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.
1KBW
Biol. Unit 2
Info
Asym.Unit (306 KB)
Biol.Unit 1 (152 KB)
Biol.Unit 2 (152 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 THE SOLUBLE DOMAIN OF ANIA FROM NEISSERIA GONORRHOEAE
Authors
:
M. J. Boulanger, M. E. P. Murphy
Date
:
06 Nov 01 (Deposition) - 05 Dec 01 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C (1x)
Biol. Unit 2: D,E,F (1x)
Keywords
:
Ania, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. J. Boulanger, M. E. Murphy
Crystal Structure Of The Soluble Domain Of The Major Anaerobically Induced Outer Membrane Protein (Ania) From Pathogenic Neisseria: A New Class Of Copper-Containing Nitrite Reductases.
J. Mol. Biol. V. 315 1111 2002
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(0, 0)
Info
All Hetero Components
1a: COPPER (II) ION (CUa)
1b: COPPER (II) ION (CUb)
1c: COPPER (II) ION (CUc)
1d: COPPER (II) ION (CUd)
1e: COPPER (II) ION (CUe)
1f: COPPER (II) ION (CUf)
1g: COPPER (II) ION (CUg)
1h: COPPER (II) ION (CUh)
1i: COPPER (II) ION (CUi)
1j: COPPER (II) ION (CUj)
1k: COPPER (II) ION (CUk)
1l: COPPER (II) ION (CUl)
View:
Select:
Label:
Sorry, no Info available
[
close Hetero component info
]
Sites
(6, 6)
Info
All Sites
1: AC7 (SOFTWARE)
2: AC8 (SOFTWARE)
3: AC9 (SOFTWARE)
4: BC1 (SOFTWARE)
5: BC2 (SOFTWARE)
6: BC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC7
SOFTWARE
HIS D:94 , CYS D:135 , HIS D:143 , MET D:148
BINDING SITE FOR RESIDUE CU D 501
2
AC8
SOFTWARE
ASP D:97 , HIS D:99 , HIS D:134 , HOH D:710 , HIS E:240 , HIS E:289
BINDING SITE FOR RESIDUE CU D 502
3
AC9
SOFTWARE
HIS E:94 , CYS E:135 , HIS E:143 , MET E:148
BINDING SITE FOR RESIDUE CU E 501
4
BC1
SOFTWARE
HIS E:99 , HIS E:134 , HOH E:693 , HIS F:289
BINDING SITE FOR RESIDUE CU E 502
5
BC2
SOFTWARE
HIS F:94 , CYS F:135 , HIS F:143 , MET F:148
BINDING SITE FOR RESIDUE CU F 501
6
BC3
SOFTWARE
HIS D:240 , HIS D:289 , HIS F:99 , HIS F:134 , HOH F:657 , HOH F:658
BINDING SITE FOR RESIDUE CU F 502
[
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
(1, 12)
Info
All SCOP Domains
1a: SCOP_d1kbwa1 (A:13-163)
1b: SCOP_d1kbwa2 (A:164-314)
1c: SCOP_d1kbwb1 (B:13-163)
1d: SCOP_d1kbwb2 (B:164-314)
1e: SCOP_d1kbwc1 (C:13-163)
1f: SCOP_d1kbwc2 (C:164-314)
1g: SCOP_d1kbwd1 (D:13-163)
1h: SCOP_d1kbwd2 (D:164-314)
1i: SCOP_d1kbwe1 (E:13-163)
1j: SCOP_d1kbwe2 (E:164-314)
1k: SCOP_d1kbwf1 (F:13-163)
1l: SCOP_d1kbwf2 (F:164-314)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Cupredoxin-like
(545)
Superfamily
:
Cupredoxins
(543)
Family
:
Multidomain cupredoxins
(146)
Protein domain
:
Nitrite reductase, NIR
(79)
Neisseria gonorrhoeae, AniA [TaxId: 485]
(2)
1a
d1kbwa1
A:13-163
1b
d1kbwa2
A:164-314
1c
d1kbwb1
B:13-163
1d
d1kbwb2
B:164-314
1e
d1kbwc1
C:13-163
1f
d1kbwc2
C:164-314
1g
d1kbwd1
D:13-163
1h
d1kbwd2
D:164-314
1i
d1kbwe1
E:13-163
1j
d1kbwe2
E:164-314
1k
d1kbwf1
F:13-163
1l
d1kbwf2
F:164-314
[
close SCOP info
]
CATH Domains
(1, 12)
Info
all CATH domains
1a: CATH_1kbwA01 (A:13-156)
1b: CATH_1kbwE01 (E:13-156)
1c: CATH_1kbwF01 (F:13-156)
1d: CATH_1kbwA02 (A:161-314)
1e: CATH_1kbwB02 (B:161-314)
1f: CATH_1kbwC02 (C:161-314)
1g: CATH_1kbwD02 (D:161-314)
1h: CATH_1kbwE02 (E:161-314)
1i: CATH_1kbwF02 (F:161-314)
1j: CATH_1kbwB01 (B:13-156)
1k: CATH_1kbwC01 (C:13-156)
1l: CATH_1kbwD01 (D:13-156)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Cupredoxins - blue copper proteins
(420)
Neisseria gonorrhoeae. Organism_taxid: 485.
(2)
1a
1kbwA01
A:13-156
1b
1kbwE01
E:13-156
1c
1kbwF01
F:13-156
1d
1kbwA02
A:161-314
1e
1kbwB02
B:161-314
1f
1kbwC02
C:161-314
1g
1kbwD02
D:161-314
1h
1kbwE02
E:161-314
1i
1kbwF02
F:161-314
1j
1kbwB01
B:13-156
1k
1kbwC01
C:13-156
1l
1kbwD01
D:13-156
[
close CATH info
]
Pfam Domains
(1, 6)
Info
all PFAM domains
1a: PFAM_Cu_oxidase_3_1kbwF01 (F:44-159)
1b: PFAM_Cu_oxidase_3_1kbwF02 (F:44-159)
1c: PFAM_Cu_oxidase_3_1kbwF03 (F:44-159)
1d: PFAM_Cu_oxidase_3_1kbwF04 (F:44-159)
1e: PFAM_Cu_oxidase_3_1kbwF05 (F:44-159)
1f: PFAM_Cu_oxidase_3_1kbwF06 (F:44-159)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
CU_oxidase
(192)
Family
:
Cu-oxidase_3
(79)
Neisseria gonorrhoeae
(2)
1a
Cu-oxidase_3-1kbwF01
F:44-159
1b
Cu-oxidase_3-1kbwF02
F:44-159
1c
Cu-oxidase_3-1kbwF03
F:44-159
1d
Cu-oxidase_3-1kbwF04
F:44-159
1e
Cu-oxidase_3-1kbwF05
F:44-159
1f
Cu-oxidase_3-1kbwF06
F:44-159
[
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 D
Chain E
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 (306 KB)
Header - Asym.Unit
Biol.Unit 1 (152 KB)
Header - Biol.Unit 1
Biol.Unit 2 (152 KB)
Header - Biol.Unit 2
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
1KBW
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
