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.
3O5A
Asym. Unit
Info
Asym.Unit (175 KB)
Biol.Unit 1 (166 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 PARTIALLY REDUCED PERIPLASMIC NITRATE REDUCTASE FROM CUPRIAVIDUS NECATOR USING IONIC LIQUIDS
Authors
:
C. Coelho, J. Trincao, M. J. Romao
Date
:
28 Jul 10 (Deposition) - 06 Apr 11 (Release) - 07 Dec 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.72
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Oxidoreductase, Heterodimeric Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. Coelho, P. J. Gonzalez, J. J. G. Moura, I. Moura, J. Trincao, M. J. Romao
The Crystal Structure Of Cupriavidus Necator Nitrate Reductase In Oxidized And Partially Reduced States
J. Mol. Biol. V. 408 932 2011
[
close entry info
]
Hetero Components
(7, 27)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
2a: FORMIC ACID (FMTa)
2b: FORMIC ACID (FMTb)
2c: FORMIC ACID (FMTc)
2d: FORMIC ACID (FMTd)
2e: FORMIC ACID (FMTe)
2f: FORMIC ACID (FMTf)
2g: FORMIC ACID (FMTg)
2h: FORMIC ACID (FMTh)
2i: FORMIC ACID (FMTi)
2j: FORMIC ACID (FMTj)
2k: FORMIC ACID (FMTk)
2l: FORMIC ACID (FMTl)
2m: FORMIC ACID (FMTm)
2n: FORMIC ACID (FMTn)
2o: FORMIC ACID (FMTo)
2p: FORMIC ACID (FMTp)
2q: FORMIC ACID (FMTq)
2r: FORMIC ACID (FMTr)
2s: FORMIC ACID (FMTs)
3a: HEME C (HECa)
3b: HEME C (HECb)
4a: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,... (MGDa)
4b: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,... (MGDb)
5a: DIOXOTHIOMOLYBDENUM(VI) ION (MOSa)
6a: CYSTEINESULFONIC ACID (OCSa)
7a: IRON/SULFUR CLUSTER (SF4a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
1
Ligand/Ion
CHLORIDE ION
2
FMT
19
Ligand/Ion
FORMIC ACID
3
HEC
2
Ligand/Ion
HEME C
4
MGD
2
Ligand/Ion
2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINEDINUCLEOTIDE
5
MOS
1
Ligand/Ion
DIOXOTHIOMOLYBDENUM(VI) ION
6
OCS
1
Mod. Amino Acid
CYSTEINESULFONIC ACID
7
SF4
1
Ligand/Ion
IRON/SULFUR CLUSTER
[
close Hetero Component info
]
Sites
(25, 25)
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)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
CYS A:19 , PHE A:21 , CYS A:22 , GLY A:25 , CYS A:26 , ASN A:53 , CYS A:54 , GLY A:57 , PRO A:194
BINDING SITE FOR RESIDUE SF4 A 1801
02
AC2
SOFTWARE
CYS A:152 , GLN A:384 , MGD A:1803 , MGD A:1804
BINDING SITE FOR RESIDUE MOS A 1802
03
AC3
SOFTWARE
ARG A:20 , GLN A:123 , ASN A:148 , CYS A:152 , GLN A:350 , GLN A:384 , VAL A:454 , ASN A:455 , ASN A:456 , ASN A:457 , ALA A:460 , SER A:482 , ASP A:483 , ALA A:484 , THR A:487 , SER A:499 , ALA A:500 , MET A:501 , LYS A:505 , ASP A:532 , THR A:692 , ARG A:694 , TRP A:699 , HIS A:700 , SER A:701 , SER A:703 , TRP A:768 , ASN A:776 , PHE A:792 , LYS A:793 , HOH A:820 , HOH A:826 , HOH A:860 , MOS A:1802 , MGD A:1804
BINDING SITE FOR RESIDUE MGD A 1803
04
AC4
SOFTWARE
