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.
4GIS
Biol. Unit 1
Info
Asym.Unit (160 KB)
Biol.Unit 1 (599 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 AN ENOLASE FAMILY MEMBER FROM VIBRIO HARVEYI (EFI-TARGET 501692) WITH HOMOLOGY TO MANNONATE DEHYDRATASE, WITH MG, GLYCEROL AND DICARBOXYLATES BOUND (MIXED LOOPS, SPACE GROUP I4122)
Authors
:
M. W. Vetting, R. Toro, R. Bhosle, N. F. Al Obaidi, L. L. Morisco, S. R. Wa S. Sojitra, E. Washington, A. Scott Glenn, S. Chowdhury, B. Evans, J. B. Hillerich, J. Love, R. D. Seidel, H. J. Imker, J. A. Gerlt, S. C. Almo, Function Initiative (Efi)
Date
:
08 Aug 12 (Deposition) - 29 Aug 12 (Release) - 29 Apr 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (4x)
Keywords
:
Enolase, Putative Mannonate Dehydratase, Enzyme Function Initiative, Efi, Structural Genomics, Lyase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. W. Vetting, R. Toro, R. Bhosle, N. F. Al Obaidi, L. L. Morisco, S. R. Wasserman, S. Sojitra, E. Washington, A. Scott Glenn, S. Chowdhury, B. Evans, J. Hammonds, B. Hillerich, J. Love, R. D. Seidel, H. J. Imker, J. A. Gerlt, S. C. Almo, Enzyme Function Initiative (Efi)
Crystal Structure Of An Enolase Family Member From Vibrio Harveyi (Efi-Target 501692) With Homology To Mannonate Dehydratase, With Mg, Glycerol And Dicarboxylates Bound (Mixed Loops, Space Group I4122)
To Be Published
[
close entry info
]
Hetero Components
(3, 20)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
1c: CHLORIDE ION (CLc)
1d: CHLORIDE ION (CLd)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
3a: MALEIC ACID (MAEa)
4a: MAGNESIUM ION (MGa)
4b: MAGNESIUM ION (MGb)
5a: MALONIC ACID (MLAa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
-1
Ligand/Ion
CHLORIDE ION
2
GOL
12
Ligand/Ion
GLYCEROL
3
MAE
4
Ligand/Ion
MALEIC ACID
4
MG
-1
Ligand/Ion
MAGNESIUM ION
5
MLA
4
Ligand/Ion
MALONIC ACID
[
close Hetero Component info
]
Sites
(11, 11)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:382 , PRO A:383 , HIS A:384 , GLU A:385 , HOH A:608 , HOH A:700
BINDING SITE FOR RESIDUE CL A 401
02
AC2
SOFTWARE
ARG A:193 , LYS A:198 , PHE A:200 , HIS A:201 , HOH A:883
BINDING SITE FOR RESIDUE GOL A 402
03
AC3
SOFTWARE
ARG A:18 , HIS A:19 , GLN A:41 , ARG A:382 , HIS A:384 , TRP A:386
BINDING SITE FOR RESIDUE MLA A 403
04
AC4
SOFTWARE
GLN A:41 , GLN A:42 , HIS A:207 , GLU A:257 , HIS A:307 , PRO A:309 , ASP A:311 , HOH A:876 , TYR B:79 , TRP B:80
BINDING SITE FOR RESIDUE GOL A 404
05
AC5
SOFTWARE
ASP A:205 , GLU A:231 , GLU A:257 , HOH A:501 , HOH A:502 , HOH A:894
BINDING SITE FOR RESIDUE MG A 405
06
AC6
SOFTWARE
THR A:166
BINDING SITE FOR RESIDUE CL A 406
07
AC7
SOFTWARE
ASN A:82 , GLY A:83 , PRO A:84 , VAL A:85 , ILE A:86 , ASN B:82 , GLY B:83 , PRO B:84 , VAL B:85 , ILE B:86
BINDING SITE FOR RESIDUE CL A 407
08
AC8
SOFTWARE
ARG B:382 , PRO B:383 , HIS B:384 , GLU B:385 , MAE B:404 , HOH B:603
BINDING SITE FOR RESIDUE CL B 401
09
AC9
SOFTWARE
TYR A:79 , TRP A:80 , GLN B:41 , GLN B:42 , HIS B:207 , GLU B:257 , HIS B:307 , PRO B:309 , ASP B:311 , HOH B:831
BINDING SITE FOR RESIDUE GOL B 402
10
BC1
SOFTWARE
ASP B:205 , GLU B:231 , GLU B:257 , HOH B:501 , HOH B:608 , HOH B:890
BINDING SITE FOR RESIDUE MG B 403
11
BC2
SOFTWARE
ARG B:18 , HIS B:19 , GLN B:41 , ARG B:382 , HIS B:384 , TRP B:386 , CL B:401 , HOH B:513
BINDING SITE FOR RESIDUE MAE B 404
[
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 A
Chain B
Asymmetric Unit 1
Asymmetric Unit 2
Asymmetric Unit 3
Asymmetric Unit 4
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 (160 KB)
Header - Asym.Unit
Biol.Unit 1 (599 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
4GIS
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
