Structure of PDB 6vdd Chain D Binding Site BS01

Receptor Information

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

GRALEPGELAAWLSEHSLGSRFGVAVVGTHKAYDADATALAIVAADGDGR
YIDTSTLTPEDEAALASWLADPGPPKALHEAKLAMHDLAGRGWTLRGVTS
DTALAAYLVRPGQRSFTLDDLAVRYLHRELRQAVQTVILRACAVLDLADA
LDQELARIDSLSLLSRMELPVQRTLAEMEHAGIAVDLGMLEQLQSEFADQ
IRDAAEAAYSVIGKQINLGSPKQLQAVLFDELEMPKTKKTKTGYTTDADA
LQSLFEKTGHPFLQHLLAHRDATRLKVTVDGLLNSVASDGRIHTTFNQTI
AATGRLSSTEPNLQNIPIRTEAGRRIRDAFVVGEGYAELMTADYSQIEMR
IMAHLSRDAGLIEAFNTGEDLHSFVASRAFSVPIDEVTPELRRRVKAMSY
GLAYGLSAYGLAQQLKISTEEAKVQMEQYFDRFGGVRDYLRDVVDQARKD
GYTSTVLGRRRYLPELDSSNRQVREAAERAALNAPIQGSAADIIKVAMIN
VDQAIKDAGLRSRILLQVHDELLFEVSEGEQGELEQLVREHMGNAYPLDV
PLEVSVGYGRSWDAAAH

Ligand information

>6vdd Chain E (length=11)

gcgatcacgta

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): T581 K582 T583 T586 T587 D588 A589 R611 R615 R646 N656 I657 P658 I659 R660 H860 D861
• Binding residue (residue number reindexed from 1): T240 K241 T242 T245 T246 D247 A248 R270 R274 R305 N315 I316 P317 I318 R319 H519 D520

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