Structure of PDB 5wm3 Chain A Binding Site BS01

Receptor Information

>5wm3 Chain A (length=537) Species: 1649596 (Streptomyces gandocaensis)

SHMLDGWVPWPESFARRYRAAGYWEGRPLDRLLRERAAADPDRIALVDAA
GDRWTYAELDRHADRQAAGLRRLGIGAGDRVVVQLPNTDAFVVLFFALLR
AGAVPVLTLPAHRESEIVHVAETAGATAYVIPDVLDGFDHRALARAARKA
VPSIEHVLVAGEAAEFTALADVDAAPVPLAEPDPGDVALLLLSGGTTGKP
KLIPRTHDDYTYNVRASAEVCGFDSDTVYLVVLPTAHNFALACPGLLGTL
MVGGTVVLAPTPSPEDAFELIEREKVTATAVVPPVALLWLDAVEWEDADL
SSLRLLQVGGSKLGAEPAARVRPALGCTLQQVFGMAEGLLNYTRLDDPSD
LVIQTQGRPLSPDDEIRVVDEDGRDVAPGETGELLTRGPYTLRGYYRAPE
HNARTFSDDGFYRTGDLVRVLPSGHLVVEGRAKDQINRGGDKISAEELEN
HIMAHPGVHDAAVVGMPDATMGERTCACLVPRAGRSAPAQRELAAFLTDR
GVAAYKLPDRVEVMDAFPRTSVGKTDKKELGRRIAGQ

Ligand information

• Ligand ID: B5V
• InChI: InChI=1S/C17H18N5O9P/c18-14-11-15(20-6-19-14)22(7-21-11)16-13(25)12(24)10(30-16)5-29-32(27,28)31-17(26)8-3-1-2-4-9(8)23/h1-4,6-7,10,12-13,16,23-25H,5H2,(H,27,28)(H2,18,19,20)/t10-,12+,13+,16+/m0/s1
• InChIKey: AESBJQJIAHTCHE-MZXFEWSRSA-N
• SMILES:
  OpenEye OEToolkits 2.0.6: c1ccc(c(c1)C(=O)OP(=O)(O)OCC2C(C(C(O2)n3cnc4c3ncnc4N)O)O)O
  ACDLabs 12.01: C2(COP(OC(=O)c1ccccc1O)(=O)O)OC(C(C2O)O)n4cnc3c(N)ncnc34
  CACTVS 3.385: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)OC(=O)c4ccccc4O)[CH](O)[CH]3O
  CACTVS 3.385: Nc1ncnc2n(cnc12)[C@@H]3O[C@@H](CO[P](O)(=O)OC(=O)c4ccccc4O)[C@@H](O)[C@H]3O
  OpenEye OEToolkits 2.0.6: c1ccc(c(c1)C(=O)OP(=O)(O)OC[C@H]2[C@H]([C@H]([C@@H](O2)n3cnc4c3ncnc4N)O)O)O
• Formula: C17 H18 N5 O9 P
• Name: 9-(5-O-{(S)-hydroxy[(2-hydroxybenzene-1-carbonyl)oxy]phosphoryl}-alpha-L-lyxofuranosyl)-9H-purin-6-amine
• PDB chain: 5wm3 Chain A Residue 601

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5wm3 A Defined and Flexible Pocket Explains Aryl Substrate Promiscuity of the Cahuitamycin Starter Unit-Activating Enzyme CahJ.
• Resolution: 1.679 Å
• Binding residue (original residue number in PDB): N256 F257 G328 S329 K330 V350 F351 G352 M353 A354 D434 K451 K460
• Binding residue (residue number reindexed from 1): N238 F239 G310 S311 K312 V332 F333 G334 M335 A336 D416 K433 K442
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): S211 N231 H255 A354 E355 N455 K460 K542
• Catalytic site (residue number reindexed from 1): S193 N213 H237 A336 E337 N437 K442 K524

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0003824 catalytic activity
• GO:0016874 ligase activity
• GO:0046872 metal ion binding

External links

• PDB: RCSB:5wm3, PDBe:5wm3, PDBj:5wm3
• PDBsum: 5wm3
• PubMed: 29742306
• UniProt: A0A140DJY3