schilling, A. J. Wolfe
Structural, Kinetic And Proteomic Characterization Of Acety Phosphate-Dependent Bacterial Protein Acetylation.
Plos One V. 9 94816 2014
[
close entry info
]
Hetero Components
(3, 4)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
2a: N(6)-ACETYLLYSINE (ALYa)
2b: N(6)-ACETYLLYSINE (ALYb)
2c: N(6)-ACETYLLYSINE (ALYc)
2d: N(6)-ACETYLLYSINE (ALYd)
2e: N(6)-ACETYLLYSINE (ALYe)
2f: N(6)-ACETYLLYSINE (ALYf)
2g: N(6)-ACETYLLYSINE (ALYg)
2h: N(6)-ACETYLLYSINE (ALYh)
2i: N(6)-ACETYLLYSINE (ALYi)
2j: N(6)-ACETYLLYSINE (ALYj)
2k: N(6)-ACETYLLYSINE (ALYk)
2l: N(6)-ACETYLLYSINE (ALYl)
2m: N(6)-ACETYLLYSINE (ALYm)
2n: N(6)-ACETYLLYSINE (ALYn)
2o: N(6)-ACETYLLYSINE (ALYo)
2p: N(6)-ACETYLLYSINE (ALYp)
2q: N(6)-ACETYLLYSINE (ALYq)
2r: N(6)-ACETYLLYSINE (ALYr)
2s: N(6)-ACETYLLYSINE (ALYs)
2t: N(6)-ACETYLLYSINE (ALYt)
2u: N(6)-ACETYLLYSINE (ALYu)
2v: N(6)-ACETYLLYSINE (ALYv)
3a: CHLORIDE ION (CLa)
3aa: CHLORIDE ION (CLaa)
3ab: CHLORIDE ION (CLab)
3ac: CHLORIDE ION (CLac)
3ad: CHLORIDE ION (CLad)
3ae: CHLORIDE ION (CLae)
3af: CHLORIDE ION (CLaf)
3ag: CHLORIDE ION (CLag)
3ah: CHLORIDE ION (CLah)
3ai: CHLORIDE ION (CLai)
3aj: CHLORIDE ION (CLaj)
3ak: CHLORIDE ION (CLak)
3al: CHLORIDE ION (CLal)
3am: CHLORIDE ION (CLam)
3an: CHLORIDE ION (CLan)
3ao: CHLORIDE ION (CLao)
3ap: CHLORIDE ION (CLap)
3aq: CHLORIDE ION (CLaq)
3ar: CHLORIDE ION (CLar)
3as: CHLORIDE ION (CLas)
3at: CHLORIDE ION (CLat)
3au: CHLORIDE ION (CLau)
3av: CHLORIDE ION (CLav)
3aw: CHLORIDE ION (CLaw)
3b: CHLORIDE ION (CLb)
3c: CHLORIDE ION (CLc)
3d: CHLORIDE ION (CLd)
3e: CHLORIDE ION (CLe)
3f: CHLORIDE ION (CLf)
3g: CHLORIDE ION (CLg)
3h: CHLORIDE ION (CLh)
3i: CHLORIDE ION (CLi)
3j: CHLORIDE ION (CLj)
3k: CHLORIDE ION (CLk)
3l: CHLORIDE ION (CLl)
3m: CHLORIDE ION (CLm)
3n: CHLORIDE ION (CLn)
3o: CHLORIDE ION (CLo)
3p: CHLORIDE ION (CLp)
3q: CHLORIDE ION (CLq)
3r: CHLORIDE ION (CLr)
3s: CHLORIDE ION (CLs)
3t: CHLORIDE ION (CLt)
3u: CHLORIDE ION (CLu)
3v: CHLORIDE ION (CLv)
3w: CHLORIDE ION (CLw)
3x: CHLORIDE ION (CLx)
3y: CHLORIDE ION (CLy)
3z: CHLORIDE ION (CLz)
5a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
5b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
5c: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADc)
5d: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADd)
5e: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADe)
5f: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADf)
5g: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADg)
4a: SODIUM ION (NAa)
4b: SODIUM ION (NAb)
4c: SODIUM ION (NAc)
4d: SODIUM ION (NAd)
5e: SODIUM ION (NAe)
5f: SODIUM ION (NAf)
5g: SODIUM ION (NAg)
5h: SODIUM ION (NAh)
5i: SODIUM ION (NAi)
5j: SODIUM ION (NAj)
5k: SODIUM ION (NAk)
5l: SODIUM ION (NAl)
6a: DI(HYDROXYETHYL)ETHER (PEGa)
7a: TETRAETHYLENE GLYCOL (PG4a)
