Structure of PDB 5wm4 Chain A Binding Site BS01

Receptor Information

>5wm4 Chain A (length=534) Species: 1649596 (Streptomyces gandocaensis)

SHMLDGWVPWPESFARRYRAAGYWEGRPLDRLLRERAAADPDRIALVDAA
GDRWTYAELDRHADRQAAGLRRLGIGAGDRVVVQLPNTDAFVVLFFALLR
AGAVPVLTLPAHRESEIVHVAETAGATAYVIPDVLDGFDHRALARAARKA
VPSIEHVLVAGEAAEFTALADVDAAPVPLAEPDPGDVALLLLSGGTTGKP
KLIPRTHDDYTYNVRASAEVCGFDSDTVYLVVLPTAHNFALACPGLLGTL
MVGGTVVLAPTPSPEDAFELIEREKVTATAVVPPVALLWLDAVEWEDADL
SSLRLLQVGGSKLGAEPAARVRPALGCTLQQVFGMAEGLLNYTRLDDPSD
LVIQTQGRPLSPDDEIRVVDEDGRDVAPGETGELLTRGPYTLRGYYRAPE
HNARTFSDDGFYRTGDLVRVLPSGHLVVEGRAKDQINRGGDKISAEELEN
HIMAHPGVHDAAVVGMPDATMGERTCACLVPRAGRSAPAQRELAAFLTDR
GVAAYKLPDRVEVMDAFPRTKTDKKELGRRIAGQ

Ligand information

• Ligand ID: B5M
• InChI: InChI=1S/C18H20N5O9P/c1-8-3-2-4-9(24)11(8)18(27)32-33(28,29)30-5-10-13(25)14(26)17(31-10)23-7-22-12-15(19)20-6-21-16(12)23/h2-4,6-7,10,13-14,17,24-26H,5H2,1H3,(H,28,29)(H2,19,20,21)/t10-,13+,14+,17+/m0/s1
• InChIKey: YIFBGYAAIZMTKM-NBCLGQJJSA-N
• SMILES:
  OpenEye OEToolkits 2.0.6: Cc1cccc(c1C(=O)OP(=O)(O)OCC2C(C(C(O2)n3cnc4c3ncnc4N)O)O)O
  CACTVS 3.385: Cc1cccc(O)c1C(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)n3cnc4c(N)ncnc34
  ACDLabs 12.01: C2(COP(OC(=O)c1c(C)cccc1O)(=O)O)OC(C(C2O)O)n4cnc3c(N)ncnc34
  OpenEye OEToolkits 2.0.6: Cc1cccc(c1C(=O)OP(=O)(O)OC[C@H]2[C@H]([C@H]([C@@H](O2)n3cnc4c3ncnc4N)O)O)O
  CACTVS 3.385: Cc1cccc(O)c1C(=O)O[P](O)(=O)OC[C@@H]2O[C@H]([C@H](O)[C@@H]2O)n3cnc4c(N)ncnc34
• Formula: C18 H20 N5 O9 P
• Name: 9-(5-O-{(S)-hydroxy[(2-hydroxy-6-methylbenzene-1-carbonyl)oxy]phosphoryl}-alpha-L-lyxofuranosyl)-9H-purin-6-amine
• PDB chain: 5wm4 Chain A Residue 601

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5wm4 A Defined and Flexible Pocket Explains Aryl Substrate Promiscuity of the Cahuitamycin Starter Unit-Activating Enzyme CahJ.
• Resolution: 1.781 Å
• Binding residue (original residue number in PDB): N256 F257 C261 G327 G328 S329 K330 V350 F351 G352 M353 A354 L358 D434 K451 K460
• Binding residue (residue number reindexed from 1): N238 F239 C243 G309 G310 S311 K312 V332 F333 G334 M335 A336 L340 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 K521

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:5wm4, PDBe:5wm4, PDBj:5wm4
• PDBsum: 5wm4
• PubMed: 29742306
• UniProt: A0A140DJY3