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1W6S
Asym. Unit
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Asym.Unit (486 KB)
Biol.Unit 1 (479 KB)
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(1)
Title
:
THE HIGH RESOLUTION STRUCTURE OF METHANOL DEHYDROGENASE FROM METHYLOBACTERIUM EXTORQUENS
Authors
:
P. A. Williams, L. Coates, F. Mohammed, R. Gill, P. T. Erskine, S. P. Wood, C. Anthony, J. B. Cooper
Date
:
23 Aug 04 (Deposition) - 21 Dec 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.20
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Anisotropic, Electron Transfer, Oxidoreductase, Calcium- Binding, Methanol Utilization, Pqq
(Keyword Search:
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)
Reference
:
P. A. Williams, L. Coates, F. Mohammed, R. Gill, P. T. Erskine, S. P. Wood, C. Anthony, J. B. Cooper
The Atomic Resolution Structure Of Methanol Dehydrogenase From Methylobacterium Extorquens
Acta Crystallogr. , Sect. D V. 61 75 2005
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Hetero Components
(3, 7)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
3a: PYRROLOQUINOLINE QUINONE (PQQa)
3b: PYRROLOQUINOLINE QUINONE (PQQb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
2
Ligand/Ion
CALCIUM ION
2
GOL
3
Ligand/Ion
GLYCEROL
3
PQQ
2
Ligand/Ion
PYRROLOQUINOLINE QUINONE
[
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Sites
(7, 7)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLU A:177 , ASN A:261 , ASP A:303 , PQQ A:1596
BINDING SITE FOR RESIDUE CA A1599
2
AC2
SOFTWARE
GLU C:2177 , ASN C:2261 , ASP C:2303 , PQQ C:3597
BINDING SITE FOR RESIDUE CA C3599
3
AC3
SOFTWARE
GLU A:55 , 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 , ASN A:261 , ARG A:331 , ASN A:394 , TRP A:476 , GLY A:539 , TRP A:540 , CA A:1599 , HOH A:2329 , HOH A:2602
BINDING SITE FOR RESIDUE PQQ A1596
4
AC4
SOFTWARE
GLU C:2055 , CYS C:2104 , VAL C:2107 , ARG C:2109 , THR C:2159 , SER C:2174 , GLY C:2175 , ALA C:2176 , GLU C:2177 , THR C:2241 , TRP C:2243 , ASN C:2261 , ARG C:2331 , ASN C:2394 , TRP C:2476 , GLY C:2539 , TRP C:2540 , CA C:3599 , HOH C:4356 , HOH C:4609
BINDING SITE FOR RESIDUE PQQ C3597
5
AC5
SOFTWARE
ALA A:43 , GLY A:584 , PRO A:585 , TYR A:586 , ASP A:587 , HOH A:2603 , HOH A:2604 , ARG C:2041 , TRP C:2508 , LYS C:2509
BINDING SITE FOR RESIDUE GOL A1597
6
AC6
SOFTWARE
HIS A:525 , THR A:528 , TYR A:530 , LYS A:583 , PRO A:585 , HOH A:2132 , HOH A:2135 , HOH A:2605
BINDING SITE FOR RESIDUE GOL A1598
7
AC7
SOFTWARE
TRP A:508 , LYS A:509 , HOH A:2095 , ALA C:2043 , GLY C:2582 , GLY C:2584 , PRO C:2585 , TYR C:2586 , ASP C:2587 , HOH C:4610
BINDING SITE FOR RESIDUE GOL C3598
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: BACTERIAL_PQQ_1 (A:13-41,C:2013-2041)
2: BACTERIAL_PQQ_2 (A:243-264,C:2243-2264)
;
View:
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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_METEA
40-68
2
A:13-41
C:2013-2041
2
BACTERIAL_PQQ_2
PS00364
Bacterial quinoprotein dehydrogenases signature 2.
DHM1_METEA
270-291
2
A:243-264
C:2243-2264
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Exons
(0, 0)
Info
All Exons
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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
(2, 4)
Info
All SCOP Domains
1a: SCOP_d1w6sb_ (B:)
1b: SCOP_d1w6sd_ (D:)
2a: SCOP_d1w6sa_ (A:)
2b: SCOP_d1w6sc_ (C:)
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Classes
(
)
(
)
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(
)
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(
)
(
)
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)
Methylobacterium extorquens [TaxId: 408]
(3)
1a
d1w6sb_
B:
1b
d1w6sd_
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)
Methylobacterium extorquens [TaxId: 408]
(3)
2a
d1w6sa_
A:
2b
d1w6sc_
C:
[
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CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1w6sB00 (B:1001-1073)
1b: CATH_1w6sD00 (D:3001-3073)
2a: CATH_1w6sA00 (A:1-596)
2b: CATH_1w6sC00 (C:2001-2597)
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)
(
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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)
Methylobacterium extorquens. Organism_taxid: 408.
(3)
1a
1w6sB00
B:1001-1073
1b
1w6sD00
D:3001-3073
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)
Methylobacterium extorquens. Organism_taxid: 408.
(3)
2a
1w6sA00
A:1-596
2b
1w6sC00
C:2001-2597
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Pfam Domains
(2, 10)
Info
all PFAM domains
1a: PFAM_PQQ_1w6sC01 (C:2485-2522)
1b: PFAM_PQQ_1w6sC02 (C:2485-2522)
1c: PFAM_PQQ_1w6sC03 (C:2485-2522)
1d: PFAM_PQQ_1w6sC04 (C:2485-2522)
1e: PFAM_PQQ_1w6sC05 (C:2485-2522)
1f: PFAM_PQQ_1w6sC06 (C:2485-2522)
1g: PFAM_PQQ_1w6sC07 (C:2485-2522)
1h: PFAM_PQQ_1w6sC08 (C:2485-2522)
2a: PFAM_MDH_1w6sD01 (D:3001-3071)
2b: PFAM_MDH_1w6sD02 (D:3001-3071)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Beta_propeller
(192)
Family
:
PQQ
(3)
Methylobacterium extorquens (strain ATCC 14718 / DSM 1338 / AM1)
(1)
1a
PQQ-1w6sC01
C:2485-2522
1b
PQQ-1w6sC02
C:2485-2522
1c
PQQ-1w6sC03
C:2485-2522
1d
PQQ-1w6sC04
C:2485-2522
1e
PQQ-1w6sC05
C:2485-2522
1f
PQQ-1w6sC06
C:2485-2522
1g
PQQ-1w6sC07
C:2485-2522
1h
PQQ-1w6sC08
C:2485-2522
Clan
:
no clan defined [family: MDH]
(2)
Family
:
MDH
(2)
Methylobacterium extorquens (strain ATCC 14718 / DSM 1338 / AM1)
(1)
2a
MDH-1w6sD01
D:3001-3071
2b
MDH-1w6sD02
D:3001-3071
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