Structure of PDB 2po3 Chain B Binding Site BS02

Receptor Information

>2po3 Chain B (length=392) Species: 54571 (Streptomyces venezuelae)

ALSDLAFFGGPAAFDQPLLVGRPNRIDRARLYERLDRALDSQWLSNGGPL
VREFEERVAGLAGVRHAVATCNATAGLQLLAHAAGLTGEVIMPSMTFAAT
PHALRWIGLTPVFADIDPDTGNLDPDQVAAAVTPRTSAVVGVHLWGRPCA
ADQLRKVADEHGLRLYFDAAHALGCAVDGRPAGSLGDAEVFSFHATKAVN
AFEGGAVVTDDADLAARIRALHNFGFDLPGGSPAGGTNAKMSEAAAAMGL
TSLDAFPEVIDRNRRNHAAYREHLADLPGVLVADHDRHGLNNHQYVIVEI
DEATTGIHRDLVMEVLKAEGVHTRAYFSPGCHELEPYRGQPHAPLPHTER
LAARVLSLPTGTAIGDDDIRRVADLLRLCATRGRELTARHRD

Ligand information

• Ligand ID: T4K
• InChI: InChI=1S/C24H35N4O19P3/c1-10-7-28(24(34)27-22(10)33)17-4-15(29)16(45-17)9-43-49(38,39)47-50(40,41)46-23-21(32)20(31)18(12(3)44-23)26-6-14-13(8-42-48(35,36)37)5-25-11(2)19(14)30/h5-7,12,15-18,20-21,23,29-32H,4,8-9H2,1-3H3,(H,38,39)(H,40,41)(H,27,33,34)(H2,35,36,37)/b26-6+/t12-,15+,16-,17-,18-,20+,21-,23-/m1/s1
• InChIKey: LEIRFGMKEVPNBT-ZBVJAJKCSA-N
• SMILES:
  ACDLabs 10.04: O=P(OC2OC(C(/N=C/c1c(cnc(c1O)C)COP(=O)(O)O)C(O)C2O)C)(O)OP(=O)(O)OCC4OC(N3C=C(C(=O)NC3=O)C)CC4O
  CACTVS 3.341: C[C@H]1O[C@H](O[P@@](O)(=O)O[P@@](O)(=O)OC[C@H]2O[C@H](C[C@@H]2O)N3C=C(C)C(=O)NC3=O)[C@H](O)[C@@H](O)[C@@H]1N=Cc4c(O)c(C)ncc4CO[P](O)(O)=O
  CACTVS 3.341: C[CH]1O[CH](O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH](C[CH]2O)N3C=C(C)C(=O)NC3=O)[CH](O)[CH](O)[CH]1N=Cc4c(O)c(C)ncc4CO[P](O)(O)=O
  OpenEye OEToolkits 1.5.0: Cc1c(c(c(cn1)COP(=O)(O)O)C=NC2C(OC(C(C2O)O)OP(=O)(O)OP(=O)(O)OCC3C(CC(O3)N4C=C(C(=O)NC4=O)C)O)C)O
  OpenEye OEToolkits 1.5.0: Cc1c(c(c(cn1)COP(=O)(O)O)\C=N\[C@@H]2[C@H](O[C@@H]([C@@H]([C@H]2O)O)O[P@](=O)(O)O[P@](=O)(O)OC[C@@H]3[C@H](C[C@@H](O3)N4C=C(C(=O)NC4=O)C)O)C)O
• Formula: C24 H35 N4 O19 P3
• Name: (2R,3R,4S,5S,6R)-3,4-DIHYDROXY-5-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)IMINO]-6-METHYLTETRAHYDRO-2H-PYRAN-2-YL [(2R,3S,5R)-3-HYDROXY-5-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)TETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN DIPHOSPHATE
• ZINC: ZINC000098209432
• PDB chain: 2po3 Chain B Residue 2500

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2po3 Molecular Architecture of DesI: A Key Enzyme in the Biosynthesis of Desosamine
• Resolution: 2.1 Å
• Binding residue (original residue number in PDB): V2023 G2024 P2026 A2076 T2077 F2100 D2171 A2173 H2174 S2195 H2197 T2199 K2200 Y2329
• Binding residue (residue number reindexed from 1): V20 G21 P23 A73 T74 F97 D168 A170 H171 S192 H194 T196 K197 Y326
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): F2100 D2171 H2174 H2197 K2200 G2233 K2243
• Catalytic site (residue number reindexed from 1): F97 D168 H171 H194 K197 G230 K240

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

External links

• PDB: RCSB:2po3, PDBe:2po3, PDBj:2po3
• PDBsum: 2po3
• PubMed: 17630700
• UniProt: Q9ZGH0