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.
5UEJ
Asym. Unit
Info
Asym.Unit (295 KB)
Biol.Unit 1 (287 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
1.30 A CRYSTAL STRUCTURE OF DAPE ENZYME FROM NEISSERIA MENINGITIDIS MC58
Authors
:
B. Nocek, A. Joachimiak, W. F. Anderson, Center For Structural Geno Infectious Diseases (Csgid)
Date
:
02 Jan 17 (Deposition) - 01 Feb 17 (Release) - 08 Feb 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.30
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
M20 Peptidase, Zn-Dependent Enzyme, High Resolution, Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
B. Nocek, T. Heath, D. Becker, A. Joachimiak, W. F. Anderson, Center For Structural Genomics Of Infectious Diseases (Csgid)
1. 30 A Crystal Structure Of Dape Enzyme From Neisseria Meningitidis Mc58
To Be Published
[
close entry info
]
Hetero Components
(2, 10)
Info
All Hetero Components
1a: SULFATE ION (SO4a)
1b: SULFATE ION (SO4b)
1c: SULFATE ION (SO4c)
1d: SULFATE ION (SO4d)
1e: SULFATE ION (SO4e)
2a: ZINC ION (ZNa)
2b: ZINC ION (ZNb)
2c: ZINC ION (ZNc)
2d: ZINC ION (ZNd)
2e: ZINC ION (ZNe)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
SO4
5
Ligand/Ion
SULFATE ION
2
ZN
5
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(10, 10)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:68 , ASP A:101 , GLU A:164 , ZN A:402 , HOH A:857
binding site for residue ZN A 401
02
AC2
SOFTWARE
ASP A:101 , GLU A:136 , HIS A:350 , ZN A:401 , HOH A:857
binding site for residue ZN A 402
03
AC3
SOFTWARE
ARG A:179 , GLY A:325 , ASN A:346 , HOH A:539 , HOH A:634 , HOH A:665 , HOH A:748 , TYR B:198
binding site for residue SO4 A 403
04
AC4
SOFTWARE
SER A:182 , ARG A:259 , SER A:291 , HOH A:523 , HOH A:602 , HOH A:673 , HOH A:765
binding site for residue SO4 A 404
05
AC5
SOFTWARE
ASP B:101 , GLU B:136 , HIS B:350 , ZN B:402 , HOH B:863
binding site for residue ZN B 401
06
AC6
SOFTWARE
HIS B:68 , ASP B:101 , GLU B:164 , ZN B:401 , HOH B:863
binding site for residue ZN B 402
07
AC7
SOFTWARE
HIS B:120 , GLU B:223 , HOH B:793 , HOH B:882 , HOH B:965
binding site for residue ZN B 403
08
AC8
SOFTWARE
SER B:182 , ARG B:259 , SER B:291 , HOH B:523 , HOH B:547 , HOH B:561 , HOH B:670 , HOH B:713 , HOH B:743 , HOH B:806
binding site for residue SO4 B 404
09
AC9
SOFTWARE
TYR A:198 , ARG B:179 , GLY B:325 , HOH B:506 , HOH B:544 , HOH B:567 , HOH B:815
binding site for residue SO4 B 405
10
AD1
SOFTWARE
ARG B:374 , HOH B:588
binding site for residue SO4 B 406
[
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
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 (295 KB)
Header - Asym.Unit
Biol.Unit 1 (287 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
5UEJ
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