CYS A:22 , LYS A:56 , CYS A:152 , TRP A:185 , GLY A:186 , ASN A:188 , GLU A:191 , MET A:192 , SER A:216 , THR A:217 , PHE A:218 , HIS A:220 , PHE A:232 , GLN A:235 , ASP A:237 , THR A:345 , MET A:346 , GLY A:347 , PHE A:348 , GLY A:383 , GLN A:384 , GLY A:693 , ARG A:694 , VAL A:695 , LEU A:696 , HIS A:698 , TRP A:699 , HIS A:700 , LYS A:793 , LYS A:794 , HOH A:871 , HOH A:888 , HOH A:894 , HOH A:940 , HOH A:1030 , MOS A:1802 , MGD A:1803
BINDING SITE FOR RESIDUE MGD A 1804
05
AC5
SOFTWARE
PHE A:397 , HIS A:399 , ARG A:400 , HOH A:1090 , HOH A:1200
BINDING SITE FOR RESIDUE FMT A 803
06
AC6
SOFTWARE
LEU A:241 , ASN A:242 , ALA A:245 , MET A:360 , ASN A:363 , LEU A:364
BINDING SITE FOR RESIDUE FMT A 804
07
AC7
SOFTWARE
SER A:15 , LYS A:16 , HIS A:520 , TYR A:587 , FMT A:815 , HOH A:883 , HOH A:1216
BINDING SITE FOR RESIDUE FMT A 805
08
AC8
SOFTWARE
ARG A:150 , HIS A:399 , ILE A:786 , HOH A:1279 , HOH A:1297
BINDING SITE FOR RESIDUE FMT A 806
09
AC9
SOFTWARE
ASP A:167 , GLU A:168 , ARG A:392 , GLU A:393 , ASP A:404 , HIS A:616 , TRP A:632 , HOH A:817
BINDING SITE FOR RESIDUE FMT A 807
10
BC1
SOFTWARE
ARG A:734
BINDING SITE FOR RESIDUE FMT A 809
11
BC2
SOFTWARE
ALA A:627 , ARG A:628 , HOH A:1361
BINDING SITE FOR RESIDUE FMT A 810
12
BC3
SOFTWARE
GLY A:229 , ILE A:230 , ILE A:231 , LYS A:325 , HOH A:1126
BINDING SITE FOR RESIDUE FMT A 811
13
BC4
SOFTWARE
ARG A:203 , HOH A:1322
BINDING SITE FOR RESIDUE FMT A 812
14
BC5
SOFTWARE
ARG A:733 , ARG A:734 , HOH A:1408
BINDING SITE FOR RESIDUE FMT A 813
15
BC6
SOFTWARE
GLY A:527 , GLU A:528 , ALA A:529 , ARG A:530 , HOH A:960
BINDING SITE FOR RESIDUE FMT A 814
16
BC7
SOFTWARE
GLU A:626 , FMT A:805
BINDING SITE FOR RESIDUE FMT A 815
17
BC8
SOFTWARE
SER A:772 , LEU A:774 , LYS A:777 , ARG B:7
BINDING SITE FOR RESIDUE CL A 816
18
BC9
SOFTWARE
PRO B:40 , THR B:41 , ILE B:42 , PRO B:43 , HIS B:44 , ILE B:46 , TYR B:49 , ARG B:57 , CYS B:58 , CYS B:61 , HIS B:62 , ALA B:72 , ILE B:73 , CYS B:98 , HIS B:102 , FMT B:140 , HOH B:355 , HOH B:667
BINDING SITE FOR RESIDUE HEC B 1128
19
CC1
SOFTWARE
ASN A:53 , TYR A:58 , GLN B:38 , PRO B:39 , PRO B:40 , ILE B:73 , VAL B:75 , SER B:76 , THR B:78 , HIS B:79 , ARG B:95 , PHE B:97 , CYS B:98 , CYS B:101 , HIS B:102 , HOH B:162 , HOH B:409 , HOH B:568 , HOH B:667
BINDING SITE FOR RESIDUE HEC B 1129
20
CC2
SOFTWARE
GLY B:48 , TYR B:49 , GLN B:50 , ARG B:57
BINDING SITE FOR RESIDUE FMT B 135
21
CC3
SOFTWARE
LYS A:109 , ARG A:746 , ALA B:13 , ASN B:14 , GLU B:15 , HOH B:144
BINDING SITE FOR RESIDUE FMT B 136
22
CC4
SOFTWARE
GLY B:113 , ASN B:114
BINDING SITE FOR RESIDUE FMT B 137
23
CC5
SOFTWARE
LEU B:2 , VAL B:3 , HOH B:767
BINDING SITE FOR RESIDUE FMT B 138
24
CC6
SOFTWARE
LEU A:491 , VAL B:3 , ASP B:4 , ARG B:7 , GLY B:8 , HOH B:684 , HOH B:710
BINDING SITE FOR RESIDUE FMT B 139
25
CC7
SOFTWARE
HIS B:44 , TYR B:49 , HEC B:1128
BINDING SITE FOR RESIDUE FMT B 140
[
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
(3, 3)
Info
All PROSITE Patterns/Profiles
1: 4FE4S_MOW_BIS_MGD (A:12-68)
2: MOLYBDOPTERIN_PROK_1 (A:17-35)
3: MULTIHEME_CYTC (B:53-107)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
4FE4S_MOW_BIS_MGD
PS51669
Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile.
