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.
1KRH
Biol. Unit 2
Info
Asym.Unit (120 KB)
Biol.Unit 1 (62 KB)
Biol.Unit 2 (58 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
X-RAY STRUCTURE OF BENZOATE DIOXYGENASE REDUCTASE
Authors
:
A. Karlsson, Z. M. Beharry, D. M. Eby, E. D. Coulter, E. L. Niedle, D. M. Ku H. Eklund, S. Ramaswamy
Date
:
09 Jan 02 (Deposition) - 15 May 02 (Release) - 01 Feb 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.50
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Alpha-Beta, Fad-Binding, Ferredoxin, Nadh-Binding, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Karlsson, Z. M. Beharry, D. Matthew Eby, E. D. Coulter, E. L. Neidle D. M. Kurtz Jr. , H. Eklund, S. Ramaswamy
X-Ray Crystal Structure Of Benzoate 1, 2-Dioxygenase Reductase From Acinetobacter Sp. Strain Adp1.
J. Mol. Biol. V. 318 261 2002
[
close entry info
]
Hetero Components
(3, 4)
Info
All Hetero Components
1a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
1b: FLAVIN-ADENINE DINUCLEOTIDE (FADb)
2a: FE2/S2 (INORGANIC) CLUSTER (FESa)
2b: FE2/S2 (INORGANIC) CLUSTER (FESb)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
3d: SULFATE ION (SO4d)
3e: SULFATE ION (SO4e)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FAD
1
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
2
FES
1
Ligand/Ion
FE2/S2 (INORGANIC) CLUSTER
3
SO4
2
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(7, 7)
Info
All Sites
1: AC2 (SOFTWARE)
2: AC3 (SOFTWARE)
3: AC4 (SOFTWARE)
4: AC5 (SOFTWARE)
5: AC7 (SOFTWARE)
6: AC8 (SOFTWARE)
7: AC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC2
SOFTWARE
ARG A:32 , HOH A:655 , HOH A:722 , HOH A:723 , HOH A:725 , ARG B:174 , GLY B:219 , THR B:248 , HOH B:617
BINDING SITE FOR RESIDUE SO4 A 401
2
AC3
SOFTWARE
ARG A:174 , GLY A:219 , THR A:248 , ASP A:252 , HOH A:635 , HOH A:637 , HOH A:721 , HOH A:724 , HOH A:727 , ARG B:32
BINDING SITE FOR RESIDUE SO4 A 402
3
AC4
SOFTWARE
ARG A:284 , THR B:153 , HOH B:602 , HOH B:603
BINDING SITE FOR RESIDUE SO4 B 403
4
AC5
SOFTWARE
LYS B:210 , ARG B:211 , ASN B:329
BINDING SITE FOR RESIDUE SO4 B 404
5
AC7
SOFTWARE
TYR A:144 , ARG A:156 , SER A:157 , TYR A:158 , SER A:159 , VAL A:172 , VAL A:173 , ARG A:174 , GLY A:179 , LYS A:180 , MET A:181 , SER A:182 , THR A:220 , GLU A:333 , PHE A:335 , SER A:336 , ALA A:337 , ASN A:338 , HOH A:528 , HOH A:638 , HOH A:639 , HOH A:719 , HOH A:726 , ARG B:16 , GLN B:34
BINDING SITE FOR RESIDUE FAD A 501
6
AC8
SOFTWARE
MET B:39 , ASP B:40 , CYS B:41 , ARG B:42 , GLY B:44 , GLU B:45 , CYS B:46 , GLY B:47 , CYS B:49 , CYS B:83
BINDING SITE FOR RESIDUE FES B 600
7
AC9
SOFTWARE
ARG A:16 , GLN A:34 , HOH A:507 , HOH A:508 , TYR B:144 , ARG B:156 , SER B:157 , TYR B:158 , SER B:159 , VAL B:172 , VAL B:173 , ARG B:174 , VAL B:176 , GLY B:179 , LYS B:180 , MET B:181 , SER B:182 , THR B:220 , ALA B:223 , GLU B:333 , LYS B:334 , PHE B:335 , SER B:336 , ALA B:337 , ASN B:338 , HOH B:611 , HOH B:627
BINDING SITE FOR RESIDUE FAD B 601
[
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
(3, 3)
Info
All PROSITE Patterns/Profiles
1: 2FE2S_FER_2 (B:4-99)
2: 2FE2S_FER_1 (B:41-49)
3: FAD_FR (B:106-207)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
2FE2S_FER_2
PS51085
2Fe-2S ferredoxin-type iron-sulfur binding domain profile.
