Structure of PDB 4c7y Chain A Binding Site BS05

Receptor Information

>4c7y Chain A (length=907) Species: 879 (Megalodesulfovibrio gigas)

MIQKVITVNGIEQNLFVDAEALLSDVLRQQLGLTGVKVGCEQGQCGACSV
ILDGKVVRACVTKMKRVADGAQITTIEGVGQPENLHPLQKAWVLHGGAQC
GFCSPGFIVSAKGLLDTNADPSREDVRDWFQKHRNACRCTGYKPLVDAVM
DAAAVINGKKPETDLEFKMPADGRIWGSKYPRPTAVAKVTGTLDYGADLG
LKMPAGTLHLAMVQAKVSHANIKGIDTSEALTMPGVHSVITHKDVKGKNR
ITGLITFPTNKGDGWDRPILCDEKVFQYGDCIALVCADSEANARAAAEKV
KVDLEELPAYMSGPAAAAEDAIEIHPGTPNVYFEQPIVKGEDTGPIFASA
DVTVEGDFYVGRQPHMPIEPDVAFAYMGDDGKCYIHSKSIGVHLHLYMIA
PGVGLEPDQLVLVANPMGGTFGYKFSPTSEALVAVAAMATGRPVHLRYNY
QQQQQYTGKRSPWEMNVKFAAKKDGTLLAMESDWLVDHGPYSEFGDLLTL
RGAQFIGAGYNIPNIRGLGRTVATNHVWGSAFRGYGAPQSMFASECLMDM
LAEKLGMDPLELRYKNAYRPGDTNPTGQEPEVFSLPDMIDQLRPKYQAAL
EKAQKESTATHKKGVGISIGVYGSGLDGPDASEAWAELNADGTITVHTAW
EDHGQGADIGCVGTAHEALRPMGVAPEKIKFTWPNTATTPNSGPSGGSRQ
QVMTGNAIRVACENLLKACEKPGGGYYTYDELKAADKPTKITGNWTASGA
THCDAVTGLGKPFVVYMYGVFMAEVTVDVATGQTTVDGMTLMADLGSLCN
QLATDGQIYGGLAQGIGLALSEDFEDIKKHATLVGAGFPFIKQIPDKLDI
VYVNHPRPDGPFGASGVGELPLTSPHAAIINAIKSATGVRIYRLPAYPEK
VLEALKA

Ligand information

• Ligand ID: PCD
• InChI: InChI=1S/C19H26N8O13P2S2.Mo.H2O.2O/c20-7-1-2-27(19(31)22-7)17-11(29)10(28)5(39-17)3-36-41(32,33)40-42(34,35)37-4-6-12(43)13(44)8-16(38-6)24-14-9(23-8)15(30)26-18(21)25-14;;;;/h1-2,5-6,8,10-11,16-17,23,28-29,43-44H,3-4H2,(H,32,33)(H,34,35)(H2,20,22,31)(H4,21,24,25,26,30);;1H2;;/q;+2;;;/p-2/t5-,6-,8+,10-,11-,16-,17-;;;;/m1..../s1
• InChIKey: YEBYDVFRFUQMER-MQPNXHJTSA-L
• SMILES:
  CACTVS 3.385: O.NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@H]3O[C@H]4Nc5nc(N)nc(O)c5N[C@H]4C6=C3S[Mo](=O)(=O)S6)[C@@H](O)[C@H]2O
  OpenEye OEToolkits 2.0.7: C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OCC3C4=C(C5C(O3)Nc6c(c(nc(n6)N)O)N5)S[Mo](=O)(=O)(S4)[OH2])O)O
  CACTVS 3.385: O.NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]4Nc5nc(N)nc(O)c5N[CH]4C6=C3S[Mo](=O)(=O)S6)[CH](O)[CH]2O
  OpenEye OEToolkits 2.0.7: C1=CN(C(=O)N=C1N)[C@H]2C([C@@H]([C@H](O2)CO[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]3C4=C([C@H]5[C@@H](O3)Nc6c(c(nc(n6)N)O)N5)S[Mo](=O)(=O)(S4)[OH2])O)O
• Formula: C19 H26 Mo N8 O16 P2 S2
• Name: (MOLYBDOPTERIN-CYTOSINE DINUCLEOTIDE-S,S)-DIOXO-AQUA-MOLYBDENUM(V);
  MOLYBDENUM COFACTOR;
  MOCO
• PDB chain: 4c7y Chain A Residue 921

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4c7y Kinetic and Structural Studies of Aldehyde Oxidoreductase from Desulfovibrio Gigas Reveal a Dithiolene-Based Chemistry for Enzyme Activation and Inhibition by H2O2.
• Resolution: 1.57 Å
• Binding residue (original residue number in PDB): Q99 C139 T420 F421 G422 R533 W650 H653 G654 Q655 G656 S695 G696 Q700 Q701 C799 N800 T804 Q807 S865 G866 V867 G868 E869
• Binding residue (residue number reindexed from 1): Q99 C139 T420 F421 G422 R533 W650 H653 G654 Q655 G656 S695 G696 Q700 Q701 C799 N800 T804 Q807 S865 G866 V867 G868 E869
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): I390 F425 R501 F505 R533 E869 L870
• Catalytic site (residue number reindexed from 1): I390 F425 R501 F505 R533 E869 L870
• Enzyme Commision number: 1.2.99.7: aldehyde dehydrogenase (FAD-independent).

Gene Ontology

Molecular Function

• GO:0005506 iron ion binding
• GO:0016491 oxidoreductase activity
• GO:0033727 aldehyde dehydrogenase (FAD-independent) activity
• GO:0046872 metal ion binding
• GO:0051536 iron-sulfur cluster binding
• GO:0051537 2 iron, 2 sulfur cluster binding

External links

• PDB: RCSB:4c7y, PDBe:4c7y, PDBj:4c7y
• PDBsum: 4c7y
• PubMed: 24391748
• UniProt: Q46509|MOP_MEGGA Aldehyde oxidoreductase (Gene Name=mop)