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2D0V
Biol. Unit 2
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Asym.Unit (338 KB)
Biol.Unit 1 (225 KB)
Biol.Unit 2 (221 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF METHANOL DEHYDROGENASE FROM HYPHOMICROBIUM DENITRIFICANS
Authors
:
M. Nojiri, D. Hira, K. Yamaguchi, S. Suzuki
Date
:
09 Aug 05 (Deposition) - 09 Aug 06 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.49
Chains
:
Asym. Unit : A,B,D,E,I,J
Biol. Unit 1: A,B (2x)
Biol. Unit 2: D,E,I,J (1x)
Keywords
:
Electron Transfer, Oxidoreductase, Calcium Binding, Methanol, Pqq
(Keyword Search:
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Reference
:
M. Nojiri, D. Hira, K. Yamaguchi, T. Okajima, K. Tanizawa, S. Suzuki
Crystal Structures Of Cytochrome C(L) And Methanol Dehydrogenase From Hyphomicrobium Denitrificans: Structural And Mechanistic Insights Into Interactions Between The Two Proteins
Biochemistry V. 45 3481 2006
(for further references see the
PDB file header
)
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Hetero Components
(1, 2)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
2a: PYRROLOQUINOLINE QUINONE (PQQa)
2b: PYRROLOQUINOLINE QUINONE (PQQb)
2c: PYRROLOQUINOLINE QUINONE (PQQc)
View:
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Label:
No.
Name
Count
Type
Full Name
1
CA
-1
Ligand/Ion
CALCIUM ION
2
PQQ
2
Ligand/Ion
PYRROLOQUINOLINE QUINONE
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Sites
(4, 4)
Info
All Sites
1: AC2 (SOFTWARE)
2: AC3 (SOFTWARE)
3: AC5 (SOFTWARE)
4: AC6 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC2
SOFTWARE
GLU D:177 , ASN D:261 , ASP D:303 , PQQ D:601
BINDING SITE FOR RESIDUE CA D 775
2
AC3
SOFTWARE
GLU I:177 , ASN I:261 , PQQ I:601
BINDING SITE FOR RESIDUE CA I 775
3
AC5
SOFTWARE
GLU D:55 , ARG D:109 , THR D:159 , SER D:174 , GLY D:175 , ALA D:176 , GLU D:177 , THR D:241 , TRP D:243 , ASN D:261 , ASP D:303 , ARG D:331 , ASN D:394 , GLN D:395 , TRP D:476 , GLY D:539 , TRP D:540 , PRO D:541 , CA D:775 , HOH D:788
BINDING SITE FOR RESIDUE PQQ D 601
4
AC6
SOFTWARE
GLU I:55 , CYS I:104 , ARG I:109 , THR I:159 , SER I:174 , GLY I:175 , ALA I:176 , GLU I:177 , THR I:241 , TRP I:243 , ASP I:303 , ARG I:331 , ASN I:394 , GLN I:395 , TRP I:476 , GLY I:539 , TRP I:540 , CA I:775 , HOH I:926
BINDING SITE FOR RESIDUE PQQ I 601
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SAPs(SNPs)/Variants
(0, 0)
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PROSITE Patterns/Profiles
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Exons
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Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
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SCOP Domains
(2, 6)
Info
All SCOP Domains
1a: SCOP_d2d0vb_ (B:)
1b: SCOP_d2d0ve_ (E:)
1c: SCOP_d2d0vj_ (J:)
2a: SCOP_d2d0va_ (A:)
2b: SCOP_d2d0vd_ (D:)
2c: SCOP_d2d0vi_ (I:)
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Non-globular all-alpha subunits of globular proteins
(135)
Superfamily
:
Methanol dehydrogenase subunit
(10)
Family
:
Methanol dehydrogenase subunit
(10)
Protein domain
:
automated matches
(1)
Hyphomicrobium denitrificans [TaxId: 53399]
(1)
1a
d2d0vb_
B:
1b
d2d0ve_
E:
1c
d2d0vj_
J:
Class
:
All beta proteins
(24004)
Fold
:
8-bladed beta-propeller
(135)
Superfamily
:
Quinoprotein alcohol dehydrogenase-like
(14)
Family
:
Quinoprotein alcohol dehydrogenase-like
(13)
Protein domain
:
automated matches
(1)
Hyphomicrobium denitrificans [TaxId: 53399]
(1)
2a
d2d0va_
A:
2b
d2d0vd_
D:
2c
d2d0vi_
I:
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CATH Domains
(2, 6)
Info
all CATH domains
1a: CATH_2d0vE00 (E:1-68)
1b: CATH_2d0vB00 (B:1-70)
1c: CATH_2d0vJ00 (J:1-70)
2a: CATH_2d0vI00 (I:1-595)
2b: CATH_2d0vA00 (A:1-597)
2c: CATH_2d0vD00 (D:1-597)
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Organisms
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(
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Class
:
Few Secondary Structures
(1120)
Architecture
:
Irregular
(1120)
Topology
:
Methanol Dehydrogenase; Chain B
(10)
Homologous Superfamily
:
Methanol Dehydrogenase, chain B
(10)
Hyphomicrobium denitrificans. Organism_taxid: 53399. Strain: a3151.
(1)
1a
2d0vE00
E:1-68
1b
2d0vB00
B:1-70
1c
2d0vJ00
J:1-70
Class
:
Mainly Beta
(13760)
Architecture
:
8 Propellor
(110)
Topology
:
Methanol Dehydrogenase; Chain A
(110)
Homologous Superfamily
:
[code=2.140.10.10, no name defined]
(14)
Hyphomicrobium denitrificans. Organism_taxid: 53399. Strain: a3151.
(1)
2a
2d0vI00
I:1-595
2b
2d0vA00
A:1-597
2c
2d0vD00
D:1-597
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Pfam Domains
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Asymmetric Unit 1
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Asym.Unit (338 KB)
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Header - Biol.Unit 1
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