Structure of PDB 6vdc Chain A Binding Site BS01

Receptor Information

>6vdc Chain A (length=497) Species: 1772 (Mycolicibacterium smegmatis)

GRALEPGELAAWLSEHSLGSRFGVAVVGTHKAYDADATALAIVAADGDGR
YIDTSTLTPEDEAALASWLADPGPPKALHEAKLAMHDLAGRGWTLRGVTS
DTALAAYLVRPGQRSFTLDDLAVRYLHRELRGVDEQAVQTVILRACAVLD
LADALDQELARIDSLSLLSRMELPVQRTLAEMEHAGIAVDLGMLEQLQSE
FADQIRDAPFLQHLLAHRDATRLKVTVDGLLNSVASDGRIHTTFNQTIAA
TGRLSSTEPNLQNIPIRTEAGRRIRDAFVVGEGYAELMTADYSQIEMRIM
AHLSRDAGLIEAFNTGEDLHSFVASRAFSVPEVTPELRRRVKAMSYGLAE
EAKVQMEQYFDRFGGVRDYLRDVVDQARKDGYTSTVLGRRRYLPELDSSN
RQVREAAERAALNAPIQGSAADIIKVAMINVDQAIKDAGLRSRILLQVHD
ELLFEVSEGEQGELEQLVREHMGNAYPLDVPLEVSVGYGRSWDAAAH

Ligand information

• Ligand ID: MN
• InChI: InChI=1S/Mn/q+2
• InChIKey: WAEMQWOKJMHJLA-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Mn+2]
  CACTVS 3.341: [Mn++]
• Formula: Mn
• Name: MANGANESE (II) ION
• DrugBank: DB06757
• PDB chain: 6vdc Chain A Residue 1001

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6vdc Mycobacterial DNA polymerase I: activities and crystal structures of the POL domain as apoenzyme and in complex with a DNA primer-template and of the full-length FEN/EXO-POL enzyme.
• Resolution: 2.402 Å
• Binding residue (original residue number in PDB): H337 D367 D369
• Binding residue (residue number reindexed from 1): H16 D46 D48
• Annotation score: 1

Enzymatic activity

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

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding
• GO:0003677 DNA binding
• GO:0003887 DNA-directed DNA polymerase activity
• GO:0008408 3'-5' exonuclease activity

Biological Process

• GO:0006139 nucleobase-containing compound metabolic process
• GO:0006260 DNA replication
• GO:0006261 DNA-templated DNA replication

External links

• PDB: RCSB:6vdc, PDBe:6vdc, PDBj:6vdc
• PDBsum: 6vdc
• PubMed: 32034423
• UniProt: A0QYZ2