Structure of PDB 5k85 Chain A Binding Site BS01

Receptor Information

>5k85 Chain A (length=652) Species: 235443 (Cryptococcus neoformans var. grubii H99)

VHHVHPLPDSVPESEDLFAPPPRMQGKEGRPKPHIGPNYESYVKEWAKTV
GPNSDEWWAAKARETLDWYDDFKTVRAGGFEHGDVQWFPEGTLNAAYNCL
DRHYYKNPKKTAIIYEADEPSESREVSYEELMQETCRVANVLKSYGVKKG
DAVSIYLPMTWQAAAAFLACARIGAIHSAVFAGFSAESLRDRVNDCECKV
LITTDEGRRGGKTIATKQIVDAALQQCPLVENVLVLRRTGNKVPMTEGRD
KWWDEECAKMPAYCPCERMASEDPLFILYTSGKPKGVVHSTAGYLLGTAL
TLKYVFDAHPDDRFACMADIGWITGHSYIIYGPLANGITTAVFESTPVYP
TPSRYWDFVDKWKATQLYTAPTAIRLLRRMGEDHVKNHDLSSLRVLGSVG
EPINPEAWHWYNDFAGKNQCAIVDTYWMTETGSISIAPLPGAISTKPGSA
TFPFFGMDVDIIDPQTGQVLEGNDVEGVLVARRPWPSIARTVYRDHKRYL
ETYMKPYPGYFFFGDGAARDYDGYMWIKGRVDDVINVSGHRLSTAEVESA
LILHKGVAETAVVGCADDLTGQAVYAFVTMKPEFDLKATKEADLSKELAI
QVRKVIGPFAAPKKIYLVSDLPKTRSGKIMRRVLRKIVAGPQIVEEVKQK
VT

Ligand information

• Ligand ID: PRX
• InChI: InChI=1S/C13H20N5O7P/c1-2-3-23-26(21,22)24-4-7-9(19)10(20)13(25-7)18-6-17-8-11(14)15-5-16-12(8)18/h5-7,9-10,13,19-20H,2-4H2,1H3,(H,21,22)(H2,14,15,16)/t7-,9-,10-,13-/m1/s1
• InChIKey: XAMXMSZRQHPMRX-QYVSTXNMSA-N
• SMILES:
  OpenEye OEToolkits 1.7.6: CCCOP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
  CACTVS 3.385: CCCO[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
  ACDLabs 12.01: OC1C(OC(COP(=O)(O)OCCC)C1O)n2cnc3c2ncnc3N
  OpenEye OEToolkits 1.7.6: CCCO[P@@](=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O
  CACTVS 3.385: CCCO[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
• Formula: C13 H20 N5 O7 P
• Name: ADENOSINE-5'-MONOPHOSPHATE-PROPYL ESTER;
  ADENOSINE-5'-PROPYLPHOSPHATE
• DrugBank: DB03230
• ZINC: ZINC000015894146
• PDB chain: 5k85 Chain A Residue 701

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5k85 CRYSTAL STRUCTURE OF ACETYL-COA SYNTHETASE IN COMPLEX WITH ADENOSINE-5'-PROPYLPHOSPHATE AND COENZYME A FROM CRYPTOCOCCUS NEOFORMANS H99
• Resolution: 2.3 Å
• Binding residue (original residue number in PDB): W334 I335 V411 G412 E413 P414 T437 Y438 W439 M440 T441 D527 R542
• Binding residue (residue number reindexed from 1): W322 I323 V399 G400 E401 P402 T425 Y426 W427 M428 T429 D515 R530
• Annotation score: 3

Enzymatic activity

• Catalytic site (original residue number in PDB): T289 T441 E442 N548 R553 K640
• Catalytic site (residue number reindexed from 1): T280 T429 E430 N536 R541 K628
• Enzyme Commision number: 6.2.1.1: acetate--CoA ligase.

Gene Ontology

Molecular Function

• GO:0003987 acetate-CoA ligase activity
• GO:0005524 ATP binding
• GO:0016208 AMP binding
• GO:0016874 ligase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0006085 acetyl-CoA biosynthetic process
• GO:0019427 acetyl-CoA biosynthetic process from acetate

Cellular Component

• GO:0005829 cytosol

External links

• PDB: RCSB:5k85, PDBe:5k85, PDBj:5k85
• PDBsum: 5k85
• UniProt: J9VFT1