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1E5V
Asym. Unit
Info
Asym.Unit (258 KB)
Biol.Unit 1 (128 KB)
Biol.Unit 2 (128 KB)
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(1)
Title
:
OXIDIZED DMSO REDUCTASE EXPOSED TO HEPES BUFFER
Authors
:
S. Bailey, B. Bennett, B. Adams, A. T. Smith, R. C. Bray
Date
:
03 Aug 00 (Deposition) - 25 Aug 00 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A,C
Biol. Unit 1: A (1x)
Biol. Unit 2: C (1x)
Keywords
:
Oxidoreductase, Reductase, Dmso, Molybdopterin
(Keyword Search:
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)
Reference
:
R. C. Bray, B. Adams, A. T. Smith, B. Bennett, S. Bailey
Reversible Dissociation Of Thiolate Ligands From Molybdenum In An Enzyme Of The Dimethyl Sulfoxide Reductase Family
Biochemistry V. 39 11258 2000
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Hetero Components
(3, 8)
Info
All Hetero Components
1a: MOLYBDENUM (IV)OXIDE (2MOa)
1b: MOLYBDENUM (IV)OXIDE (2MOb)
2a: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,... (PGDa)
2b: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,... (PGDb)
2c: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,... (PGDc)
2d: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,... (PGDd)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
2MO
2
Ligand/Ion
MOLYBDENUM (IV)OXIDE
2
PGD
4
Ligand/Ion
2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
3
SO4
2
Ligand/Ion
SULFATE ION
[
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Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
LYS A:117 , ARG A:121 , ASN A:124 , TRP A:196 , HOH A:2048 , HOH A:2260 , HOH A:2261
BINDING SITE FOR RESIDUE SO4 A 901
2
AC2
SOFTWARE
LYS C:117 , ARG C:121 , ASN C:124 , TRP C:196 , HOH C:2046
BINDING SITE FOR RESIDUE SO4 C 901
3
AC3
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 , ARG A:481 , ASP A:511 , ALA A:641 , HIS A:643 , LEU A:648 , HIS A:649 , SER A:650 , GLN A:651 , GLU A:715 , ASN A:737 , GLY A:754 , GLN A:755 , PGD A:802 , 2MO A:803 , HOH A:2230 , HOH A:2257 , HOH A:2258
BINDING SITE FOR RESIDUE PGD A 801
4
AC4
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:801 , 2MO A:803 , HOH A:2069 , HOH A:2071 , HOH A:2226 , HOH A:2259
BINDING SITE FOR RESIDUE PGD A 802
5
AC5
SOFTWARE
TYR A:114 , TRP A:116 , TYR A:146 , SER A:147 , PGD A:801 , PGD A:802
BINDING SITE FOR RESIDUE 2MO A 803
6
AC6
SOFTWARE
TYR C:114 , GLY C:115 , TRP C:116 , LYS C:117 , SER C:118 , TYR C:146 , SER C:147 , ARG C:326 , GLY C:432 , GLY C:433 , ASN C:434 , HIS C:438 , GLN C:440 , HIS C:458 , ASP C:459 , PHE C:460 , THR C:463 , ALA C:475 , ARG C:481 , ASP C:511 , ALA C:641 , HIS C:643 , HIS C:649 , SER C:650 , GLN C:651 , GLU C:715 , ASN C:737 , GLY C:754 , GLN C:755 , PGD C:802 , 2MO C:803 , HOH C:2157 , HOH C:2180 , HOH C:2203 , HOH C:2204 , HOH C:2205
BINDING SITE FOR RESIDUE PGD C 801
7
AC7
SOFTWARE
MET C:41 , TRP C:116 , SER C:147 , ALA C:185 , LYS C:190 , THR C:191 , GLN C:193 , ILE C:194 , ILE C:220 , ASP C:221 , PRO C:222 , PRO C:240 , GLN C:241 , ASP C:243 , GLY C:321 , TRP C:322 , SER C:323 , ARG C:326 , MET C:327 , HIS C:359 , SER C:642 , HIS C:643 , PRO C:644 , PHE C:645 , ARG C:647 , LEU C:648 , HIS C:649 , GLN C:755 , PGD C:801 , 2MO C:803 , HOH C:2063 , HOH C:2065 , HOH C:2177 , HOH C:2206
BINDING SITE FOR RESIDUE PGD C 802
8
AC8
SOFTWARE
TYR C:114 , TRP C:116 , TYR C:146 , SER C:147 , PGD C:801 , PGD C:802
BINDING SITE FOR RESIDUE 2MO C 803
[
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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: MOLYBDOPTERIN_PROK_2 (A:463-480,C:463-480)
2: MOLYBDOPTERIN_PROK_3 (A:676-703,C:676-703)
;
View:
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Label:
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
2
A:463-480
C:463-480
2
MOLYBDOPTERIN_PROK_3
PS00932
Prokaryotic molybdopterin oxidoreductases signature 3.
DSTOR_RHOCA
718-745
2
A:676-703
C:676-703
[
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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_d1e5va1 (A:626-781)
1b: SCOP_d1e5vc1 (C:626-781)
2a: SCOP_d1e5va2 (A:3-625)
2b: SCOP_d1e5vc2 (C:3-625)
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(
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Protein Domains
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)
(
)
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
d1e5va1
A:626-781
1b
d1e5vc1
C: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
d1e5va2
A:3-625
2b
d1e5vc2
C:3-625
[
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CATH Domains
(4, 8)
Info
all CATH domains
1a: CATH_1e5vA02 (A:147-366,A:579-604)
1b: CATH_1e5vC02 (C:147-366,C:579-604)
2a: CATH_1e5vA01 (A:54-145,A:378-481,A:507-529)
2b: CATH_1e5vC01 (C:54-145,C:378-481,C:507-529)
3a: CATH_1e5vA03 (A:5-32,A:482-499,A:530-570)
3b: CATH_1e5vC03 (C:5-32,C:482-499,C:530-570)
4a: CATH_1e5vA04 (A:612-774)
4b: CATH_1e5vC04 (C:612-774)
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)
(
)
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
1e5vA02
A:147-366,A:579-604
1b
1e5vC02
C:147-366,C: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
1e5vA01
A:54-145,A:378-481,A:507-529
2b
1e5vC01
C:54-145,C:378-481,C: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
1e5vA03
A:5-32,A:482-499,A:530-570
3b
1e5vC03
C:5-32,C:482-499,C: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
1e5vA04
A:612-774
4b
1e5vC04
C:612-774
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Pfam Domains
(0, 0)
Info
all PFAM domains
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