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1DMR
Asym. Unit
Info
Asym.Unit (139 KB)
Biol.Unit 1 (134 KB)
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(1)
Title
:
OXIDIZED DMSO REDUCTASE FROM RHODOBACTER CAPSULATUS
Authors
:
A. S. Mcalpine, S. Bailey
Date
:
22 Apr 97 (Deposition) - 18 Mar 98 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.82
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Oxidoreductase, Reductase, Dmso, Molybdopterin
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. S. Mcalpine, A. G. Mcewan, A. Shaw, S. Bailey
Molybdenum Active Centre Of Dmso Reductase From Rhodobacter Capsulatus: Crystal Structure Of The Oxidised Enzyme At 1. 82-A Resolution And The Dithionite-Reduced Enzyme At 2. 8-A Resolution
J. Biol. Inorg. Chem. V. 2 690 1997
(for further references see the
PDB file header
)
[
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Hetero Components
(3, 5)
Info
All Hetero Components
1a: MOLYBDENUM(VI) ION (6MOa)
2a: OXYGEN ATOM (Oa)
2b: OXYGEN ATOM (Ob)
3a: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,... (PGDa)
3b: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,... (PGDb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
6MO
1
Ligand/Ion
MOLYBDENUM(VI) ION
2
O
2
Ligand/Ion
OXYGEN ATOM
3
PGD
2
Ligand/Ion
2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINEDINUCLEOTIDE
[
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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: MO (UNKNOWN)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
TYR A:114 , GLY A:115 , TRP A:116 , LYS A:117 , SER A:118 , TYR A:146 , SER A:147 , ARG A:326 , GLY A:432 , GLY A:433 , ASN A:434 , HIS A:438 , GLN A:440 , HIS A:458 , ASP A:459 , PHE A:460 , THR A:463 , ALA A:475 , ARG A:481 , ASP A:511 , ALA A:641 , HIS A:643 , HIS A:649 , SER A:650 , GLN A:651 , GLU A:715 , ASN A:737 , GLY A:754 , GLN A:755 , PGD A:783 , 6MO A:784 , O A:785 , O A:786 , HOH A:799 , HOH A:814 , HOH A:832 , HOH A:840 , HOH A:915
BINDING SITE FOR RESIDUE PGD A 782
2
AC2
SOFTWARE
TRP A:116 , SER A:147 , ALA A:185 , LYS A:190 , THR A:191 , GLN A:193 , ILE A:194 , ILE A:220 , ASP A:221 , PRO A:222 , THR A:225 , PRO A:240 , GLN A:241 , ASP A:243 , GLY A:321 , TRP A:322 , SER A:323 , ARG A:326 , MET A:327 , HIS A:359 , SER A:642 , HIS A:643 , PRO A:644 , PHE A:645 , ARG A:647 , LEU A:648 , HIS A:649 , GLN A:755 , PGD A:782 , 6MO A:784 , O A:786 , HOH A:801 , HOH A:813 , HOH A:824 , HOH A:854
BINDING SITE FOR RESIDUE PGD A 783
3
AC3
SOFTWARE
SER A:147 , PGD A:782 , PGD A:783 , O A:785 , O A:786
BINDING SITE FOR RESIDUE 6MO A 784
4
AC4
SOFTWARE
TYR A:114 , SER A:147 , PGD A:782 , 6MO A:784 , O A:786
BINDING SITE FOR RESIDUE O A 785
5
AC5
SOFTWARE
TYR A:114 , TRP A:116 , SER A:147 , PGD A:782 , PGD A:783 , 6MO A:784 , O A:785 , HOH A:974
BINDING SITE FOR RESIDUE O A 786
6
MO
UNKNOWN
SER A:147
SER SITE.
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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, 2)
Info
All PROSITE Patterns/Profiles
1: MOLYBDOPTERIN_PROK_2 (A:463-480)
2: MOLYBDOPTERIN_PROK_3 (A:676-703)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
MOLYBDOPTERIN_PROK_2
PS00490
Prokaryotic molybdopterin oxidoreductases signature 2.
DSTOR_RHOCA
505-522
1
A:463-480
2
MOLYBDOPTERIN_PROK_3
PS00932
Prokaryotic molybdopterin oxidoreductases signature 3.
DSTOR_RHOCA
718-745
1
A:676-703
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Exons
(0, 0)
Info
All Exons
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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, 2)
Info
All SCOP Domains
1a: SCOP_d1dmra1 (A:626-781)
2a: SCOP_d1dmra2 (A:3-625)
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Classes
(
)
(
)
Folds
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)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Double psi beta-barrel
(111)
Superfamily
:
ADC-like
(88)
Family
:
Formate dehydrogenase/DMSO reductase, C-terminal domain
(41)
Protein domain
:
Dimethylsulfoxide reductase (DMSO reductase)
(11)
Rhodobacter capsulatus [TaxId: 1061]
(10)
1a
d1dmra1
A:626-781
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Formate dehydrogenase/DMSO reductase, domains 1-3
(53)
Superfamily
:
Formate dehydrogenase/DMSO reductase, domains 1-3
(53)
Family
:
Formate dehydrogenase/DMSO reductase, domains 1-3
(53)
Protein domain
:
Dimethylsulfoxide reductase (DMSO reductase)
(11)
Rhodobacter capsulatus [TaxId: 1061]
(10)
2a
d1dmra2
A:3-625
[
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]
CATH Domains
(4, 4)
Info
all CATH domains
1a: CATH_1dmrA02 (A:147-366,A:579-604)
2a: CATH_1dmrA01 (A:54-145,A:378-481,A:507-529)
3a: CATH_1dmrA03 (A:5-32,A:482-499,A:530-570)
4a: CATH_1dmrA04 (A:612-774)
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Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Dimethylsulfoxide Reductase; domain 2
(37)
Homologous Superfamily
:
Dimethylsulfoxide Reductase, domain 2
(37)
Rhodobacter capsulatus. Organism_taxid: 1061. Strain: h123.
(9)
1a
1dmrA02
A:147-366,A:579-604
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.740, no name defined]
(37)
Rhodobacter capsulatus. Organism_taxid: 1061. Strain: h123.
(9)
2a
1dmrA01
A:54-145,A:378-481,A:507-529
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Dimethylsulfoxide Reductase; domain 3
(12)
Homologous Superfamily
:
Dimethylsulfoxide Reductase, domain 3
(12)
Rhodobacter capsulatus. Organism_taxid: 1061. Strain: h123.
(9)
3a
1dmrA03
A:5-32,A:482-499,A:530-570
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
Barwin-like endoglucanases
(75)
Homologous Superfamily
:
[code=2.40.40.20, no name defined]
(63)
Rhodobacter capsulatus. Organism_taxid: 1061. Strain: h123.
(9)
4a
1dmrA04
A:612-774
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Chain A
Asymmetric Unit 1
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Asym.Unit (139 KB)
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