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.
1KMK
Asym. Unit
Info
Asym.Unit (79 KB)
Biol.Unit 1 (147 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
E. COLI NIFS/CSDB PROTEIN AT 2.20A WITH THE CYSTEINE PERSELENIDE INTERMEDIATE (RESIDUE CSZ).
Authors
:
C. D. Lima, S. K. Burley, New York Sgx Research Center For Structu Genomics (Nysgxrc)
Date
:
16 Dec 01 (Deposition) - 21 Dec 01 (Release) - 09 Apr 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A
Biol. Unit 1: A (2x)
Keywords
:
Nifs Selenocysteine Cysteine Persulfide Perselenide Xray, Structural Genomics, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Lyase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. D. Lima
Analysis Of The E. Coli Nifs Csdb Protein At 2. 0 A Reveals The Structural Basis For Perselenide And Persulfide Intermediate Formation.
J. Mol. Biol. V. 315 1199 2002
[
close entry info
]
Hetero Components
(3, 3)
Info
All Hetero Components
1a: S-SELANYL CYSTEINE (CSZa)
2a: PYRIDOXAL-5'-PHOSPHATE (PLPa)
3a: SELENOCYSTEINE (SECa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CSZ
1
Mod. Amino Acid
S-SELANYL CYSTEINE
2
PLP
1
Ligand/Ion
PYRIDOXAL-5'-PHOSPHATE
3
SEC
1
Ligand/Ion
SELENOCYSTEINE
[
close Hetero Component info
]
Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ALA A:30 , HIS A:123 , ASN A:175 , GLN A:203 , LYS A:226 , ARG A:359 , ARG A:379 , PLP A:500 , HOH A:601 , HOH A:732
BINDING SITE FOR RESIDUE SEC A 502
2
AC2
SOFTWARE
THR A:94 , THR A:95 , HIS A:123 , ALA A:125 , ASN A:175 , ASP A:200 , ALA A:202 , GLN A:203 , SER A:223 , HIS A:225 , LYS A:226 , GLY A:277 , THR A:278 , SEC A:502 , HOH A:582 , HOH A:601
BINDING SITE FOR RESIDUE PLP A 500
[
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
(1, 1)
Info
All PROSITE Patterns/Profiles
1: AA_TRANSFER_CLASS_5 (A:217-236)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
AA_TRANSFER_CLASS_5
PS00595
Aminotransferases class-V pyridoxal-phosphate attachment site.
SUFS_ECOLI
217-236
1
A:217-236
[
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, 1)
Info
All SCOP Domains
1a: SCOP_d1kmka_ (A:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
PLP-dependent transferase-like
(627)
Superfamily
:
PLP-dependent transferases
(625)
Family
:
Cystathionine synthase-like
(64)
Protein domain
:
NifS-like protein/selenocysteine lyase
(7)
Escherichia coli [TaxId: 562]
(5)
1a
d1kmka_
A:
[
close SCOP info
]
CATH Domains
(2, 2)
Info
all CATH domains
1a: CATH_1kmkA02 (A:38-297)
2a: CATH_1kmkA01 (A:3-37,A:298-401)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Aspartate Aminotransferase; domain 2
(384)
Homologous Superfamily
:
Type I PLP-dependent aspartate aminotransferase-like (Major domain)
(384)
Escherichia coli. Organism_taxid: 562.
(56)
1a
1kmkA02
A:38-297
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Aspartate Aminotransferase, domain 1
(355)
Homologous Superfamily
:
Aspartate Aminotransferase, domain 1
(354)
Escherichia coli. Organism_taxid: 562.
(56)
2a
1kmkA01
A:3-37,A:298-401
[
close CATH info
]
Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_Aminotran_5_1kmkA01 (A:25-394)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
PLP_aminotran
(240)
Family
:
Aminotran_5
(20)
Escherichia coli (strain K12)
(3)
1a
Aminotran_5-1kmkA01
A:25-394
[
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
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 (79 KB)
Header - Asym.Unit
Biol.Unit 1 (147 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
1KMK
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help