Structure of PDB 5k3x Chain A Binding Site BS01

Receptor Information

>5k3x Chain A (length=343) Species: 266834 (Sinorhizobium meliloti 1021)

LETKRSEFGTSIITPEEKLYIKNNVNTPPESILADRDGWKVEISGVKEPR
TLTVAELKTLGLVTAATVLQCSGNGRKYFKDQLTGDQKMSGTPWTVGAAG
CVIWSGVPLKAVVDALGGPAEGARFITGTGGEELPAGLDPKLLVVERSVP
ISNLDNVILAWEMNGRPLSLAHGGPLRMVVPGYSGVNNIKYVKAVAMTEV
ETDAKIQKTSYRVHALGEKGSPDQPSVWEQPVKSWITTPHEAAKAGQVQI
AGVAFGGMNACKSVEVSVDGGQTWQEAEFIGPDLGRFAWRVFALSADLAR
GTYTLVSRATDTEGNVQPEETEMNGAGYGHNGWRAPAVKLTVA

Ligand information

• Ligand ID: MSS
• InChI: InChI=1S/C10H14N5O6PS2.Mo.O/c11-10-14-7-4(8(16)15-10)12-3-6(24)5(23)2(21-9(3)13-7)1-20-22(17,18)19;;/h2-3,9,12,23-24H,1H2,(H2,17,18,19)(H4,11,13,14,15,16);;/q;+2;/p-2/t2-,3+,9-;;/m1../s1
• InChIKey: BDXDYZBRBRKVRM-MRZGRPIRSA-L
• SMILES:
  CACTVS 3.341: NC1=NC2=C(N[CH]3[CH](N2)O[CH](CO[P](O)(O)=O)C4=C3S[Mo](=O)S4)C(=O)N1
  CACTVS 3.341: NC1=NC2=C(N[C@@H]3[C@H](N2)O[C@H](CO[P](O)(O)=O)C4=C3S[Mo](=O)S4)C(=O)N1
  OpenEye OEToolkits 1.5.0: C(C1C2=C(C3C(O1)NC4=C(N3)C(=O)NC(=N4)N)S[Mo](=O)S2)OP(=O)(O)O
  OpenEye OEToolkits 1.5.0: C([C@@H]1C2=C([C@H]3[C@@H](O1)NC4=C(N3)C(=O)NC(=N4)N)S[Mo](=O)S2)OP(=O)(O)O
  ACDLabs 10.04: O=P(O)(O)OCC2OC3NC=4N=C(N)NC(=O)C=4NC3C=1S[Mo](=O)SC=12
• Formula: C10 H12 Mo N5 O7 P S2
• Name: (MOLYBDOPTERIN-S,S)-OXO-MOLYBDENUM
• PDB chain: 5k3x Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5k3x The central active site arginine in sulfite oxidizing enzymes alters kinetic properties by controlling electron transfer and redox interactions.
• Resolution: 1.6 Å
• Binding residue (original residue number in PDB): Y76 I77 K78 N79 N80 L125 C127 S128 E188 V201 H228 R233 G241 V242 N244 K246 Y247
• Binding residue (residue number reindexed from 1): Y20 I21 K22 N23 N24 L69 C71 S72 E132 V145 H172 R177 G185 V186 N188 K190 Y191
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): K78 C127 S266 Y267
• Catalytic site (residue number reindexed from 1): K22 C71 S210 Y211
• Enzyme Commision number: 1.8.3.1: sulfite oxidase.

Gene Ontology

Molecular Function

• GO:0008482 sulfite oxidase activity
• GO:0016491 oxidoreductase activity
• GO:0020037 heme binding
• GO:0030151 molybdenum ion binding
• GO:0043546 molybdopterin cofactor binding
• GO:0046872 metal ion binding

Biological Process

• GO:0006790 sulfur compound metabolic process

External links

• PDB: RCSB:5k3x, PDBe:5k3x, PDBj:5k3x
• PDBsum: 5k3x
• PubMed: 28986298
• UniProt: Q92M24