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...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
2ZPG
Asym. Unit
Info
Asym.Unit (85 KB)
Biol.Unit 1 (79 KB)
Biol.Unit 2 (156 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
COMPLEX OF FE-TYPE NITRILE HYDRATASE WITH TERT-BUTYLISONITRILE, PHOTO-ACTIVATED FOR 120MIN AT 293K
Authors
:
K. Hashimoto, H. Suzuki, K. Taniguchi, T. Noguchi, M. Yohda, M. Odaka
Date
:
11 Jul 08 (Deposition) - 21 Oct 08 (Release) - 16 Dec 08 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.39
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Biol. Unit 2: A,B (2x)
Keywords
:
Lyase, Iron, Metal-Binding, Oxidation
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. Hashimoto, H. Suzuki, K. Taniguchi, T. Noguchi, M. Yohda, M. Odaka
Catalytic Mechanism Of Nitrile Hydratase Proposed By Time-Resolved X-Ray Crystallography Using A Novel Substrate, Tert-Butylisonitrile
J. Biol. Chem. V. 283 36617 2008
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(5, 9)
Info
All Hetero Components
1a: 3-SULFINOALANINE (CSDa)
2a: S-HYDROXYCYSTEINE (CSOa)
3a: FE (III) ION (FEa)
4a: MAGNESIUM ION (MGa)
4b: MAGNESIUM ION (MGb)
4c: MAGNESIUM ION (MGc)
4d: MAGNESIUM ION (MGd)
4e: MAGNESIUM ION (MGe)
5a: TERT-BUTYL ISOCYANIDE (TB0a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CSD
1
Mod. Amino Acid
3-SULFINOALANINE
2
CSO
1
Mod. Amino Acid
S-HYDROXYCYSTEINE
3
FE
1
Ligand/Ion
FE (III) ION
4
MG
5
Ligand/Ion
MAGNESIUM ION
5
TB0
1
Ligand/Ion
TERT-BUTYL ISOCYANIDE
[
close Hetero Component info
]
Sites
(7, 7)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
CYS A:109 , CSD A:112 , SER A:113 , CSO A:114 , TB0 A:301
BINDING SITE FOR RESIDUE FE A 300
2
AC2
SOFTWARE
GLN A:90 , CSD A:112 , SER A:113 , CSO A:114 , FE A:300 , TYR B:72
BINDING SITE FOR RESIDUE TB0 A 301
3
AC3
SOFTWARE
HOH A:1363 , HOH A:1397 , HOH A:1423 , HOH A:1449 , HOH A:1477 , HOH A:1491
BINDING SITE FOR RESIDUE MG A1302
4
AC4
SOFTWARE
HOH A:1460 , HOH A:1505 , HOH B:1629
BINDING SITE FOR RESIDUE MG A1303
5
AC5
SOFTWARE
HOH A:1367 , HOH A:1394 , HOH A:1463 , HOH A:1561 , HOH A:1591
BINDING SITE FOR RESIDUE MG A1304
6
AC6
SOFTWARE
HOH B:1327 , HOH B:1370 , HOH B:1397 , HOH B:1400 , HOH B:1410 , HOH B:1413
BINDING SITE FOR RESIDUE MG B1301
7
AC7
SOFTWARE
HOH B:1399 , HOH B:1407 , HOH B:1447 , HOH B:1465 , HOH B:1471 , HOH B:1501
BINDING SITE FOR RESIDUE MG B1305
[
close Site info
]
SAPs(SNPs)/Variants
(1, 1)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_NHAB_RHOER_001 (M40V, chain B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_NHAB_RHOER_001
*
M
40
V
NHAB_RHOER
---
---
B
M
40
V
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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
(2, 2)
Info
All SCOP Domains
1a: SCOP_d2zpgb_ (B:)
2a: SCOP_d2zpga_ (A:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
SH3-like barrel
(1035)
Superfamily
:
Electron transport accessory proteins
(58)
Family
:
Nitrile hydratase beta chain
(30)
Protein domain
:
Iron-containing nitrile hydratase
(21)
Rhodococcus erythropolis [TaxId: 1833]
(21)
1a
d2zpgb_
B:
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Nitrile hydratase alpha chain
(36)
Superfamily
:
Nitrile hydratase alpha chain
(36)
Family
:
Nitrile hydratase alpha chain
(35)
Protein domain
:
automated matches
(25)
Rhodococcus erythropolis [TaxId: 1833]
(17)
2a
d2zpga_
A:
[
close SCOP info
]
CATH Domains
(3, 3)
Info
all CATH domains
1a: CATH_2zpgA00 (A:9-204)
2a: CATH_2zpgB01 (B:1-110)
3a: CATH_2zpgB02 (B:111-211)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Nitrile Hydratase; Chain A
(34)
Homologous Superfamily
:
Nitrile Hydratase; Chain A
(34)
Rhodococcus erythropolis. Organism_taxid: 1833. Strain: n771.
(12)
1a
2zpgA00
A:9-204
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Cyclin A; domain 1
(136)
Homologous Superfamily
:
[code=1.10.472.20, no name defined]
(29)
Rhodococcus erythropolis. Organism_taxid: 1833. Strain: n771.
(12)
2a
2zpgB01
B:1-110
Class
:
Mainly Beta
(13760)
Architecture
:
Roll
(1513)
Topology
:
SH3 type barrels.
(648)
Homologous Superfamily
:
[code=2.30.30.50, no name defined]
(46)
Rhodococcus erythropolis. Organism_taxid: 1833. Strain: n771.
(12)
3a
2zpgB02
B:111-211
[
close CATH info
]
Pfam Domains
(2, 2)
Info
all PFAM domains
1a: PFAM_NHase_alpha_2zpgA01 (A:13-201)
2a: PFAM_NHase_beta_2zpgB01 (B:1-211)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: NHase_alpha]
(12)
Family
:
NHase_alpha
(12)
Rhodococcus erythropolis (Arthrobacter picolinophilus)
(7)
1a
NHase_alpha-2zpgA01
A:13-201
Clan
:
no clan defined [family: NHase_beta]
(11)
Family
:
NHase_beta
(11)
Rhodococcus erythropolis (Arthrobacter picolinophilus)
(7)
2a
NHase_beta-2zpgB01
B:1-211
[
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 (85 KB)
Header - Asym.Unit
Biol.Unit 1 (79 KB)
Header - Biol.Unit 1
Biol.Unit 2 (156 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
2ZPG
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