BENC_ACIAD
14-109
1
-
B:4-99
2
2FE2S_FER_1
PS00197
2Fe-2S ferredoxin-type iron-sulfur binding region signature.
BENC_ACIAD
51-59
1
-
B:41-49
3
FAD_FR
PS51384
Ferredoxin reductase-type FAD binding domain profile.
BENC_ACIAD
116-217
1
-
B:106-207
[
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
(3, 6)
Info
All SCOP Domains
1a: SCOP_d1krha1 (A:106-205)
1b: SCOP_d1krhb1 (B:106-205)
2a: SCOP_d1krha3 (A:2-105)
2b: SCOP_d1krhb3 (B:2-105)
3a: SCOP_d1krha2 (A:206-338)
3b: SCOP_d1krhb2 (B:206-338)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Reductase/isomerase/elongation factor common domain
(381)
Superfamily
:
Riboflavin synthase domain-like
(130)
Family
:
Ferredoxin reductase FAD-binding domain-like
(72)
Protein domain
:
Benzoate dioxygenase reductase
(1)
Acinetobacter sp. [TaxId: 472]
(1)
1a
d1krha1
A:106-205
1b
d1krhb1
B:106-205
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
beta-Grasp (ubiquitin-like)
(1032)
Superfamily
:
2Fe-2S ferredoxin-like
(174)
Family
:
2Fe-2S ferredoxin domains from multidomain proteins
(82)
Protein domain
:
Benzoate dioxygenase reductase, N-terminal domain
(1)
Acinetobacter sp. [TaxId: 472]
(1)
2a
d1krha3
A:2-105
2b
d1krhb3
B:2-105
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Ferredoxin reductase-like, C-terminal NADP-linked domain
(120)
Superfamily
:
Ferredoxin reductase-like, C-terminal NADP-linked domain
(120)
Family
:
Aromatic dioxygenase reductase-like
(3)
Protein domain
:
Benzoate dioxygenase reductase
(1)
Acinetobacter sp. [TaxId: 472]
(1)
3a
d1krha2
A:206-338
3b
d1krhb2
B:206-338
[
close SCOP info
]
CATH Domains
(3, 6)
Info
all CATH domains
1a: CATH_1krhA03 (A:202-335)
1b: CATH_1krhB03 (B:202-335)
2a: CATH_1krhA01 (A:2-104)
2b: CATH_1krhB01 (B:2-104)
3a: CATH_1krhA02 (A:105-201)
3b: CATH_1krhB02 (B:105-201)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module
(85)
Acinetobacter sp.. Organism_taxid: 472.
(1)
1a
1krhA03
A:202-335
1b
1krhB03
B:202-335
Architecture
:
Roll
(3276)
Topology
:
Ubiquitin-like (UB roll)
(674)
Homologous Superfamily
:
[code=3.10.20.30, no name defined]
(153)
Acinetobacter sp.. Organism_taxid: 472.
(1)
2a
1krhA01
A:2-104
2b
1krhB01
B:2-104
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
Elongation Factor Tu (Ef-tu); domain 3
(323)
Homologous Superfamily
:
Translation factors
(223)
Acinetobacter sp.. Organism_taxid: 472.
(1)
3a
1krhA02
A:105-201
3b
1krhB02
B:105-201
[
close CATH info
]
Pfam Domains
(3, 6)
Info
all PFAM domains
1a: PFAM_FAD_binding_6_1krhB01 (B:110-206)
1b: PFAM_FAD_binding_6_1krhB02 (B:110-206)
2a: PFAM_Fer2_1krhB03 (B:9-88)
2b: PFAM_Fer2_1krhB04 (B:9-88)
3a: PFAM_NAD_binding_1_1krhB05 (B:215-318)
3b: PFAM_NAD_binding_1_1krhB06 (B:215-318)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
FAD_Lum_binding
(30)
Family
:
FAD_binding_6
(24)
Acinetobacter sp. (strain ADP1)
(1)
1a
FAD_binding_6-1krhB01
B:110-206
1b
FAD_binding_6-1krhB02
B:110-206
Clan
:
Fer2
(69)
Family
:
Fer2
(60)
Acinetobacter sp. (strain ADP1)
(1)
2a
Fer2-1krhB03
B:9-88
2b
Fer2-1krhB04
B:9-88
Clan
:
NAD_Ferredoxin
(30)
Family
:
NAD_binding_1
(30)
Acinetobacter sp. (strain ADP1)
(1)
3a
NAD_binding_1-1krhB05
B:215-318
3b
NAD_binding_1-1krhB06
B:215-318
[
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 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 (120 KB)
Header - Asym.Unit
Biol.Unit 1 (62 KB)
Header - Biol.Unit 1
Biol.Unit 2 (58 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
1KRH
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
