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.
1NIR
Asym. Unit
Info
Asym.Unit (199 KB)
Biol.Unit 1 (192 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
OXYDIZED NITRITE REDUCTASE FROM PSEUDOMONAS AERUGINOSA
Authors
:
D. Nurizzo, M. Tegoni, C. Cambillau
Date
:
17 Jun 97 (Deposition) - 03 Dec 97 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.15
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Nitrite Reductase, Pseudomonas Aeruginosa, Hemoprotein, Denitrification, Domain Swapping
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. Nurizzo, M. C. Silvestrini, M. Mathieu, F. Cutruzzola, D. Bourgeois, V. Fulop, J. Hajdu, M. Brunori, M. Tegoni, C. Cambillau
N-Terminal Arm Exchange Is Observed In The 2. 15 A Crystal Structure Of Oxidized Nitrite Reductase From Pseudomonas Aeruginosa.
Structure V. 5 1157 1997
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(5, 10)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
2a: HEME D (DHEa)
2b: HEME D (DHEb)
3a: HEME C (HECa)
3b: HEME C (HECb)
4a: HYDROXIDE ION (OHa)
4b: HYDROXIDE ION (OHb)
5a: PHOSPHATE ION (PO4a)
5b: PHOSPHATE ION (PO4b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
2
Ligand/Ion
CHLORIDE ION
2
DHE
2
Ligand/Ion
HEME D
3
HEC
2
Ligand/Ion
HEME C
4
OH
2
Ligand/Ion
HYDROXIDE ION
5
PO4
2
Ligand/Ion
PHOSPHATE ION
[
close Hetero Component info
]
Sites
(12, 12)
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: NIA (UNKNOWN)
12: NIB (UNKNOWN)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HOH A:673 , HIS B:335 , HIS B:540 , HOH B:770
BINDING SITE FOR RESIDUE PO4 A 604
02
AC2
SOFTWARE
SER A:265 , GLY B:268 , MET B:269
BINDING SITE FOR RESIDUE CL A 605
03
AC3
SOFTWARE
HIS A:369 , DHE A:602 , TYR B:10
BINDING SITE FOR RESIDUE OH A 603
04
AC4
SOFTWARE
HIS A:335 , HIS A:540 , HOH A:744 , HOH B:984
BINDING SITE FOR RESIDUE PO4 B 604
05
AC5
SOFTWARE
GLY A:268 , MET A:269 , SER B:265
BINDING SITE FOR RESIDUE CL B 605
06
AC6
SOFTWARE
TYR A:10 , HIS B:369 , DHE B:602
BINDING SITE FOR RESIDUE OH B 603
07
AC7
SOFTWARE
ARG A:46 , CYS A:47 , CYS A:50 , HIS A:51 , THR A:59 , LEU A:63 , ARG A:71 , LEU A:79 , THR A:84 , LEU A:86 , GLY A:87 , MET A:88 , PRO A:89 , TRP A:91 , HOH A:722 , HOH A:770 , HOH A:822 , HOH A:895 , GLU B:8
BINDING SITE FOR RESIDUE HEC A 601
08
AC8
SOFTWARE
ARG A:156 , HIS A:182 , ILE A:183 , ARG A:185 , ARG A:198 , ARG A:225 , SER A:226 , TYR A:245 , ALA A:283 , ALA A:284 , ILE A:285 , HIS A:327 , ARG A:372 , PHE A:425 , GLN A:483 , GLY A:531 , PHE A:533 , OH A:603 , HOH A:645 , HOH A:656 , HOH A:876 , HOH A:877 , HOH A:880 , HOH A:901 , HOH A:907 , HOH A:1010 , TYR B:10 , ALA B:13 , HOH B:884
BINDING SITE FOR RESIDUE DHE A 602
09
AC9
SOFTWARE
GLU A:8 , ARG B:46 , CYS B:47 , CYS B:50 , HIS B:51 , THR B:59 , LEU B:63 , ARG B:71 , LEU B:79 , THR B:84 , LEU B:86 , GLY B:87 , MET B:88 , PRO B:89 , TRP B:91 , HOH B:639 , HOH B:682 , HOH B:725 , HOH B:849
BINDING SITE FOR RESIDUE HEC B 601
10
BC1
SOFTWARE
TYR A:10 , ARG B:156 , HIS B:182 , ARG B:185 , ARG B:198 , ARG B:225 , SER B:226 , TYR B:245 , ALA B:284 , ILE B:285 , HIS B:327 , ARG B:372 , PHE B:425 , PHE B:441 , GLN B:483 , GLY B:531 , PHE B:533 , OH B:603 , HOH B:609 , HOH B:640 , HOH B:662 , HOH B:711 , HOH B:863 , HOH B:872 , HOH B:890 , HOH B:891 , HOH B:980 , HOH B:981
BINDING SITE FOR RESIDUE DHE B 602
11
NIA
UNKNOWN
HIS A:327 , HIS A:369 , DHE A:602
ACTIVE SITE.
