Structure of PDB 2vg2 Chain B Binding Site BS01

Receptor Information

>2vg2 Chain B (length=283) Species: 1773 (Mycobacterium tuberculosis)

FPQLPPAPDDYPTFPDTSTWPVVFPELPAAPYGGPCRPPQHTSKAAAPRI
PADRLPNHVAIVMDGNGRWATQRGLARTEGHKMGEAVVIDIACGAIELGI
KWLSLYAFSTENWKRSPEEVRFLMGFNRDVVRRRRDTLKKLGVRIRWVGS
RPRLWRSVINELAVAEEMTKSNDVITINYCVNYGGRTEITEATREIAREV
AAGRLNPERITESTIARHLQRPDIPDVDLFLRTSGEQRSSNFMLWQAAYA
EYIFQDKLWPDYDRRDLWAACEEYASRTRRFGS

Ligand information

• Ligand ID: DPO
• InChI: InChI=1S/H4O7P2/c1-8(2,3)7-9(4,5)6/h(H2,1,2,3)(H2,4,5,6)/p-4
• InChIKey: XPPKVPWEQAFLFU-UHFFFAOYSA-J
• SMILES:
  CACTVS 3.370: [O-][P]([O-])(=O)O[P]([O-])([O-])=O
  OpenEye OEToolkits 1.7.2: [O-]P(=O)([O-])OP(=O)([O-])[O-]
  ACDLabs 12.01: [O-]P([O-])(=O)OP([O-])([O-])=O
• Formula: O7 P2
• Name: DIPHOSPHATE
• PDB chain: 2vg2 Chain B Residue 1296

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2vg2 The structural basis of chain length control in Rv1086.
• Resolution: 1.95 Å
• Binding residue (original residue number in PDB): D76 G77 N78 G79 R80 R89 H93 R127
• Binding residue (residue number reindexed from 1): D64 G65 N66 G67 R68 R77 H81 R115
• Annotation score: 5

Enzymatic activity

• Catalytic site (original residue number in PDB): D76 H93 I187
• Catalytic site (residue number reindexed from 1): D64 H81 I175
• Enzyme Commision number: 2.5.1.86: trans,polycis-decaprenyl diphosphate synthase.
  2.5.1.87: ditrans,polycis-polyprenyl diphosphate synthase [(2E,6E)-farnesyl diphosphate specific].

Gene Ontology

Molecular Function

• GO:0000287 magnesium ion binding
• GO:0004659 prenyltransferase activity
• GO:0008834 di-trans,poly-cis-undecaprenyl-diphosphate synthase activity
• GO:0016740 transferase activity
• GO:0016765 transferase activity, transferring alkyl or aryl (other than methyl) groups
• GO:0030145 manganese ion binding
• GO:0033850 Z-farnesyl diphosphate synthase activity
• GO:0045547 dehydrodolichyl diphosphate synthase activity
• GO:0046872 metal ion binding
• GO:0052923 all-trans-nonaprenyl-diphosphate synthase (geranyl-diphosphate specific) activity

Biological Process

• GO:0016094 polyprenol biosynthetic process

Cellular Component

• GO:0005829 cytosol
• GO:0005886 plasma membrane

External links

• PDB: RCSB:2vg2, PDBe:2vg2, PDBj:2vg2
• PDBsum: 2vg2
• PubMed: 18597781
• UniProt: P9WFF7|DPDS_MYCTU Decaprenyl diphosphate synthase (Gene Name=uppS)