BioLiP

Receptor Information

>1dms Chain A (length=766) Species: 1061 (Rhodobacter capsulatus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

LANGTVMSGSHWGVFTATVENGRATAFTPWEKDPHPTPMLEGVLDSIYSP
TRIKYPMVRREFLEKGVNADRSTRGNGDFVRVSWDQALDLVAAEVKRVEE
TYGPQGVFGGSYGWKSPGRLHNCTTLLRRMLTLAGGYVNGAGDYSTGAAQ
VIMPHVVGTLEVYEQQTAWPVLAENTEVMVFWAADPIKTSQIGWVIPEHG
AYPGLEALKAKGTKVIVIDPVRTKTVEFFGADHVTPKPQTDVAIMLGMAH
TLVAEDLYDKDFIANYTSGFDKFLPYLMGETDSTPKTAEWASDISGVPAE
TIKELARLFKSKRTMLAAGWSMQRMHHGEQAHWMLVTLASMLGQIGLPGG
GFGLSYHYSGGGTPSSSGPALSGITDGGASVIPVARVVDMLENPGAEFDF
NGTRSKFPDVKMAYWVGGNPFVHHQDRNRMVKAWEKLETFIVHDFQWTPT
ARHADIVLPATTSYERNDIETIGDYSNTGILAMKKIVEPLYEARSDYDIF
AAVAERLGKGKEFTEGKDEMGWIKSFYDDAAKQGKAGGVEMPAFDAFWAE
GIVEFPVTDGADFVRYASFREDPLLNPLGTPTGLIEIYSKNIEKMGYDDC
PAHPTWMEPLERLDGPGAKYPLHIAASHPFNRLHSQLNGTVLREGYAVQG
HEPCLMHPDDAAARGIADGDVVRVHNDRGQILTGVKVTDAVMKGVIQIYE
GGWYDPSDVTEAGTLDKYGDVNVLSADIGTSKLAQGNCGQTVLAEVEKYT
GPAVTLTGFVAPKAAE

Ligand ID

PGD

InChI

InChI=1S/C20H24N10O13P2S2/c21-19-26-13-7(15(33)28-19)24-6-12(47)11(46)5(41-17(6)25-13)2-40-45(37,38)43-44(35,36)39-1-4-9(31)10(32)18(42-4)30-3-23-8-14(30)27-20(22)29-16(8)34/h3-6,9-10,17-18,31-32,46-47H,1-2H2,(H,35,36)(H,37,38)(H3,22,27,29,34)(H3,21,25,26,28,33)/t4-,5-,6+,9-,10-,17-,18-/m1/s1

InChIKey

SOFMTHSWCZNJTQ-ILXWUORBSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 1.5.0	c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(=C(C5C(O4)NC6=NC(=NC(=O)C6=N5)N)S)S)O)O)N=C(NC2=O)N
ACDLabs 10.04	O=C6N=C(N=C1C6=NC2C(S)=C(S)C(OC2N1)COP(=O)(O)OP(=O)(O)OCC5OC(n4cnc3c4N=C(N)NC3=O)C(O)C5O)N
CACTVS 3.341	NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)OC[C@H]4O[C@H]5NC6=NC(=NC(=O)C6=N[C@H]5C(=C4S)S)N)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0	c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]4C(=C([C@H]5[C@@H](O4)NC6=NC(=NC(=O)C6=N5)N)S)S)O)O)N=C(NC2=O)N
CACTVS 3.341	NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]5NC6=NC(=NC(=O)C6=N[CH]5C(=C4S)S)N)[CH](O)[CH]3O

Formula

C20 H24 N10 O13 P2 S2

Name

2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE

PDB chain

1dms Chain A Residue 782 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	1dms Crystal structure of dimethyl sulfoxide reductase from Rhodobacter capsulatus at 1.88 A resolution.
Resolution	1.88 Å
Binding residue (original residue number in PDB)	Y114 G115 W116 K117 S118 C125 Y146 S147 R326 G432 G433 H438 H458 D459 F460 R481 D511 A641 H643 H649 S650 Q651 E715 N737 G754
Binding residue (residue number reindexed from 1)	Y112 G113 W114 K115 S116 C123 Y144 S145 R324 G417 G418 H423 H443 D444 F445 R466 D496 A626 H628 H634 S635 Q636 E700 N722 G739
Annotation score	1

Catalytic site (original residue number in PDB)	M41 Y114 W116 D145 S147 T148 V153 I154 W322 S357 Y358 H359 Y360
Catalytic site (residue number reindexed from 1)	M39 Y112 W114 D143 S145 T146 V151 I152 W320 S355 Y356 H357 Y358
Enzyme Commision number	1.7.2.3: trimethylamine-N-oxide reductase. 1.8.5.3: respiratory dimethylsulfoxide reductase.

	Molecular Function
GO:0009055	electron transfer activity
GO:0016491	oxidoreductase activity
GO:0030151	molybdenum ion binding
GO:0043546	molybdopterin cofactor binding
GO:0046872	metal ion binding
GO:0050626	trimethylamine-N-oxide reductase (cytochrome c) activity

	Biological Process
GO:0009061	anaerobic respiration

	Cellular Component
GO:0030288	outer membrane-bounded periplasmic space
GO:0042597	periplasmic space

PDB	RCSB:1dms, PDBe:1dms, PDBj:1dms
PDBsum	1dms
PubMed	8890912
UniProt	Q52675\|DSTOR_RHOCA Dimethyl sulfoxide/trimethylamine N-oxide reductase (Gene Name=dorA)

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Structure of PDB 1dms Chain A Binding Site BS01