Structure of PDB 6eqo Chain B Binding Site BS02

Receptor Information
>6eqo Chain B (length=1803) Species: 237727 (Erythrobacter sp. NAP1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
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 IDNAP
InChIInChI=1S/C21H28N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1-4,7-8,10-11,13-16,20-21,29-31H,5-6H2,(H7-,22,23,24,25,32,33,34,35,36,37,38,39)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyXJLXINKUBYWONI-NNYOXOHSSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)OP(=O)(O)O)O)O)O)C(=O)N
CACTVS 3.341NC(=O)c1ccc[n+](c1)[CH]2O[CH](CO[P]([O-])(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O[P](O)(O)=O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
CACTVS 3.341NC(=O)c1ccc[n+](c1)[C@@H]2O[C@H](CO[P]([O-])(=O)O[P@@](O)(=O)OC[C@H]3O[C@H]([C@H](O[P](O)(O)=O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)([O-])O[P@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)OP(=O)(O)O)O)O)O)C(=O)N
FormulaC21 H28 N7 O17 P3
NameNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE;
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
ChEMBLCHEMBL295069
DrugBankDB03461
ZINC
PDB chain6eqo Chain B Residue 1902 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6eqo The multicatalytic compartment of propionyl-CoA synthase sequesters a toxic metabolite.
Resolution2.7 Å
Binding residue
(original residue number in PDB)		F1300 W1304 T1418 T1442 G1443 T1444 V1463 S1464 R1468 R1483 H1531 A1532 A1536 Y1553 S1556 W1752 H1769 L1770 H1813
Binding residue
(residue number reindexed from 1)		F1260 W1264 T1378 T1402 G1403 T1404 V1423 S1424 R1428 R1443 H1491 A1492 A1496 Y1513 S1516 W1712 H1729 L1730 H1773
Annotation score3
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6eqo, PDBe:6eqo, PDBj:6eqo
PDBsum6eqo
PubMed30374166
UniProtA3WE14

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