Structure of PDB 5agv Chain B Binding Site BS01

Receptor Information

>5agv Chain B (length=393) Species: 83332 (Mycobacterium tuberculosis H37Rv)

LTDLTFRLLRESFADAVSWVAKNLPARPAVPVLSGVLLTGSDNGLTISGF
DYEVSAEAQVGAEIVSPGSVLVSGRLLSDITRALPNKPVDVHVEGNRVAL
TCGNARFSLPTMPVEDYPTLPTLPEETGLLPAELFAEAISQVAIAAGRDD
TLPMLTGIRVEILGETVVLAATDRFRLAVRELKWSASSPDIEAAVLVPAK
TLAEAAKAGIGGSDVRLSLGTGPGVGKDGLLGISGNGKRSTTRLLDAEFP
KFRQLLPTEHTAVATMDVAELIEAIKLVALVADRGAQVRMEFADGSVRLS
AGADDVGRAEEDLVVDYAGEPLTIAFNPTYLTDGLSSLRSERVSFGFTTA
GKPALLRPVSGDDRPVAGLNGNGPFPAVSTDYVYLLMPVRLPG

Ligand information

>5agv Chain D (length=10)

VPTLPLVPLG

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5agv Antibiotics. Targeting Dnan for Tuberculosis Therapy Using Novel Griselimycins.
• Resolution: 1.93 Å
• Binding residue (original residue number in PDB): R183 F184 R185 E257 L264 M396 P397 V398 R399
• Binding residue (residue number reindexed from 1): R174 F175 R176 E248 L255 M387 P388 V389 R390

Enzymatic activity

• Enzyme Commision number: 2.7.7.7: DNA-directed DNA polymerase.

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0003887 DNA-directed DNA polymerase activity
• GO:0008408 3'-5' exonuclease activity
• GO:0042802 identical protein binding

Biological Process

• GO:0006260 DNA replication
• GO:0006271 DNA strand elongation involved in DNA replication
• GO:0046677 response to antibiotic
• GO:0071897 DNA biosynthetic process

Cellular Component

• GO:0005576 extracellular region
• GO:0005737 cytoplasm
• GO:0009274 peptidoglycan-based cell wall
• GO:0009360 DNA polymerase III complex

External links

• PDB: RCSB:5agv, PDBe:5agv, PDBj:5agv
• PDBsum: 5agv
• PubMed: 26045430
• UniProt: P9WNU1|DPO3B_MYCTU Beta sliding clamp (Gene Name=dnaN)