Structure of PDB 4yak Chain C Binding Site BS01

Receptor Information

>4yak Chain C (length=463) Species: 374847 (Candidatus Korarchaeum cryptofilum OPF8)

NDLERLFNPSAIAVVGASKDPSKIGSQILRNLLSYGFKGKVYPINPTADE
LMGLKCYPKVSDVPDKVDVAVISVPSDKVLGVIDDCGKAGVKFAVVITSG
FKEVGNEELEEELVRRAHSYGMRVLGPNIFGYLYAPARLNATFGPKDVLS
GNVAFISQSGALGIALMGYTVVENIGISSIVSVGNKADLDDVDLLDFFDK
DPNTGVIMIYLEGIAPGRGRMFIDVASRVSLRKPIIVIKAGRTEVGARAA
ASHTGSIAGSVAIYESAFKQSGILMAKSVEDAFDWTKALSWNPIPEGERL
IVLTNGGGAGVQSTDTFADNGIYLSKPPESLIQEIKKFVPPFASFANPID
ITGMAPDDWYYMGTLAALKNPDVDALTVLYCQTAVTTPIGVAKGIVDAIK
EAGNSKPVTVGMVGGPEVAEAVSFLNKQRIAAYPTPERASSAMSALYAYA
RARSYVMKSLAVR

Ligand information

• Ligand ID: ACO
• InChI: InChI=1S/C23H38N7O17P3S/c1-12(31)51-7-6-25-14(32)4-5-26-21(35)18(34)23(2,3)9-44-50(41,42)47-49(39,40)43-8-13-17(46-48(36,37)38)16(33)22(45-13)30-11-29-15-19(24)27-10-28-20(15)30/h10-11,13,16-18,22,33-34H,4-9H2,1-3H3,(H,25,32)(H,26,35)(H,39,40)(H,41,42)(H2,24,27,28)(H2,36,37,38)/t13-,16-,17-,18+,22-/m1/s1
• InChIKey: ZSLZBFCDCINBPY-ZSJPKINUSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: CC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)O
  CACTVS 3.341: CC(=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
  ACDLabs 10.04: O=C(SCCNC(=O)CCNC(=O)C(O)C(C)(C)COP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3OP(=O)(O)O)C
  CACTVS 3.341: CC(=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
  OpenEye OEToolkits 1.5.0: CC(=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
• Formula: C23 H38 N7 O17 P3 S
• Name: ACETYL COENZYME *A
• ChEMBL: CHEMBL1230809
• ZINC: ZINC000008551095
• PDB chain: 4yak Chain C Residue 500

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4yak Structure of NDP-forming Acetyl-CoA synthetase ACD1 reveals a large rearrangement for phosphoryl transfer.
• Resolution: 2.464 Å
• Binding residue (original residue number in PDB): G17 S19 K24 N46 P47 V75 P76 S100 N129 I130 F144
• Binding residue (residue number reindexed from 1): G16 S18 K23 N45 P46 V74 P75 S99 N128 I129 F143
• Annotation score: 4

Enzymatic activity

• Catalytic site (original residue number in PDB): I215 H254
• Catalytic site (residue number reindexed from 1): I214 H253

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0043758 acetate-CoA ligase (ADP-forming) activity
• GO:0046872 metal ion binding

External links

• PDB: RCSB:4yak, PDBe:4yak, PDBj:4yak
• PDBsum: 4yak
• PubMed: 26787904
• UniProt: B1L3C9