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.
1JMZ
Biol. Unit 2
Info
Asym.Unit (157 KB)
Biol.Unit 1 (151 KB)
Biol.Unit 2 (298 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 QUINOHEMOPROTEIN AMINE DEHYDROGENASE FROM PSEUDOMONAS PUTIDA WITH INHIBITOR
Authors
:
A. Satoh, I. Miyahara, K. Hirotsu
Date
:
20 Jul 01 (Deposition) - 16 Jan 02 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B,G
Biol. Unit 1: A,B,G (1x)
Biol. Unit 2: A,B,G (2x)
Keywords
:
Amine Dehydrogenase, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Satoh, J. K. Kim, I. Miyahara, B. Devreese, I. Vandenberghe, A. Hacisalihoglu, T. Okajima, S. Kuroda, O. Adachi, J. A. Duine, J. Van Beeumen, K. Tanizawa, K. Hirotsu
Crystal Structure Of Quinohemoprotein Amine Dehydrogenase From Pseudomonas Putida. Identification Of A Novel Quinone Cofactor Encaged By Multiple Thioether Cross-Bridges.
J. Biol. Chem. V. 277 2830 2002
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 8)
Info
All Hetero Components
1a: HEME C (HECa)
1b: HEME C (HECb)
2a: NICKEL (II) ION (NIa)
3a: P-NITROPHENYLHYDRAZINE (PNDa)
4a: 2-AMINO-3-(6,7-DIOXO-6,7-DIHYDRO-1... (TRQa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
HEC
4
Ligand/Ion
HEME C
2
NI
-1
Ligand/Ion
NICKEL (II) ION
3
PND
2
Ligand/Ion
P-NITROPHENYLHYDRAZINE
4
TRQ
2
Mod. Amino Acid
2-AMINO-3-(6,7-DIOXO-6,7-DIHYDRO-1H-INDOL-3-YL)-PROPIONIC ACID
[
close Hetero Component info
]
Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLU A:367 , HOH A:2061 , HIS B:11
BINDING SITE FOR RESIDUE NI A 2001
2
AC2
SOFTWARE
LEU B:198 , PHE B:200 , TRP B:201 , TYR B:298 , THR B:341 , ASP G:12 , ASP G:33 , GLY G:36 , TRQ G:43
BINDING SITE FOR RESIDUE PND G 101
3
AC3
SOFTWARE
SER A:40 , ARG A:43 , THR A:99 , CYS A:100 , CYS A:103 , HIS A:104 , ARG A:108 , VAL A:109 , GLN A:112 , LEU A:122 , HIS A:126 , TRP A:130 , GLN A:136 , ASN A:489 , PRO A:491 , HEC A:1002 , HOH A:2019 , HOH A:2093 , PRO G:44 , HOH G:104
BINDING SITE FOR RESIDUE HEC A 1001
4
AC4
SOFTWARE
LYS A:11 , CYS A:12 , CYS A:15 , HIS A:16 , ARG A:26 , ILE A:27 , GLN A:30 , ARG A:43 , MET A:44 , HIS A:48 , LEU A:50 , ARG A:114 , PHE A:125 , HEC A:1001 , HOH A:2003 , HOH A:2088 , LEU B:116 , ASN B:117 , ASP B:118 , HIS B:119
BINDING SITE FOR RESIDUE HEC A 1002
[
close Site info
]
SAPs(SNPs)/Variants
(2, 4)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_QADG_PSEPU_001 (S62T, chain G, )
2: VAR_QADG_PSEPU_002 (E66D, chain G, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_QADG_PSEPU_001
*
S
62
T
QADG_PSEPU
---
---
G
S
62
T
2
UniProt
VAR_QADG_PSEPU_002
*
E
66
D
QADG_PSEPU
---
---
G
E
66
D
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(, 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.
