Structure of PDB 5ydm Chain A Binding Site BS01

Receptor Information

>5ydm Chain A (length=408) Species: 1571532 (Streptomyces sp. CNQ431)

NLYFQGSGRRLVLPVSARTSGALRGQAHALARRLEERPGLRLDDVAGALR
ADRPALRHRLTVSASSVPEAVEALRAAVPAVPPVPDEPPKVAFLLPGGGT
QYVGMGSGLYRENDVYRDTVDRCAAVLRPALGSDLRTALFEEVEPGSTAA
FMALFVTEYALARTLMEEGVRPDALIGHSLGEYTAACLAGVMEIDEALPV
VAERIRLIASSGGATVGVAACADTVLPLLGEGLSLAAVNSPVACTVAGDT
DAVDRLEAELTRRGVPFRRLRMPAAAHSHVLDPILESFAGHLRTLTLRPP
RIPYVTNVTGDWATDAQATDVGHWVDHTRRTVRFADGIAALWERERPVLV
EIGPGDSLTKLARARLDGEGPVTVTTMRHAKAQAADGFVLAEALGRLWSA
GVDAALPH

Ligand information

• Ligand ID: DUW
• InChI: InChI=1S/C10H10O3/c11-7-9(10(12)13)6-8-4-2-1-3-5-8/h1-5,7,9H,6H2,(H,12,13)/t9-/m1/s1
• InChIKey: NAYOGLQOGCMXAU-SECBINFHSA-N
• SMILES:
  OpenEye OEToolkits 2.0.6: c1ccc(cc1)C[C@H](C=O)C(=O)O
  CACTVS 3.385: OC(=O)[C@H](Cc1ccccc1)C=O
  CACTVS 3.385: OC(=O)[CH](Cc1ccccc1)C=O
  OpenEye OEToolkits 2.0.6: c1ccc(cc1)CC(C=O)C(=O)O
• Formula: C10 H10 O3
• Name: (2R)-2-methanoyl-3-phenyl-propanoic acid
• PDB chain: 5ydm Chain A Residue 501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5ydm Structural Basis of a Broadly Selective Acyltransferase from the Polyketide Synthase of Splenocin.
• Resolution: 2.5 Å
• Binding residue (original residue number in PDB): S173 L174 R198 I202 M266 A268
• Binding residue (residue number reindexed from 1): S179 L180 R204 I208 M272 A274
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): G92 S173 L174 R198 H271 H321
• Catalytic site (residue number reindexed from 1): G98 S179 L180 R204 H277 H327

Gene Ontology

Molecular Function

• GO:0016740 transferase activity

External links

• PDB: RCSB:5ydm, PDBe:5ydm, PDBj:5ydm
• PDBsum: 5ydm
• PubMed: 29536601
• UniProt: A0A0E3JLZ0