Structure of PDB 6vde Chain B

Receptor sequence
>6vdeB (length=860) Species: 1772 (Mycolicibacterium smegmatis) [Search protein sequence]
DTPTLMLLDGNSLAFRAFYALPAENFKTQSGLTTNAVYGFTAMLINLLRD
EQPTHIAAAFDVATPDEFRGQIDITKEVLGALGITVLAEPGFEADDIIAT
LATQAEQEGYRVLVVTGDRDSLQLVSDQVTVLYPRKGVSELTRFTPDAVV
EKYGLTPQQYPDFAALRGEKTATKWIVEYGSLQALVDNVDAVKGKVGDAL
RANLSSVILNRELTDLIRDVPLPQTPDTLRMQPWNRDQIHRLFDDLEFRV
LRDRLFETLVAVEPEVEHGFDVRGRALEPGELAAWLSEHSLGSRFGVAVV
GTHKAYDADATALAIVAADGDGRYIDTSTLTPEDEAALASWLADPGPPKA
LHEAKLAMHDLAGRGWTLRGVTSDTALAAYLVRPGQRSFTLDDLAVRYLH
RELRAETPEQQQLSLLDDSDGVDEQAVQTVILRACAVLDLADALDQELAR
IDSLSLLSRMELPVQRTLAEMEHAGIAVDLGMLEQLQSEFADQIRDAAEA
AYSVIGKQINLGSPKQLQAVLFDELEMPKTKKTKTGYTTDADALQSLFEK
TGHPFLQHLLAHRDATRLKVTVDGLLNSVASDGRIHTTFNQTIAATGRLS
STEPNLQNIPIRTEAGRRIRDAFVVGEGYAELMTADYSQIEMRIMAHLSR
DAGLIEAFNTGEDLHSFVASRAFSVPIDEVTPELRRRVKAMSYGLAYGLS
AYGLAQQLKISTEEAKVQMEQYFDRFGGVRDYLRDVVDQARKDGYTSTVL
GRRRYLPELDSSNRQVREAAERAALNAPIQGSAADIIKVAMINVDQAIKD
AGLRSRILLQVHDELLFEVSEGEQGELEQLVREHMGNAYPLDVPLEVSVG
YGRSWDAAAH
3D structure
PDB6vde 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.
ChainB
Resolution2.713 Å
3D
structure
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Enzymatic activity
Enzyme Commision number 2.7.7.7: DNA-directed DNA polymerase.
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 MN B D26 D130 D153 D9 D95 D118
BS02 MN B D153 D155 D118 D120
BS03 MN B A123 D465 D471 A88 D417 D423
Gene Ontology
Molecular Function
GO:0003676 nucleic acid binding
GO:0003677 DNA binding
GO:0003824 catalytic activity
GO:0003887 DNA-directed DNA polymerase activity
GO:0004518 nuclease activity
GO:0008408 3'-5' exonuclease activity
GO:0008409 5'-3' exonuclease activity
GO:0016788 hydrolase activity, acting on ester bonds
GO:0046872 metal ion binding
Biological Process
GO:0006139 nucleobase-containing compound metabolic process
GO:0006260 DNA replication
GO:0006261 DNA-templated DNA replication
GO:0006281 DNA repair
GO:0006302 double-strand break repair
GO:0006974 DNA damage response
GO:0071897 DNA biosynthetic process

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Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6vde, PDBe:6vde, PDBj:6vde
PDBsum6vde
PubMed32034423
UniProtA0QYZ2

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