Structure of PDB 6vdd Chain A Binding Site BS02

Receptor Information

>6vdd Chain A (length=567) Species: 1772 (Mycolicibacterium smegmatis)

RGRALEPGELAAWLSEHSLGSRFGVAVVGTHKAYDADATALAIVAADGDG
RYIDTSTLTPEDEAALASWLADPGPPKALHEAKLAMHDLAGRGWTLRGVT
SDTALAAYLVRPGQRSFTLDDLAVRYLHRELRAVQTVILRACAVLDLADA
LDQELARIDSLSLLSRMELPVQRTLAEMEHAGIAVDLGMLEQLQSEFADQ
IRDAAEAAYSVIGKQINLGSPKQLQAVLFDELEMPKTKKTKTGYTTDADA
LQSLFEKTGHPFLQHLLAHRDATRLKVTVDGLLNSVASDGRIHTTFNQTI
AATGRLSSTEPNLQNIPIRTEAGRRIRDAFVVGEGYAELMTADYSQIEMR
IMAHLSRDAGLIEAFNTGEDLHSFVASRAFSVPIDEVTPELRRRVKAMSY
GLAYGLSAYGLAQQLKISTEEAKVQMEQYFDRFGGVRDYLRDVVDQARKD
GYTSTVLGRRRYLPELDSSNRQVREAAERAALNAPIQGSAADIIKVAMIN
VDQAIKDAGLRSRILLQVHDELLFEVSEGEQGELEQLVREHMGNAYPLDV
PLEVSVGYGRSWDAAAH

Ligand information

>6vdd Chain C (length=14)

cgtacgtgatcgca

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6vdd 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: 1.9 Å
• Binding residue (original residue number in PDB): N558 G560 S561 K563 Q564 I641 A642 A643 T644 S648 S649 T650 E651 N653 Y745 L747 S748 Y750 G751 R802 R820 Q828
• Binding residue (residue number reindexed from 1): N217 G219 S220 K222 Q223 I300 A301 A302 T303 S307 S308 T309 E310 N312 Y404 L406 S407 Y409 G410 R461 R479 Q487

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:6vdd, PDBe:6vdd, PDBj:6vdd
• PDBsum: 6vdd
• PubMed: 32034423
• UniProt: A0QYZ2