Structure of PDB 6xbt Chain A Binding Site BS02

Receptor Information

>6xbt Chain A (length=140) Species: 100226 (Streptomyces coelicolor A3(2))

SLTRIDHIGIACHDLDATVEFYRATYGFEVFHTEVNEEQGVREAMLKIND
TSDGGASYLALLEPTREDSAVGKWLAKNGEGVHHIAFGTADVDADAADIR
DKGVRVLYDEPRRGSMGSRITFLHPKDCHGVLTELVTSAA

Ligand information

• Ligand ID: KFV
• InChI: InChI=1S/C24H38N8O19P3S/c1-12(32(38)39)23(37)55-7-6-26-14(33)4-5-27-21(36)18(35)24(2,3)9-48-54(45,46)51-53(43,44)47-8-13-17(50-52(40,41)42)16(34)22(49-13)31-11-30-15-19(25)28-10-29-20(15)31/h10-11,13,16-18,22,34-35H,4-9H2,1-3H3,(H8-,25,26,27,28,29,33,36,37,38,39,40,41,42,43,44,45,46)/q-1/t13-,16-,17-,18+,22-/m1/s1
• InChIKey: BLWVPDVKNPMTPY-ZSJPKINUSA-N
• SMILES:
  CACTVS 3.385: CC(C(=O)SCCNC(=O)CCNC(=O)[CH](O)C(C)(C)CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O[P](O)(O)=O)n2cnc3c(N)ncnc23)=[N+]([O-])[O-]
  ACDLabs 12.01: n1cnc2c(c1N)ncn2C3C(O)C(C(O3)COP(OP(OCC(C(C(=O)NCCC(=O)NCCSC(\C(=[N+](\[O-])[O-])C)=O)O)(C)C)(=O)O)(O)=O)OP(O)(O)=O
  OpenEye OEToolkits 2.0.7: CC(=[N+]([O-])[O-])C(=O)SCCNC(=O)CCNC(=O)C(C(C)(C)COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)O
  OpenEye OEToolkits 2.0.7: CC(=[N+]([O-])[O-])C(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)COP(=O)(O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)O
  CACTVS 3.385: CC(C(=O)SCCNC(=O)CCNC(=O)[C@H](O)C(C)(C)CO[P](O)(=O)O[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O[P](O)(O)=O)n2cnc3c(N)ncnc23)=[N+]([O-])[O-]
• Formula: C24 H38 N8 O19 P3 S
• Name: [1-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethylsulfanyl]-1-oxidanylidene-propan-2-ylidene]-bis(oxidanidyl)azanium
• PDB chain: 6xbt Chain A Residue 204

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6xbt Streptomyces coelicolor methylmalonyl-CoA epimerase (Q60A) in complex with 2-nitronate-propionyl-CoA
• Resolution: 1.49 Å
• Binding residue (original residue number in PDB): H7 Q39 A70 K73 W74 H83 H84 L107 G114 S115 P125 K126 L132 E134
• Binding residue (residue number reindexed from 1): H7 Q39 A70 K73 W74 H83 H84 L107 G114 S115 P125 K126 L132 E134
• Annotation score: 2

Enzymatic activity

• Catalytic site (original residue number in PDB): H7 E43 A60 H84 E134
• Catalytic site (residue number reindexed from 1): H7 E43 A60 H84 E134

Gene Ontology

Molecular Function

• GO:0004493 methylmalonyl-CoA epimerase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0046491 L-methylmalonyl-CoA metabolic process

External links

• PDB: RCSB:6xbt, PDBe:6xbt, PDBj:6xbt
• PDBsum: 6xbt
• UniProt: Q9L2C2