Structure of PDB 5k8f Chain B Binding Site BS02

Receptor Information

>5k8f Chain B (length=655) Species: 235443 (Cryptococcus neoformans var. grubii H99)

HHVHPLPDSVPESEDLFAPPPRMQGKEGRPKPHIGPNYESYVKEWAKTVG
PNSDEWWAAKARETLDWYDDFKTVRAGGFEHGDVQWFPEGTLNAAYNCLD
RHYYKNPKKTAIIYEADEPSESREVSYEELMQETCRVANVLKSYGVKKGD
AVSIYLPMTWQAAAAFLACARIGAIHSAVFAGFSAESLRDRVNDCECKVL
ITTDEGRRGGKTIATKQIVDAALQQCPLVENVLVLRRTGNKVPMTEGRDK
WWDEECAKMPAYCPCERMASEDPLFILYTSGSTGKPKGVVHSTAGYLLGT
ALTLKYVFDAHPDDRFACMADIGWITGHSYIIYGPLANGITTAVFESTPV
YPTPSRYWDFVDKWKATQLYTAPTAIRLLRRMGEDHVKNHDLSSLRVLGS
VGEPINPEAWHWYNDFAGKNQCAIVDTYWMTETGSISIAPLPGAISTKPG
SATFPFFGMDVDIIDPQTGQVLEGNDVEGVLVARRPWPSIARTVYRDHKR
YLETYMKPYPGYFFFGDGAARDYDGYMWIKGRVDDVINVSGHRLSTAEVE
SALILHKGVAETAVVGCADDLTGQAVYAFVTMKPEFDLKATKEADLSKEL
AIQVRKVIGPFAAPKKIYLVSDLPKTRSGKIMRRVLRKIVAGEPQIVEEV
KQKVT

Ligand information

• Ligand ID: 6R9
• InChI: InChI=1S/C12H16N5O8P/c1-5(18)25-26(21,22)23-2-6-8(19)9(20)12(24-6)17-4-16-7-10(13)14-3-15-11(7)17/h3-4,6,8-9,12,19-20H,2H2,1H3,(H,21,22)(H2,13,14,15)/t6-,8-,9-,12-/m1/s1
• InChIKey: UBPVOHPZRZIJHM-WOUKDFQISA-N
• SMILES:
  CACTVS 3.385: CC(=O)O[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
  OpenEye OEToolkits 2.0.5: CC(=O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
  CACTVS 3.385: CC(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
  OpenEye OEToolkits 2.0.5: CC(=O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O
• Formula: C12 H16 N5 O8 P
• Name: [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] ethanoate
• ZINC: ZINC000004096994
• PDB chain: 5k8f Chain B Residue 702

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5k8f Crystal structure of Acetyl-CoA Synthetase in complex with ATP and Acetyl-AMP from Cryptococcus neoformans H99
• Resolution: 2.45 Å
• Binding residue (original residue number in PDB): I335 G412 E413 P414 T437 Y438 W439 M440 T441 D527 I539 K640
• Binding residue (residue number reindexed from 1): I325 G402 E403 P404 T427 Y428 W429 M430 T431 D517 I529 K630
• 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): T279 T431 E432 N538 R543 K630
• 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:5k8f, PDBe:5k8f, PDBj:5k8f
• PDBsum: 5k8f
• UniProt: J9VFT1