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1PBY
Asym. Unit
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Asym.Unit (176 KB)
Biol.Unit 1 (170 KB)
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(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
)
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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:
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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
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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:
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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
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
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;
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End label:
Sorry, no Info available
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Exons
(0, 0)
Info
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All Exon Boundaries
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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)
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)
(
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(
)
(
)
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)
(
)
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
[
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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)
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)
Homologous Superfamilies
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)
(
)
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
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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:
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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
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