Structure of PDB 5n9x Chain B Binding Site BS01

Receptor Information

>5n9x Chain B (length=486) Species: 1931 (Streptomyces sp.)

FGATLVDLFSRAAMEMPDRTALHIDDEKISYGLLHSWAEGLADLLHDAGV
RKGDRVALRMPPGANAIAAMLGILRAGAAYVPLDIRNPPARNAFIVTDSQ
VVALVGDPTGPLVTEENVAALRDREGPERPGPQDVAYIIYTSGTTGRPKG
VPVRHGNVTALFEACSRLFSFSADDRWLLFHSMAFDFSVWEIWGALSTGA
ELVVLPTARTPVETARVVRDRGITVLNQTPTAFGALTTAVLGEGIDLPEL
RYVVFGGEKLTPAVVRPWAKRFGLDRPHLINMYGITETTVHATFHRLTED
DLAAEDSVIGRPLPGFTHRIVTEDGRDAATGEPGELWLAGPQVSEGYLNR
PELTAERFTTGPPRYYHSGDLVSRRAGGDLVYQGRADLQVKLRGHRIELS
DVEAAVRTHPAVVDAVVWVHEFAPGDSRLVCAYTAQADARALRAHVKTVL
PSYMQPSQYLALPELPRTINGKADRASVARAFDERR

Ligand information

• Ligand ID: 8QN
• InChI: InChI=1S/C14H21N6O9P/c1-5(21)7(15)14(24)29-30(25,26)27-2-6-9(22)10(23)13(28-6)20-4-19-8-11(16)17-3-18-12(8)20/h3-7,9-10,13,21-23H,2,15H2,1H3,(H,25,26)(H2,16,17,18)/t5-,6-,7+,9-,10-,13-/m1/s1
• InChIKey: YYBNSQASHCKPHX-DWVDDHQFSA-N
• SMILES:
  CACTVS 3.385: C[CH](O)[CH](N)C(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
  CACTVS 3.385: C[C@@H](O)[C@H](N)C(=O)O[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
  OpenEye OEToolkits 2.0.6: C[C@H]([C@@H](C(=O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O)N)O
  OpenEye OEToolkits 2.0.6: CC(C(C(=O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)O)N)O
• Formula: C14 H21 N6 O9 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] (2~{S},3~{R})-2-azanyl-3-oxidanyl-butanoate
• ZINC: ZINC000059064934
• PDB chain: 5n9x Chain B Residue 601

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5n9x Structure of the adenylation domain Thr1 involved in the biosynthesis of 4-chlorothreonine in Streptomyces sp. OH-5093-protein flexibility and molecular bases of substrate specificity.
• Resolution: 2.396 Å
• Binding residue (original residue number in PDB): T167 D212 F213 G285 E286 K287 N309 M310 Y311 G312 I313 T314 V318 D406 Y418 R421 N513 K515
• Binding residue (residue number reindexed from 1): T141 D186 F187 G257 E258 K259 N281 M282 Y283 G284 I285 T286 V290 D370 Y382 R385 N470 K472
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): T167 L187 T314 E315 K427 R432 K515
• Catalytic site (residue number reindexed from 1): T141 L161 T286 E287 K391 R396 K472

Gene Ontology

Molecular Function

• GO:0003824 catalytic activity
• GO:0005524 ATP binding
• GO:0031177 phosphopantetheine binding

Biological Process

• GO:0043041 amino acid activation for nonribosomal peptide biosynthetic process
• GO:0044550 secondary metabolite biosynthetic process

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:5n9x, PDBe:5n9x, PDBj:5n9x
• PDBsum: 5n9x
• PubMed: 28704585
• UniProt: H6SG27