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.
1PBY
Asym. Unit
Info
Asym.Unit (176 KB)
Biol.Unit 1 (170 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 PHENYLHYDRAZINE ADDUCT OF THE QUINOHEMOPROTEIN AMINE DEHYDROGENASE FROM PARACOCCUS DENITRIFICANS AT 1.7 A RESOLUTION
Authors
:
S. Datta, T. Ikeda, K. Kano, F. S. Mathews
Date
:
15 May 03 (Deposition) - 02 Sep 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.70
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (1x)
Keywords
:
Quinohemoprotein, Amine Dehydrogenase, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Datta, T. Ikeda, K. Kano, F. S. Mathews
Structure Of The Phenylhydrazine Adduct Of The Quinohemoprotein Amine Dehydrogenase From Paracoccus Denitrificans At 1. 7 A Resolution.
Acta Crystallogr. , Sect. D V. 59 1551 2003
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 7)
Info
All Hetero Components
1a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
1b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
2a: TERTIARY-BUTYL ALCOHOL (TBUa)
2b: TERTIARY-BUTYL ALCOHOL (TBUb)
2c: TERTIARY-BUTYL ALCOHOL (TBUc)
2d: TERTIARY-BUTYL ALCOHOL (TBUd)
3a: TRW3-(2-AMINO-3-HYDROXY-PROPYL)-6-... (TRWa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
HEM
2
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
2
TBU
4
Ligand/Ion
TERTIARY-BUTYL ALCOHOL
3
TRW
1
Mod. Amino Acid
TRW3-(2-AMINO-3-HYDROXY-PROPYL)-6-(N'-CYCLOHEXYL-HYDRAZINO)OCTAHYDRO-INDOL-7-OL
[
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:10 , CYS A:11 , CYS A:14 , HIS A:15 , ARG A:25 , ILE A:26 , TRP A:36 , THR A:39 , ARG A:42 , MET A:43 , HIS A:47 , VAL A:49 , ARG A:114 , PHE A:125 , HEM A:992 , HOH A:2001 , HOH A:2007 , LEU B:107 , THR B:108 , HIS B:109
BINDING SITE FOR RESIDUE HEM A 991
2
AC2
SOFTWARE
LYS A:31 , THR A:39 , ARG A:42 , ARG A:45 , THR A:99 , CYS A:100 , ARG A:102 , CYS A:103 , HIS A:104 , ARG A:108 , VAL A:109 , GLN A:112 , ARG A:114 , LEU A:122 , HIS A:126 , PHE A:130 , LEU A:133 , GLN A:136 , HEM A:991 , HOH A:1999 , HOH A:2008 , HOH A:2030 , HOH A:2176 , PRO C:44 , HOH C:80
BINDING SITE FOR RESIDUE HEM A 992
3
AC3
SOFTWARE
GLY A:236 , GLU B:162
BINDING SITE FOR RESIDUE TBU A 1993
4
AC4
SOFTWARE
HOH A:2412 , ARG B:128
BINDING SITE FOR RESIDUE TBU A 1994
5
AC5
SOFTWARE
SER A:303 , GLU A:316 , ALA A:318 , ILE B:209 , ASP B:213
BINDING SITE FOR RESIDUE TBU B 1995
6
AC6
SOFTWARE
GLU B:132 , HOH B:2247 , HOH B:2456
BINDING SITE FOR RESIDUE TBU B 1996
[
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
(5, 7)
Info
All SCOP Domains
1a: SCOP_d1pbya1 (A:1-85)
1b: SCOP_d1pbya2 (A:86-165)
2a: SCOP_d1pbyc_ (C:)
3a: SCOP_d1pbyb_ (B:)
4a: SCOP_d1pbya3 (A:274-351)
4b: SCOP_d1pbya4 (A:352-489)
5a: SCOP_d1pbya5 (A:166-273)
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)
Paracoccus denitrificans [TaxId: 266]
(2)
1a
d1pbya1
A:1-85
1b
d1pbya2
A:86-165
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)
Paracoccus denitrificans [TaxId: 266]
(2)
2a
d1pbyc_
C:
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)
Paracoccus denitrificans [TaxId: 266]
(2)
3a
d1pbyb_
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)
Paracoccus denitrificans [TaxId: 266]
(2)
4a
d1pbya3
A:274-351
4b
d1pbya4
A:352-489
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)
Paracoccus denitrificans [TaxId: 266]
(2)
5a
d1pbya5
A:166-273
[
close SCOP info
]
CATH Domains
(4, 5)
Info
all CATH domains
1a: CATH_1pbyC00 (C:1-79)
2a: CATH_1pbyB00 (B:1-337)
3a: CATH_1pbyA02 (A:169-274)
4a: CATH_1pbyA04 (A:351-481)
4b: CATH_1pbyA03 (A:275-350)
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)
Paracoccus denitrificans. Organism_taxid: 266.
(1)
1a
1pbyC00
C:1-79
Class
:
Mainly Beta
(13760)
Architecture
:
7 Propellor
(136)
Topology
:
Methylamine Dehydrogenase; Chain H
(136)
Homologous Superfamily
:
YVTN repeat-like/Quinoprotein amine dehydrogenase
(76)
Paracoccus denitrificans. Organism_taxid: 266.
(3)
2a
1pbyB00
B:1-337
Architecture
:
Beta Barrel
(4804)
Topology
:
Lipocalin
(526)
Homologous Superfamily
:
Quinohemoprotein amine dehydrogenase
(4)
Paracoccus denitrificans. Organism_taxid: 266.
(1)
3a
1pbyA02
A:169-274
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Paracoccus denitrificans. Organism_taxid: 266.
(2)
4a
1pbyA04
A:351-481
4b
1pbyA03
A:275-350
[
close CATH info
]
Pfam Domains
(4, 4)
Info
all PFAM domains
1a: PFAM_Dehyd_heme_bind_1pbyA01 (A:97-164)
2a: PFAM_DUF1927_1pbyA02 (A:275-351)
3a: PFAM_DUF1928_1pbyA03 (A:356-488)
4a: PFAM_QH_AmDH_gamma_1pbyC01 (C:2-79)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Cytochrome-c
(108)
Family
:
Dehyd-heme_bind
(4)
Paracoccus denitrificans
(2)
1a
Dehyd-heme_bind-1pbyA01
A:97-164
Clan
:
E-set
(290)
Family
:
DUF1927
(4)
Paracoccus denitrificans
(2)
2a
DUF1927-1pbyA02
A:275-351
Clan
:
no clan defined [family: DUF1928]
(4)
Family
:
DUF1928
(4)
Paracoccus denitrificans
(2)
3a
DUF1928-1pbyA03
A:356-488
Clan
:
no clan defined [family: QH-AmDH_gamma]
(4)
Family
:
QH-AmDH_gamma
(4)
Paracoccus denitrificans
(2)
4a
QH-AmDH_gamma-1pbyC01
C:2-79
[
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 C
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 (176 KB)
Header - Asym.Unit
Biol.Unit 1 (170 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
1PBY
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
