Structure of PDB 5agv Chain B Binding Site BS06

Receptor Information
>5agv Chain B (length=393) Species: 83332 (Mycobacterium tuberculosis H37Rv) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LTDLTFRLLRESFADAVSWVAKNLPARPAVPVLSGVLLTGSDNGLTISGF
DYEVSAEAQVGAEIVSPGSVLVSGRLLSDITRALPNKPVDVHVEGNRVAL
TCGNARFSLPTMPVEDYPTLPTLPEETGLLPAELFAEAISQVAIAAGRDD
TLPMLTGIRVEILGETVVLAATDRFRLAVRELKWSASSPDIEAAVLVPAK
TLAEAAKAGIGGSDVRLSLGTGPGVGKDGLLGISGNGKRSTTRLLDAEFP
KFRQLLPTEHTAVATMDVAELIEAIKLVALVADRGAQVRMEFADGSVRLS
AGADDVGRAEEDLVVDYAGEPLTIAFNPTYLTDGLSSLRSERVSFGFTTA
GKPALLRPVSGDDRPVAGLNGNGPFPAVSTDYVYLLMPVRLPG
Ligand information
Ligand IDBU3
InChIInChI=1S/C4H10O2/c1-3(5)4(2)6/h3-6H,1-2H3/t3-,4-/m1/s1
InChIKeyOWBTYPJTUOEWEK-QWWZWVQMSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C[C@H]([C@@H](C)O)O
CACTVS 3.341C[C@@H](O)[C@@H](C)O
ACDLabs 10.04OC(C)C(O)C
OpenEye OEToolkits 1.5.0CC(C(C)O)O
CACTVS 3.341C[CH](O)[CH](C)O
FormulaC4 H10 O2
Name(R,R)-2,3-BUTANEDIOL
ChEMBL
DrugBank
ZINCZINC000000901616
PDB chain5agv Chain B Residue 513 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5agv Antibiotics. Targeting Dnan for Tuberculosis Therapy Using Novel Griselimycins.
Resolution1.93 Å
Binding residue
(original residue number in PDB)		E190 D390 Y391
Binding residue
(residue number reindexed from 1)		E181 D381 Y382
Annotation score1
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5agv, PDBe:5agv, PDBj:5agv
PDBsum5agv
PubMed26045430
UniProtP9WNU1|DPO3B_MYCTU Beta sliding clamp (Gene Name=dnaN)

[Back to BioLiP]