12
NIB
UNKNOWN
HIS B:327 , HIS B:369 , DHE B:602
ACTIVE SITE.
[
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
(1, 2)
Info
All PROSITE Patterns/Profiles
1: CYTC (A:34-113,B:34-113)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
CYTC
PS51007
Cytochrome c family profile.
NIRS_PSEAE
59-138
2
A:34-113
B:34-113
[
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, 4)
Info
All SCOP Domains
1a: SCOP_d1nira1 (A:6-117)
1b: SCOP_d1nirb1 (B:5-117)
2a: SCOP_d1nira2 (A:118-543)
2b: SCOP_d1nirb2 (B:118-543)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Cytochrome c
(308)
Superfamily
:
Cytochrome c
(308)
Family
:
N-terminal (heme c) domain of cytochrome cd1-nitrite reductase
(22)
Protein domain
:
N-terminal (heme c) domain of cytochrome cd1-nitrite reductase
(22)
Pseudomonas aeruginosa [TaxId: 287]
(9)
1a
d1nira1
A:6-117
1b
d1nirb1
B:5-117
Class
:
All beta proteins
(24004)
Fold
:
8-bladed beta-propeller
(135)
Superfamily
:
C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase
(22)
Family
:
C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase
(22)
Protein domain
:
C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase
(22)
Pseudomonas aeruginosa [TaxId: 287]
(9)
2a
d1nira2
A:118-543
2b
d1nirb2
B:118-543
[
close SCOP info
]
CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1nirA01 (A:6-116)
1b: CATH_1nirB01 (B:6-116)
2a: CATH_1nirA02 (A:117-543)
2b: CATH_1nirB02 (B:117-543)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Cytochrome Bc1 Complex; Chain D, domain 2
(279)
Homologous Superfamily
:
Cytochrome c
(279)
Pseudomonas aeruginosa. Organism_taxid: 287.
(9)
1a
1nirA01
A:6-116
1b
1nirB01
B:6-116
Class
:
Mainly Beta
(13760)
Architecture
:
8 Propellor
(110)
Topology
:
Methanol Dehydrogenase; Chain A
(110)
Homologous Superfamily
:
[code=2.140.10.20, no name defined]
(22)
Pseudomonas aeruginosa. Organism_taxid: 287.
(8)
2a
1nirA02
A:117-543
2b
1nirB02
B:117-543
[
close CATH info
]
Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_Cytochrom_D1_1nirB01 (B:144-538)
1b: PFAM_Cytochrom_D1_1nirB02 (B:144-538)
2a: PFAM_Cytochrome_CBB3_1nirB03 (B:34-109)
2b: PFAM_Cytochrome_CBB3_1nirB04 (B:34-109)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Beta_propeller
(192)
Family
:
Cytochrom_D1
(5)
Pseudomonas aeruginosa
(4)
1a
Cytochrom_D1-1nirB01
B:144-538
1b
Cytochrom_D1-1nirB02
B:144-538
Clan
:
Cytochrome-c
(108)
Family
:
Cytochrome_CBB3
(20)
Pseudomonas aeruginosa
(5)
2a
Cytochrome_CBB3-1nirB03
B:34-109
2b
Cytochrome_CBB3-1nirB04
B:34-109
[
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 (199 KB)
Header - Asym.Unit
Biol.Unit 1 (192 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
1NIR
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help