NAPA_CUPNH
41-97
1
A:12-68
2
MOLYBDOPTERIN_PROK_1
PS00551
Prokaryotic molybdopterin oxidoreductases signature 1.
NAPA_CUPNH
46-64
1
A:17-35
3
MULTIHEME_CYTC
PS51008
Multiheme cytochrome c family profile.
NAPB_CUPNH
88-142
1
B:53-107
[
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
(2, 2)
Info
All SCOP Domains
1a: SCOP_d3o5aa2 (A:682-802)
2a: SCOP_d3o5aa1 (A:11-681)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Double psi beta-barrel
(111)
Superfamily
:
ADC-like
(88)
Family
:
automated matches
(19)
Protein domain
:
automated matches
(19)
Ralstonia eutropha [TaxId: 381666]
(2)
1a
d3o5aa2
A:682-802
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Formate dehydrogenase/DMSO reductase, domains 1-3
(53)
Superfamily
:
Formate dehydrogenase/DMSO reductase, domains 1-3
(53)
Family
:
Formate dehydrogenase/DMSO reductase, domains 1-3
(53)
Protein domain
:
automated matches
(12)
Ralstonia eutropha [TaxId: 381666]
(2)
2a
d3o5aa1
A:11-681
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(4, 4)
Info
all PFAM domains
1a: PFAM_Molydop_binding_3o5aA01 (A:688-796)
2a: PFAM_NapB_3o5aB01 (B:1-119)
3a: PFAM_Molybdop_Fe4S4_3o5aA02 (A:12-66)
4a: PFAM_Molybdopterin_3o5aA03 (A:69-542)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
AcetylDC-like
(37)
Family
:
Molydop_binding
(24)
Cupriavidus necator (strain ATCC 17699 / H16 / DSM 428 / Stanier 337) (Ralstonia eutropha)
(2)
1a
Molydop_binding-3o5aA01
A:688-796
Clan
:
Multiheme_cytos
(34)
Family
:
NapB
(3)
Cupriavidus necator (strain ATCC 17699 / H16 / DSM 428 / Stanier 337) (Ralstonia eutropha)
(2)
2a
NapB-3o5aB01
B:1-119
Clan
:
no clan defined [family: Molybdop_Fe4S4]
(17)
Family
:
Molybdop_Fe4S4
(17)
Cupriavidus necator (strain ATCC 17699 / H16 / DSM 428 / Stanier 337) (Ralstonia eutropha)
(2)
3a
Molybdop_Fe4S4-3o5aA02
A:12-66
Clan
:
no clan defined [family: Molybdopterin]
(24)
Family
:
Molybdopterin
(24)
Cupriavidus necator (strain ATCC 17699 / H16 / DSM 428 / Stanier 337) (Ralstonia eutropha)
(2)
4a
Molybdopterin-3o5aA03
A:69-542
[
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 (175 KB)
Header - Asym.Unit
Biol.Unit 1 (166 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
3O5A
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help