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1LRW
Asym. Unit
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Asym.Unit (231 KB)
Biol.Unit 1 (226 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF METHANOL DEHYDROGENASE FROM P. DENITRIFICANS
Authors
:
Z. -X. Xia, W. -W. Dai, Y. -N. He, S. A. White, F. S. Mathews, V. L. Davidson
Date
:
16 May 02 (Deposition) - 12 Aug 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Heavy Subunits: 8-Fold Beta-Propeller Superbarrel, Oxidoreductase
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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)
Reference
:
Z. -X. Xia, W. -W. Dai, Y. -N. He, S. A. White, F. S. Mathews, V. L. Davidson
X-Ray Structure Of Methanol Dehydrogenase From Paracoccus Denitrificans And Molecular Modeling Of Its Interactions With Cytochrome C-551I
J. Biol. Inorg. Chem. V. 8 843 2003
(for further references see the
PDB file header
)
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Hetero Components
(2, 4)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
2a: PYRROLOQUINOLINE QUINONE (PQQa)
2b: PYRROLOQUINOLINE QUINONE (PQQb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
2
Ligand/Ion
CALCIUM ION
2
PQQ
2
Ligand/Ion
PYRROLOQUINOLINE QUINONE
[
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Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLU A:177 , ASN A:261 , ASP A:303 , PQQ A:701
BINDING SITE FOR RESIDUE CA A 702
2
AC2
SOFTWARE
GLU C:177 , ASN C:261 , PQQ C:701
BINDING SITE FOR RESIDUE CA C 702
3
AC3
SOFTWARE
GLU A:55 , CYS A:103 , CYS A:104 , VAL A:107 , ARG A:109 , THR A:159 , SER A:174 , GLY A:175 , ALA A:176 , GLU A:177 , THR A:241 , TRP A:243 , ARG A:331 , TRP A:476 , GLY A:539 , TRP A:540 , CA A:702 , HOH A:726 , HOH A:820
BINDING SITE FOR RESIDUE PQQ A 701
4
AC4
SOFTWARE
GLU C:55 , CYS C:103 , ARG C:109 , THR C:159 , SER C:174 , GLY C:175 , ALA C:176 , GLU C:177 , THR C:241 , TRP C:243 , ASN C:261 , ARG C:331 , TRP C:476 , GLY C:539 , TRP C:540 , CA C:702 , HOH C:771 , HOH C:772 , HOH C:863
BINDING SITE FOR RESIDUE PQQ C 701
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: BACTERIAL_PQQ_1 (A:13-41,C:13-41)
2: BACTERIAL_PQQ_2 (A:243-264,C:243-264)
;
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
BACTERIAL_PQQ_1
PS00363
Bacterial quinoprotein dehydrogenases signature 1.
DHM1_PARDE
45-73
2
A:13-41
C:13-41
2
BACTERIAL_PQQ_2
PS00364
Bacterial quinoprotein dehydrogenases signature 2.
DHM1_PARDE
275-296
2
A:243-264
C:243-264
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Exons
(0, 0)
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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
(2, 4)
Info
All SCOP Domains
1a: SCOP_d1lrwb_ (B:)
1b: SCOP_d1lrwd_ (D:)
2a: SCOP_d1lrwa_ (A:)
2b: SCOP_d1lrwc_ (C:)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
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
:
Methanol dehydrogenase, light chain
(9)
Paracoccus denitrificans [TaxId: 266]
(1)
1a
d1lrwb_
B:
1b
d1lrwd_
D:
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
:
Methanol dehydrogenase, heavy chain
(9)
Paracoccus denitrificans [TaxId: 266]
(1)
2a
d1lrwa_
A:
2b
d1lrwc_
C:
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CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1lrwB00 (B:1-83)
1b: CATH_1lrwD00 (D:1-83)
2a: CATH_1lrwA00 (A:1-600)
2b: CATH_1lrwC00 (C:1-600)
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(
)
(
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Architectures
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)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Few Secondary Structures
(1120)
Architecture
:
Irregular
(1120)
Topology
:
Methanol Dehydrogenase; Chain B
(10)
Homologous Superfamily
:
Methanol Dehydrogenase, chain B
(10)
Paracoccus denitrificans. Organism_taxid: 266.
(1)
1a
1lrwB00
B:1-83
1b
1lrwD00
D:1-83
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)
Paracoccus denitrificans. Organism_taxid: 266.
(1)
2a
1lrwA00
A:1-600
2b
1lrwC00
C:1-600
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Pfam Domains
(2, 10)
Info
all PFAM domains
1a: PFAM_PQQ_1lrwC01 (C:485-522)
1b: PFAM_PQQ_1lrwC02 (C:485-522)
1c: PFAM_PQQ_1lrwC03 (C:485-522)
1d: PFAM_PQQ_1lrwC04 (C:485-522)
1e: PFAM_PQQ_1lrwC05 (C:485-522)
1f: PFAM_PQQ_1lrwC06 (C:485-522)
1g: PFAM_PQQ_1lrwC07 (C:485-522)
1h: PFAM_PQQ_1lrwC08 (C:485-522)
2a: PFAM_MDH_1lrwD01 (D:1-71)
2b: PFAM_MDH_1lrwD02 (D:1-71)
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Clans
(
)
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Families
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)
(
)
Organisms
(
)
(
)
Clan
:
Beta_propeller
(192)
Family
:
PQQ
(3)
Paracoccus denitrificans
(1)
1a
PQQ-1lrwC01
C:485-522
1b
PQQ-1lrwC02
C:485-522
1c
PQQ-1lrwC03
C:485-522
1d
PQQ-1lrwC04
C:485-522
1e
PQQ-1lrwC05
C:485-522
1f
PQQ-1lrwC06
C:485-522
1g
PQQ-1lrwC07
C:485-522
1h
PQQ-1lrwC08
C:485-522
Clan
:
no clan defined [family: MDH]
(2)
Family
:
MDH
(2)
Paracoccus denitrificans
(1)
2a
MDH-1lrwD01
D:1-71
2b
MDH-1lrwD02
D:1-71
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Asym.Unit (231 KB)
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