Structure of PDB 6eqo Chain B Binding Site BS01

Receptor Information

>6eqo Chain B (length=1803) Species: 237727 (Erythrobacter sp. NAP1)

ISDRDHFQRLREECRSDPGEFHGRLAKREICWLIENPAWAFYDDAAETWT
GWDASSAAPITLDLPESFEPWERAFNDDDPPNWRWFEGGLTSTAFNEVDR
HVLSGHGDEAAMIFEGDRWNMASEGGRGGPVDSEVISRRKLLLESAKCAL
ALKALGLEAGDRIALNMPSIPEQIYWTEGAKRMGIVYTPVFGGFSDKTLS
DRIADAGARVVVTADGSYRNAQMVPFKPSYTDPALDNFIAVPVAMELLGQ
ALEVVAPEHAGLIRSEVAGLLDGEVTVERSDVMRGVGKALTAIASGEAAG
GAMTPRQAAQLRIAIASALVDSPPRVDAVVVVKHTAQPDLPWNEARDHWS
HDLTAAAGEELLKAARDAGFDVADEEALLALSDTEFVRAIWAGAPVLAVD
AEYPNFIIYTSGSTGKPKGVVHVHGGYASGVAATMPAAFGAEPGDVMYVV
ADPGWITGQSYQIAASLLSRVTTVITEGSPVFPHAGRFASIIERYGVNVF
KAGVTFLKSVMQNPENLKDIQRYDLSSLKVATFCAEPVSPAVQAFAMEHI
THRYINSYWATEHGGMVWTHFADADGFPLEADAHTYPLPWIMGDVWVEDA
DGSSNGPVEYERDTPWRVAEDGEKGEIVIALPYPYLTRTIWGDVENFTVE
HVGNLARVAGGWRGDEVRYADTYWRRWKGAWAYTQGDFAMRHPDGSFSLH
GRSDDVINVSGHRIGTEEIEGAILRDKALDPNSPVGNVIVIGAPHSQKGV
TPIAFVTPVEGRRLTQDDKRRLTDLVRTEKGAVAVPQDFIELSEFPETRS
GKYMRRMVRAVVEGGEVLRNPESLDELARAVDGWKRRQSLSDTQALFERY
RFFTIQYNLVAPGKRVATVTVKNPPVNALNERALDELVIIAEHLARKDDV
AAVVFTGSGTASFVAGADIRQMLEEVNSVEEAKALPDNAQLAFRTIEEMD
KPCIAAIQGVALGGGMEFALACHYRVAEPKARFGQPEINLRLLPGYGGTQ
RLPRLLADGGGETGLRDALDLILGGRAIDADAALAVGAVDALADGSDNAL
SHAHAMVREFVRSGDDSALGKAFAARKTQTQSWHEPASIDLDAVLEDEFL
QRILNQLEWAGRDKAGERALDAVRTGWTQGMTAGLECEAQRFAEAIIDPE
GGKTGIQQFMDKQSPPLPVRRDGVWEDDQHEATKTALIEAGDLLPLGAPF
YPGVTAIPPKQLAFGIARDPDTGAPRFGPPETHERELVVNTPKPGANEAL
IYLLSSEVNFNDIWALTGIPVSPFDAHDEDVQITGSGGLALVAALGSELK
EEGRLQVGDLVSVYSGTSELLSPLAGDDPMYAGFAIQGYETKTGSHAQFL
TVQGPQLHRPPADLTLEQAGAYTLNLGTVARCLFTTLEIQAGKTAFVEGS
ATGTGLDALKSSVRTGLAVTGLVSSEDRAEFVKSHGSVGAINRKDPEIAD
CFTPVPDDPDEARQWEADGEKLLDAYRETNGGKLADYVVSHAGERAFPRS
FQLLAEGGRLAFYGASSGYHFSFMGKGGEARPDEMLARANLRGGESVLLY
YGPGSHELADEKGLEMVEAARLMKARMVIVTTSDGQREFLQSLGLEDAVE
GIVSIEGLKRRLSDFHWPDTLPRLPDARTDIENFKIGVRAYQQNTMKPFG
TAVGKLLRSPGNPRGVPDLVIERAGQDTLGVSTSLVKPFGGRVIYAEEMA
GRRYTFYAPQVWTRQRRIYMPSAEIFGTHLCNAYEVTMMNEMVAAGLLDV
TEPTMVPWEGLPEAHQAMWDNRHSGATYVVNHALPAMGLTTKDELLEYWV
AAQ

Ligand information

• Ligand ID: ACP
• InChI: InChI=1S/C11H18N5O12P3/c12-9-6-10(14-2-13-9)16(3-15-6)11-8(18)7(17)5(27-11)1-26-31(24,25)28-30(22,23)4-29(19,20)21/h2-3,5,7-8,11,17-18H,1,4H2,(H,22,23)(H,24,25)(H2,12,13,14)(H2,19,20,21)/t5-,7-,8-,11-/m1/s1
• InChIKey: UFZTZBNSLXELAL-IOSLPCCCSA-N
• SMILES:
  CACTVS 3.341: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)C[P](O)(O)=O)[CH](O)[CH]3O
  ACDLabs 10.04: O=P(O)(O)CP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(CP(=O)(O)O)O)O)O)N
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(CP(=O)(O)O)O)O)O)N
  CACTVS 3.341: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@](O)(=O)C[P](O)(O)=O)[C@@H](O)[C@H]3O
• Formula: C11 H18 N5 O12 P3
• Name: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER;
  ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE
• ChEMBL: CHEMBL133463
• DrugBank: DB03909
• ZINC: ZINC000008295124
• PDB chain: 6eqo Chain B Residue 1901

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6eqo The multicatalytic compartment of propionyl-CoA synthase sequesters a toxic metabolite.
• Resolution: 2.7 Å
• Binding residue (original residue number in PDB): C564 A565 E566 P567 N586 S587 Y588 A590 T591 D722 R748
• Binding residue (residue number reindexed from 1): C534 A535 E536 P537 N556 S557 Y558 A560 T561 D687 R713
• Annotation score: 3

Enzymatic activity

• Catalytic site (original residue number in PDB): A957 G1004 E1007 E1027 G1035
• Catalytic site (residue number reindexed from 1): A917 G964 E967 E987 G995
• Enzyme Commision number: 1.1.1.35: 3-hydroxyacyl-CoA dehydrogenase.
  6.2.1.1: acetate--CoA ligase.

Gene Ontology

Molecular Function

• GO:0003824 catalytic activity
• GO:0003857 3-hydroxyacyl-CoA dehydrogenase activity
• GO:0003987 acetate-CoA ligase activity
• GO:0005524 ATP binding
• GO:0016874 ligase activity

Biological Process

• GO:0006085 acetyl-CoA biosynthetic process

Cellular Component

• GO:0005829 cytosol

External links

• PDB: RCSB:6eqo, PDBe:6eqo, PDBj:6eqo
• PDBsum: 6eqo
• PubMed: 30374166
• UniProt: A3WE14