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.
3KOQ
Asym. Unit
Info
Asym.Unit (150 KB)
Biol.Unit 1 (73 KB)
Biol.Unit 2 (72 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 A NITROREDUCTASE FAMILY PROTEIN (CD3355) FROM CLOSTRIDIUM DIFFICILE 630 AT 1.58 A RESOLUTION
Authors
:
Joint Center For Structural Genomics (Jcsg)
Date
:
13 Nov 09 (Deposition) - 01 Dec 09 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.58
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Nitroreductase Family Protein (Yp_001089872. 1) From Clostridium Difficile 630 At 1. 58 A Resolution
To Be Published
[
close entry info
]
Hetero Components
(4, 35)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
2a: FLAVIN MONONUCLEOTIDE (FMNa)
2b: FLAVIN MONONUCLEOTIDE (FMNb)
2c: FLAVIN MONONUCLEOTIDE (FMNc)
2d: FLAVIN MONONUCLEOTIDE (FMNd)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
3c: GLYCEROL (GOLc)
3d: GLYCEROL (GOLd)
3e: GLYCEROL (GOLe)
3f: GLYCEROL (GOLf)
3g: GLYCEROL (GOLg)
3h: GLYCEROL (GOLh)
3i: GLYCEROL (GOLi)
3j: GLYCEROL (GOLj)
3k: GLYCEROL (GOLk)
3l: GLYCEROL (GOLl)
3m: GLYCEROL (GOLm)
4a: SELENOMETHIONINE (MSEa)
4b: SELENOMETHIONINE (MSEb)
4c: SELENOMETHIONINE (MSEc)
4d: SELENOMETHIONINE (MSEd)
4e: SELENOMETHIONINE (MSEe)
4f: SELENOMETHIONINE (MSEf)
4g: SELENOMETHIONINE (MSEg)
4h: SELENOMETHIONINE (MSEh)
4i: SELENOMETHIONINE (MSEi)
4j: SELENOMETHIONINE (MSEj)
4k: SELENOMETHIONINE (MSEk)
4l: SELENOMETHIONINE (MSEl)
4m: SELENOMETHIONINE (MSEm)
4n: SELENOMETHIONINE (MSEn)
4o: SELENOMETHIONINE (MSEo)
4p: SELENOMETHIONINE (MSEp)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
2
Ligand/Ion
CHLORIDE ION
2
FMN
4
Ligand/Ion
FLAVIN MONONUCLEOTIDE
3
GOL
13
Ligand/Ion
GLYCEROL
4
MSE
16
Mod. Amino Acid
SELENOMETHIONINE
[
close Hetero Component info
]
Sites
(19, 19)
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)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:10 , TYR A:11 , SER A:12 , ARG A:14 , TYR A:66 , VAL A:115 , TRP A:116 , VAL A:117 , CYS A:118 , TYR A:119 , ARG A:155 , ARG A:160 , HOH A:242 , HOH A:330 , HOH A:490 , HOH A:636 , PRO B:37 , THR B:38 , GLY B:39 , ASN B:41 , ILE B:94 , ASP B:95 , ILE B:98 , CL B:173 , LYS C:148 , HOH C:284
BINDING SITE FOR RESIDUE FMN A 300
02
AC2
SOFTWARE
LYS A:9 , PRO A:150 , HOH A:653 , HOH A:680 , HOH A:708
BINDING SITE FOR RESIDUE GOL A 173
03
AC3
SOFTWARE
GLY A:40 , TRP A:82 , HOH A:881 , GOL B:176 , FMN B:300
BINDING SITE FOR RESIDUE GOL A 174
04
AC4
SOFTWARE
ILE A:149 , PRO A:150 , GLU A:151
BINDING SITE FOR RESIDUE GOL A 175
05
AC5
SOFTWARE
MSE A:1 , ASN A:2 , PHE A:3 , GLU A:109 , MSE B:1 , PHE B:3 , LEU B:6 , GLU B:109
BINDING SITE FOR RESIDUE GOL A 176
06
AC6
SOFTWARE
PRO A:37 , THR A:38 , GLY A:39 , ASN A:41 , ILE A:94 , ASP A:95 , ILE A:98 , GOL A:174 , ARG B:10 , TYR B:11 , SER B:12 , ARG B:14 , TYR B:66 , VAL B:115 , TRP B:116 , VAL B:117 , CYS B:118 , TYR B:119 , ARG B:155 , ARG B:160 , GOL B:176 , HOH B:197 , HOH B:233 , HOH B:247