8a: TRIETHYLENE GLYCOL (PGEa)
9a: PHOSPHATE ION (PO4a)
9b: PHOSPHATE ION (PO4b)
9c: PHOSPHATE ION (PO4c)
9d: PHOSPHATE ION (PO4d)
9e: PHOSPHATE ION (PO4e)
9f: PHOSPHATE ION (PO4f)
9g: PHOSPHATE ION (PO4g)
9h: PHOSPHATE ION (PO4h)
9i: PHOSPHATE ION (PO4i)
9j: PHOSPHATE ION (PO4j)
9k: PHOSPHATE ION (PO4k)
9l: PHOSPHATE ION (PO4l)
9m: PHOSPHATE ION (PO4m)
9n: PHOSPHATE ION (PO4n)
9o: PHOSPHATE ION (PO4o)
10a: PYROPHOSPHATE 2- (POPa)
10b: PYROPHOSPHATE 2- (POPb)
10c: PYROPHOSPHATE 2- (POPc)
10d: PYROPHOSPHATE 2- (POPd)
10e: PYROPHOSPHATE 2- (POPe)
10f: PYROPHOSPHATE 2- (POPf)
11a: S-ACETYL-CYSTEINE (SCYa)
11b: S-ACETYL-CYSTEINE (SCYb)
11c: S-ACETYL-CYSTEINE (SCYc)
12a: ACETYLPHOSPHATE (UVWa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
-1
Ligand/Ion
ACETATE ION
2
ALY
2
Mod. Amino Acid
N(6)-ACETYLLYSINE
3
CL
-1
Ligand/Ion
CHLORIDE ION
4
NA
-1
Ligand/Ion
SODIUM ION
5
NAD
-1
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
6
PEG
-1
Ligand/Ion
DI(HYDROXYETHYL)ETHER
7
PG4
-1
Ligand/Ion
TETRAETHYLENE GLYCOL
8
PGE
-1
Ligand/Ion
TRIETHYLENE GLYCOL
9
PO4
1
Ligand/Ion
PHOSPHATE ION
10
POP
1
Ligand/Ion
PYROPHOSPHATE 2-
11
SCY
-1
Mod. Amino Acid
S-ACETYL-CYSTEINE
12
UVW
-1
Ligand/Ion
ACETYLPHOSPHATE
[
close Hetero Component info
]
Sites
(4, 4)
Info
All Sites
1: EC7 (SOFTWARE)
2: EC8 (SOFTWARE)
3: EC9 (SOFTWARE)
4: FC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
EC7
SOFTWARE
GLY F:133 , PHE F:136
BINDING SITE FOR RESIDUE CL F 401
2
EC8
SOFTWARE
TRP F:194 , ASP H:278
BINDING SITE FOR RESIDUE PO4 F 402
3
EC9
SOFTWARE
GLY F:11 , ARG F:12 , ILE F:13 , ALA F:181 , HOH F:507
BINDING SITE FOR RESIDUE POP F 403
4
FC9
SOFTWARE
ASP F:278 , TRP H:194
BINDING SITE FOR RESIDUE PO4 H 403
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(, 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.
(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
(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 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 (1.7 MB)
Header - Asym.Unit
Biol.Unit 1 (121 KB)
Header - Biol.Unit 1
Biol.Unit 10 (122 KB)
Header - Biol.Unit 10
Biol.Unit 11 (121 KB)
Header - Biol.Unit 11
Biol.Unit 12 (123 KB)
Header - Biol.Unit 12
Biol.Unit 13 (120 KB)
Header - Biol.Unit 13
Biol.Unit 14 (123 KB)
Header - Biol.Unit 14
Biol.Unit 15 (121 KB)
Header - Biol.Unit 15
Biol.Unit 16 (123 KB)
Header - Biol.Unit 16
Biol.Unit 2 (122 KB)
Header - Biol.Unit 2
Biol.Unit 3 (121 KB)
Header - Biol.Unit 3
Biol.Unit 4 (123 KB)
Header - Biol.Unit 4
Biol.Unit 5 (122 KB)
Header - Biol.Unit 5
Biol.Unit 6 (124 KB)
Header - Biol.Unit 6
Biol.Unit 7 (121 KB)
Header - Biol.Unit 7
Biol.Unit 8 (121 KB)
Header - Biol.Unit 8
Biol.Unit 9 (123 KB)
Header - Biol.Unit 9
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
4MVJ
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
