Structure of PDB 6vde Chain B Binding Site BS01

Receptor Information
>6vde Chain B (length=860) Species: 1772 (Mycolicibacterium smegmatis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DTPTLMLLDGNSLAFRAFYALPAENFKTQSGLTTNAVYGFTAMLINLLRD
EQPTHIAAAFDVATPDEFRGQIDITKEVLGALGITVLAEPGFEADDIIAT
LATQAEQEGYRVLVVTGDRDSLQLVSDQVTVLYPRKGVSELTRFTPDAVV
EKYGLTPQQYPDFAALRGEKTATKWIVEYGSLQALVDNVDAVKGKVGDAL
RANLSSVILNRELTDLIRDVPLPQTPDTLRMQPWNRDQIHRLFDDLEFRV
LRDRLFETLVAVEPEVEHGFDVRGRALEPGELAAWLSEHSLGSRFGVAVV
GTHKAYDADATALAIVAADGDGRYIDTSTLTPEDEAALASWLADPGPPKA
LHEAKLAMHDLAGRGWTLRGVTSDTALAAYLVRPGQRSFTLDDLAVRYLH
RELRAETPEQQQLSLLDDSDGVDEQAVQTVILRACAVLDLADALDQELAR
IDSLSLLSRMELPVQRTLAEMEHAGIAVDLGMLEQLQSEFADQIRDAAEA
AYSVIGKQINLGSPKQLQAVLFDELEMPKTKKTKTGYTTDADALQSLFEK
TGHPFLQHLLAHRDATRLKVTVDGLLNSVASDGRIHTTFNQTIAATGRLS
STEPNLQNIPIRTEAGRRIRDAFVVGEGYAELMTADYSQIEMRIMAHLSR
DAGLIEAFNTGEDLHSFVASRAFSVPIDEVTPELRRRVKAMSYGLAYGLS
AYGLAQQLKISTEEAKVQMEQYFDRFGGVRDYLRDVVDQARKDGYTSTVL
GRRRYLPELDSSNRQVREAAERAALNAPIQGSAADIIKVAMINVDQAIKD
AGLRSRILLQVHDELLFEVSEGEQGELEQLVREHMGNAYPLDVPLEVSVG
YGRSWDAAAH
Ligand information
Ligand IDMN
InChIInChI=1S/Mn/q+2
InChIKeyWAEMQWOKJMHJLA-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Mn+2]
CACTVS 3.341[Mn++]
FormulaMn
NameMANGANESE (II) ION
ChEMBL
DrugBankDB06757
ZINC
PDB chain6vde Chain B Residue 1001 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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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.
Resolution2.713 Å
Binding residue
(original residue number in PDB)		D26 D130 D153
Binding residue
(residue number reindexed from 1)		D9 D95 D118
Annotation score1
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: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

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

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