BINDING SITE FOR RESIDUE FMN B 300
07
AC7
SOFTWARE
FMN A:300 , GLY B:40 , ILE C:149
BINDING SITE FOR RESIDUE CL B 173
08
AC8
SOFTWARE
ILE B:149 , HOH B:779 , GLY C:40 , FMN D:300
BINDING SITE FOR RESIDUE CL B 174
09
AC9
SOFTWARE
PHE A:86 , ALA B:62 , ASN B:64 , TYR B:119 , HOH B:195 , HOH B:229
BINDING SITE FOR RESIDUE GOL B 175
10
BC1
SOFTWARE
GOL A:174 , HOH A:881 , ARG B:14 , FMN B:300 , HOH B:716 , HOH B:789
BINDING SITE FOR RESIDUE GOL B 176
11
BC2
SOFTWARE
TYR A:119 , HOH A:434 , HOH A:577 , ARG B:84 , PRO B:85 , PHE B:86
BINDING SITE FOR RESIDUE GOL B 177
12
BC3
SOFTWARE
ARG C:10 , TYR C:11 , SER C:12 , ARG C:14 , TYR C:66 , VAL C:115 , TRP C:116 , VAL C:117 , CYS C:118 , TYR C:119 , ARG C:155 , ARG C:160 , HOH C:264 , HOH C:336 , HOH C:709 , PRO D:37 , THR D:38 , GLY D:39 , ASN D:41 , ILE D:94 , ILE D:98 , GOL D:175
BINDING SITE FOR RESIDUE FMN C 300
13
BC4
SOFTWARE
ALA C:62 , ASN C:64 , TYR C:119 , HOH C:311 , HOH C:769 , PHE D:86
BINDING SITE FOR RESIDUE GOL C 173
14
BC5
SOFTWARE
LYS C:9 , THR C:108 , GLY C:111 , LEU C:112 , ALA C:113 , GLU C:146 , PRO C:150 , HOH C:237 , HOH C:371 , HOH C:414
BINDING SITE FOR RESIDUE GOL C 174
15
BC6
SOFTWARE
LYS C:158 , THR C:159 , ARG C:160 , VAL C:161 , ASN D:41 , GLN D:43
BINDING SITE FOR RESIDUE GOL C 175
16
BC7
SOFTWARE
LYS B:148 , CL B:174 , PRO C:37 , THR C:38 , GLY C:39 , ASN C:41 , LEU C:91 , ILE C:94 , ILE C:98 , ARG D:10 , TYR D:11 , SER D:12 , ARG D:14 , TYR D:66 , VAL D:115 , TRP D:116 , VAL D:117 , CYS D:118 , TYR D:119 , ARG D:155 , ARG D:160 , HOH D:241 , HOH D:280 , HOH D:356 , HOH D:365 , HOH D:654
BINDING SITE FOR RESIDUE FMN D 300
17
BC8
SOFTWARE
LYS D:9 , PRO D:150 , HOH D:341 , HOH D:580 , HOH D:762
BINDING SITE FOR RESIDUE GOL D 173
18
BC9
SOFTWARE
MSE C:1 , GLU C:109 , MSE D:1 , ASN D:2 , GLU D:109
BINDING SITE FOR RESIDUE GOL D 174
19
CC1
SOFTWARE
TYR C:119 , FMN C:300 , GLY D:40 , TRP D:82
BINDING SITE FOR RESIDUE GOL D 175
[
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
(1, 4)
Info
All SCOP Domains
1a: SCOP_d3koqa_ (A:)
1b: SCOP_d3koqb_ (B:)
1c: SCOP_d3koqc_ (C:)
1d: SCOP_d3koqd_ (D:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
FMN-dependent nitroreductase-like
(52)
Superfamily
:
FMN-dependent nitroreductase-like
(52)
Family
:
automated matches
(22)
Protein domain
:
automated matches
(22)
Clostridium difficile [TaxId: 272563]
(3)
1a
d3koqa_
A:
1b
d3koqb_
B:
1c
d3koqc_
C:
1d
d3koqd_
D:
[
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
Chain C
Chain D
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 (150 KB)
Header - Asym.Unit
Biol.Unit 1 (73 KB)
Header - Biol.Unit 1
Biol.Unit 2 (72 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
3KOQ
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help