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1JMZ
Asym. Unit
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Asym.Unit (157 KB)
Biol.Unit 1 (151 KB)
Biol.Unit 2 (298 KB)
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(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
)
[
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Hetero Components
(4, 5)
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
2
Ligand/Ion
HEME C
2
NI
1
Ligand/Ion
NICKEL (II) ION
3
PND
1
Ligand/Ion
P-NITROPHENYLHYDRAZINE
4
TRQ
1
Mod. Amino Acid
2-AMINO-3-(6,7-DIOXO-6,7-DIHYDRO-1H-INDOL-3-YL)-PROPIONIC ACID
[
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]
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
[
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SAPs(SNPs)/Variants
(2, 2)
Info
(mutated residues are not available)
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)
[
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]
PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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End label:
Sorry, no Info available
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Exons
(0, 0)
Info
All Exons
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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_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)
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Classes
(
)
(
)
Folds
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)
(
)
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)
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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)
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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
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