Structure of PDB 6r2d Chain A Binding Site BS04

Receptor Information

>6r2d Chain A (length=814) Species: 246196 (Mycolicibacterium smegmatis MC2 155)

KNARVIELIAAYRNRGHLMADIDPLRLDNTRFRSLTLWDLDREFQRKKLR
DILSVLRDAYCRHVGVEYTHILEPEQQRWIQERVETKHDKPTVAEQKYIL
SKLNAAEAFETFLQTKYVGQKRFSLEGAETVIPMMDAVIDQCAEHGLDEV
VIAMPHRGRLNVLANIVGKPYSQIFSEFDVKYHLGATGTYIQMFGDNDIE
VSLTANPSHLEAVDPVLEGLVRAKQDLLDTGEEGSDNRFSVVPLMLHGDA
AFAGQGVVAETLNLALLRGYRTGGTIHIVVNNQIGFTTAPTDSRSSEYCT
DVAKMIGAPIFHVNGDDPEACAWVARLAVDFRQAFKKDVVIDMLCYRRRG
HNEGDDPSMTQPYMYDVIDTKRGSRKAYTEALIGRGDISMKEAEDALRDY
QGQLERVFNEVRELEKHLATAVDKAMLQRIGDAHLALPEGFTVHPRVRPV
LEKRREMAYEGRIDWAFAELLALGSLIAEGKLVRLSGQDTQRGTFTQRHA
VIVDRKTGEEFTPLQLLATNPDGTPTGGKFLVYNSALSEFAAVGFEYGYS
VGNPDAMVLWEAQFGDFVNGAQSIIDEFISSGEAKWGQLSDVVLLLPHGH
EGQGPDHTSGRIERFLQLWAEGSMTIAMPSTPANYFHLLRRHGKDGIQRP
LIVFTPKSMLRNKAAVSDIRDFTESKFRSVLEEPMYTDGEGDRNKVTRLL
LTSGKIYYELAARKAKENREDVAIVRIEQLAPLPRRRLAETLDRYPNVKE
KFWVQEEPANQGAWPSFGLTLPEILPDHFTGLKRISRRAMSAPSSGSSKV
HAVEQQEILDTAFG

Ligand information

• Ligand ID: ZP1
• InChI: InChI=1S/C18H31N4O13P3S/c1-4-33-36(26,27)18(25,7-5-15(23)24)17-22(10-13-9-20-12(3)21-16(13)19)11(2)14(39-17)6-8-34-38(31,32)35-37(28,29)30/h9,17,25H,4-8,10H2,1-3H3,(H,23,24)(H,26,27)(H,31,32)(H2,19,20,21)(H2,28,29,30)/t17-,18+/m1/s1
• InChIKey: XUQXUYTXDQCESE-MSOLQXFVSA-N
• SMILES:
  CACTVS 3.385: CCO[P](O)(=O)[C](O)(CCC(O)=O)[CH]1SC(=C(C)N1Cc2cnc(C)nc2N)CCO[P](O)(=O)O[P](O)(O)=O
  OpenEye OEToolkits 2.0.7: CCOP(=O)(C(CCC(=O)O)(C1N(C(=C(S1)CCOP(=O)(O)OP(=O)(O)O)C)Cc2cnc(nc2N)C)O)O
  CACTVS 3.385: CCO[P](O)(=O)[C@@](O)(CCC(O)=O)[C@H]1SC(=C(C)N1Cc2cnc(C)nc2N)CCO[P](O)(=O)O[P](O)(O)=O
  OpenEye OEToolkits 2.0.7: CCOP(=O)([C@@](CCC(=O)O)([C@@H]1N(C(=C(S1)CCOP(=O)(O)OP(=O)(O)O)C)Cc2cnc(nc2N)C)O)O
• Formula: C18 H31 N4 O13 P3 S
• Name: (4~{S})-4-[(2~{R})-3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-5-[2-[oxidanyl(phosphonooxy)phosphoryl]oxyethyl]-2~{H}-1,3-thiazol-2-yl]-4-[ethoxy(oxidanyl)phosphoryl]-4-oxidanyl-butanoic acid
• PDB chain: 6r2d Chain B Residue 2001

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6r2d Conformational transitions in the active site of mycobacterial 2-oxoglutarate dehydrogenase upon binding phosphonate analogues of 2-oxoglutarate: From a Michaelis-like complex to ThDP adducts.
• Resolution: 2.3 Å
• Binding residue (original residue number in PDB): Q901 L950 E952 Q976 F980 H1020
• Binding residue (residue number reindexed from 1): Q488 L537 E539 Q563 F567 H607
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 1.2.4.2: oxoglutarate dehydrogenase (succinyl-transferring).
  2.2.1.5: 2-hydroxy-3-oxoadipate synthase.
  2.3.1.61: dihydrolipoyllysine-residue succinyltransferase.
  4.1.1.71: 2-oxoglutarate decarboxylase.

Gene Ontology

Molecular Function

• GO:0016624 oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor
• GO:0030976 thiamine pyrophosphate binding

External links

• PDB: RCSB:6r2d, PDBe:6r2d, PDBj:6r2d
• PDBsum: 6r2d
• PubMed: 31476368
• UniProt: A0R2B1|KGD_MYCS2 Multifunctional 2-oxoglutarate metabolism enzyme (Gene Name=kgd)