(no "Exon" information available for biological units yet)
SCOP Domains
(5, 7)
Info
All SCOP Domains
1a: SCOP_d1jmza1 (A:2-85)
1b: SCOP_d1jmza2 (A:86-162)
2a: SCOP_d1jmzg_ (G:)
3a: SCOP_d1jmzb_ (B:)
4a: SCOP_d1jmza3 (A:282-363)
4b: SCOP_d1jmza4 (A:364-494)
5a: SCOP_d1jmza5 (A:163-281)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Cytochrome c
(308)
Superfamily
:
Cytochrome c
(308)
Family
:
Quinohemoprotein amine dehydrogenase A chain, domains 1 and 2
(4)
Protein domain
:
Quinohemoprotein amine dehydrogenase A chain, domains 1 and 2
(4)
Pseudomonas putida [TaxId: 303]
(2)
1a
d1jmza1
A:2-85
1b
d1jmza2
A:86-162
Fold
:
Non-globular all-alpha subunits of globular proteins
(135)
Superfamily
:
Quinohemoprotein amine dehydrogenase C chain
(4)
Family
:
Quinohemoprotein amine dehydrogenase C chain
(4)
Protein domain
:
Quinohemoprotein amine dehydrogenase C chain
(4)
Pseudomonas putida [TaxId: 303]
(2)
2a
d1jmzg_
G:
Class
:
All beta proteins
(24004)
Fold
:
7-bladed beta-propeller
(245)
Superfamily
:
YVTN repeat-like/Quinoprotein amine dehydrogenase
(31)
Family
:
Quinohemoprotein amine dehydrogenase B chain
(4)
Protein domain
:
Quinohemoprotein amine dehydrogenase B chain
(4)
Pseudomonas putida [TaxId: 303]
(2)
3a
d1jmzb_
B:
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
E set domains
(509)
Family
:
Quinohemoprotein amine dehydrogenase A chain, domains 4 and 5
(4)
Protein domain
:
Quinohemoprotein amine dehydrogenase A chain, domains 4 and 5
(4)
Pseudomonas putida [TaxId: 303]
(2)
4a
d1jmza3
A:282-363
4b
d1jmza4
A:364-494
Fold
:
Streptavidin-like
(225)
Superfamily
:
Quinohemoprotein amine dehydrogenase A chain, domain 3
(4)
Family
:
Quinohemoprotein amine dehydrogenase A chain, domain 3
(4)
Protein domain
:
Quinohemoprotein amine dehydrogenase A chain, domain 3
(4)
Pseudomonas putida [TaxId: 303]
(2)
5a
d1jmza5
A:163-281
[
close SCOP info
]
CATH Domains
(4, 5)
Info
all CATH domains
1a: CATH_1jmzG00 (G:3-79)
2a: CATH_1jmzB00 (B:4-349)
3a: CATH_1jmzA02 (A:175-283)
4a: CATH_1jmzA04 (A:364-486)
4b: CATH_1jmzA03 (A:284-363)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Few Secondary Structures
(1120)
Architecture
:
Irregular
(1120)
Topology
:
Quinohemoprotein amine dehydrogenase
(4)
Homologous Superfamily
:
Quinohemoprotein amine dehydrogenase
(4)
Pseudomonas putida. Organism_taxid: 303. Pseudomonas putida. Organism_taxid: 303.
(2)
1a
1jmzG00
G:3-79
Class
:
Mainly Beta
(13760)
Architecture
:
7 Propellor
(136)
Topology
:
Methylamine Dehydrogenase; Chain H
(136)
Homologous Superfamily
:
YVTN repeat-like/Quinoprotein amine dehydrogenase
(76)
Pseudomonas putida. Organism_taxid: 303. Pseudomonas putida. Organism_taxid: 303.
(2)
2a
1jmzB00
B:4-349
Architecture
:
Beta Barrel
(4804)
Topology
:
Lipocalin
(526)
Homologous Superfamily
:
Quinohemoprotein amine dehydrogenase
(4)
Pseudomonas putida. Organism_taxid: 303. Pseudomonas putida. Organism_taxid: 303.
(2)
3a
1jmzA02
A:175-283
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Pseudomonas putida. Organism_taxid: 303. Pseudomonas putida. Organism_taxid: 303.
(2)
4a
1jmzA04
A:364-486
4b
1jmzA03
A:284-363
[
close CATH info
]
Pfam Domains
(4, 4)
Info
all PFAM domains
1a: PFAM_Dehyd_heme_bind_1jmzA01 (A:97-164)
2a: PFAM_DUF1927_1jmzA02 (A:283-363)
3a: PFAM_DUF1928_1jmzA03 (A:368-493)
4a: PFAM_QH_AmDH_gamma_1jmzG01 (G:3-79)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Cytochrome-c
(108)
Family
:
Dehyd-heme_bind
(4)
Pseudomonas putida (Arthrobacter siderocapsulatus)
(2)
1a
Dehyd-heme_bind-1jmzA01
A:97-164
Clan
:
E-set
(290)
Family
:
DUF1927
(4)
Pseudomonas putida (Arthrobacter siderocapsulatus)
(2)
2a
DUF1927-1jmzA02
A:283-363
Clan
:
no clan defined [family: DUF1928]
(4)
Family
:
DUF1928
(4)
Pseudomonas putida (Arthrobacter siderocapsulatus)
(2)
3a
DUF1928-1jmzA03
A:368-493
Clan
:
no clan defined [family: QH-AmDH_gamma]
(4)
Family
:
QH-AmDH_gamma
(4)
Pseudomonas putida (Arthrobacter siderocapsulatus)
(2)
4a
QH-AmDH_gamma-1jmzG01
G:3-79
[
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 G
Asymmetric Unit 1
Asymmetric Unit 2
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 (157 KB)
Header - Asym.Unit
Biol.Unit 1 (151 KB)
Header - Biol.Unit 1
Biol.Unit 2 (298 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
1JMZ
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help