Structure of PDB 5w70 Chain A Binding Site BS01

Receptor Information
>5w70 Chain A (length=414) Species: 80859 (Streptomyces ribosidificus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QLAVKGGEALRTRPWPAWPQPAPGVPDAVADVLGSGRWSISGPYRGTESY
ERRFARAFAAYNGVPHCVPAASGTASLMLALEACGIGAGDEVIVPGLSWV
ASGSTILGVNAVPIFCDVDPDTLCLSPEAVEAAITEHTRAIVVVHLYSAL
ADMDALSAIAERHGLPLIEDCAQAHGATYRGVKVGALATAGTFSMQHSKV
LTSGEGGAVITRDEDFARRVEHLRADGRCLSAVPPAPGAMELVETGELMG
NNRCLSEFQAAILAEQLTILDEQNETRRANAAHLDGLLGELGLRPQTTSD
GTTSRTYYTYAVRLPDGVLEDVPVTDVSCALTAELGFPVLPSYAPIPANR
LYTPHTRRRYTLGLDHERRIDPKRFALPVCEDAARRTVTLHHAALLGDAD
DMGDIAAAFAKVLR
Ligand information
Ligand ID9YM
InChIInChI=1S/C14H24N3O8P/c1-6-11(18)8(7(3-16-6)5-25-26(22,23)24)4-17-10-2-9(15)12(19)14(21)13(10)20/h3,9-10,12-14,17-21H,2,4-5,15H2,1H3,(H2,22,23,24)/t9-,10+,12+,13-,14-/m0/s1
InChIKeyQHLVFXGQUJCQEL-MYALOSSISA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6Cc1c(c(c(cn1)COP(=O)(O)O)CNC2CC(C(C(C2O)O)O)N)O
ACDLabs 12.01OP(O)(=O)OCc1cnc(c(c1CNC2C(C(C(O)C(N)C2)O)O)O)C
CACTVS 3.385Cc1ncc(CO[P](O)(O)=O)c(CN[CH]2C[CH](N)[CH](O)[CH](O)[CH]2O)c1O
OpenEye OEToolkits 2.0.6Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@@H]2C[C@@H]([C@H]([C@@H]([C@H]2O)O)O)N)O
CACTVS 3.385Cc1ncc(CO[P](O)(O)=O)c(CN[C@@H]2C[C@H](N)[C@@H](O)[C@H](O)[C@H]2O)c1O
FormulaC14 H24 N3 O8 P
Name[4-({[(1R,2S,3S,4R,5S)-5-amino-2,3,4-trihydroxycyclohexyl]amino}methyl)-5-hydroxy-6-methylpyridin-3-yl]methyl dihydrogen phosphate
ChEMBL
DrugBank
ZINC
PDB chain5w70 Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5w70 The structure of RbmB from Streptomyces ribosidificus, an aminotransferase involved in the biosynthesis of ribostamycin.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		G76 T77 W102 D173 A175 Q176 S197 Q199 K202
Binding residue
(residue number reindexed from 1)		G73 T74 W99 D170 A172 Q173 S194 Q196 K199
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) W102 D173 Q176 Q199 K202 L233 E247 C257
Catalytic site (residue number reindexed from 1) W99 D170 Q173 Q196 K199 L230 E244 C254
Enzyme Commision number 2.6.1.100: L-glutamine:2-deoxy-scyllo-inosose aminotransferase.
2.6.1.101: L-glutamine:3-amino-2,3-dideoxy-scyllo-inosose aminotransferase.
Gene Ontology
Molecular Function
GO:0008483 transaminase activity
GO:0030170 pyridoxal phosphate binding
Biological Process
GO:0000271 polysaccharide biosynthetic process
GO:0009058 biosynthetic process
GO:0017000 antibiotic biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5w70, PDBe:5w70, PDBj:5w70
PDBsum5w70
PubMed28685903
UniProtQ4R0W2|GLDSA_STRRI L-glutamine:2-deoxy-scyllo-inosose aminotransferase (Gene Name=rbmB)

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