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.
3NTD
Asym. Unit
Info
Asym.Unit (371 KB)
Biol.Unit 1 (362 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
STRUCTURE OF THE SHEWANELLA LOIHICA PV-4 NADH-DEPENDENT PERSULFIDE REDUCTASE C531S MUTANT
Authors
:
M. H. Sazinsky, M. D. Warner, V. Lukose, K. H. Lee, E. J. Crane
Date
:
03 Jul 10 (Deposition) - 08 Dec 10 (Release) - 22 Feb 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.99
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Fad, Coa, Persulfide Reductase, Rhodanese, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. D. Warner, V. Lukose, K. H. Lee, K. Lopez, M. H Sazinsky, E. J. Crane
Characterization Of An Nadh-Dependent Persulfide Reductase From Shewanella Loihica Pv-4: Implications For The Mechanis Of Sulfur Respiration Via Fad-Dependent Enzymes .
Biochemistry V. 50 194 2010
[
close entry info
]
Hetero Components
(3, 6)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
2a: COENZYME A (COAa)
2b: COENZYME A (COAb)
3a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
3b: FLAVIN-ADENINE DINUCLEOTIDE (FADb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
2
Ligand/Ion
CHLORIDE ION
2
COA
2
Ligand/Ion
COENZYME A
3
FAD
2
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
[
close Hetero Component info
]
Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ALA A:11 , ALA A:14 , ARG A:19 , ARG A:22 , SER A:39 , PHE A:40 , ASN A:42 , CYS A:43 , ALA A:321 , ASN A:325 , ARG A:329 , HOH A:636 , HOH A:638 , HOH A:655 , HOH A:659 , HOH A:711 , HOH A:792 , FAD A:900 , HOH A:948 , TYR B:446 , LYS B:454 , GLN B:459 , PHE B:462 , VAL B:463 , ASN B:466 , VAL B:533 , GLY B:534 , LEU B:535 , ASN B:538 , HOH B:708
BINDING SITE FOR RESIDUE COA A 901
2
AC2
SOFTWARE
ALA A:231 , SER A:531 , GLN A:532 , VAL A:533 , LEU A:535 , ARG A:536
BINDING SITE FOR RESIDUE CL A 566
3
AC3
SOFTWARE
GLY A:8 , VAL A:10 , ALA A:11 , GLY A:12 , GLU A:33 , ARG A:34 , ASN A:42 , CYS A:43 , HIS A:79 , GLU A:80 , VAL A:81 , SER A:112 , PRO A:113 , GLY A:114 , LEU A:133 , ARG A:134 , PHE A:161 , ILE A:162 , GLY A:302 , ASP A:303 , PRO A:319 , LEU A:320 , ALA A:321 , HOH A:597 , HOH A:606 , HOH A:631 , HOH A:665 , HOH A:669 , HOH A:695 , HOH A:719 , HOH A:857 , COA A:901 , TYR B:446 , ALA B:447 , PRO B:448
BINDING SITE FOR RESIDUE FAD A 900
4
AC4
SOFTWARE
ALA B:231 , SER B:531 , GLN B:532 , VAL B:533 , LEU B:535 , ARG B:536
BINDING SITE FOR RESIDUE CL B 566
5
AC5
SOFTWARE
TYR A:446 , ALA A:447 , PRO A:448 , ILE B:7 , GLY B:8 , VAL B:10 , ALA B:11 , GLY B:12 , GLU B:33 , ARG B:34 , ASN B:42 , CYS B:43 , HIS B:79 , GLU B:80 , VAL B:81 , SER B:112 , PRO B:113 , GLY B:114 , LEU B:133 , ARG B:134 , PHE B:161 , ILE B:162 , LEU B:271 , GLY B:302 , ASP B:303 , PRO B:319 , LEU B:320 , ALA B:321 , HOH B:574 , HOH B:575 , HOH B:585 , HOH B:598 , HOH B:610 , HOH B:639 , HOH B:657 , HOH B:683 , HOH B:763
BINDING SITE FOR RESIDUE FAD B 900
6
AC6
SOFTWARE
TYR A:446 , LYS A:454 , GLN A:459 , PHE A:462 , VAL A:463 , ASN A:466 , VAL A:533 , GLY A:534 , LEU A:535 , ASN A:538 , HOH A:613 , HOH A:637 , HOH A:663 , VAL B:10 , ALA B:11 , ALA B:14 , SER B:15 , ALA B:18 , ARG B:19 , ARG B:22 , SER B:39 , PHE B:40 , ASN B:42 , CYS B:43 , GLN B:62 , ALA B:321 , ASN B:325 , ARG B:329 , HOH B:650 , HOH B:651 , HOH B:653 , HOH B:840 , HOH B:876 , HOH B:961 , HOH B:1091
BINDING SITE FOR RESIDUE COA B 901
[
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
(4, 8)
Info
all PFAM domains
1a: PFAM_Pyr_redox_3ntdB01 (B:153-231)
1b: PFAM_Pyr_redox_3ntdB02 (B:153-231)
2a: PFAM_Pyr_redox_2_3ntdB03 (B:3-309)
2b: PFAM_Pyr_redox_2_3ntdB04 (B:3-309)
3a: PFAM_Pyr_redox_dim_3ntdB05 (B:348-457)
3b: PFAM_Pyr_redox_dim_3ntdB06 (B:348-457)
4a: PFAM_Rhodanese_3ntdB07 (B:478-564)
4b: PFAM_Rhodanese_3ntdB08 (B:478-564)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
NADP_Rossmann
(1239)
Family
:
Pyr_redox
(62)
Shewanella loihica (strain ATCC BAA-1088 / PV-4)
(3)
1a
Pyr_redox-3ntdB01
B:153-231
1b
Pyr_redox-3ntdB02
B:153-231
Family
:
Pyr_redox_2
(69)
Shewanella loihica (strain ATCC BAA-1088 / PV-4)
(3)
2a
Pyr_redox_2-3ntdB03
B:3-309
2b
Pyr_redox_2-3ntdB04
B:3-309
Clan
:
no clan defined [family: Pyr_redox_dim]
(44)
Family
:
Pyr_redox_dim
(44)
Shewanella loihica (strain ATCC BAA-1088 / PV-4)
(3)
3a
Pyr_redox_dim-3ntdB05
B:348-457
3b
Pyr_redox_dim-3ntdB06
B:348-457
Clan
:
no clan defined [family: Rhodanese]
(33)
Family
:
Rhodanese
(33)
Shewanella loihica (strain ATCC BAA-1088 / PV-4)
(3)
4a
Rhodanese-3ntdB07
B:478-564
4b
Rhodanese-3ntdB08
B:478-564
[
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 (371 KB)
Header - Asym.Unit
Biol.Unit 1 (362 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
3NTD
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help