Brand  (β version)

PDB ID: 5KFP

Hetero Atom Contents

color scheme of protein:

hetatm:

x
information
centroid:
interaction residue:

chain: Hide other chain(s)

Ligands
Code Name Link
CA Calcium ion PoSSuM
DPO Diphosphate PoSSuM
GOL Glycerol PoSSuM
MG Magnesium ion PoSSuM
STP 2'-deoxyadenosine 5'-O-(1-thiotriphosphate) PoSSuM
Modified Residues
Code Name Link
AS 2-deoxy-adenosine -5'-thio-monophosphate PoSSuM

Structure summary

Code : 5KFP   PDBj   RCSB PDB   PDBe
Header : replication, transferase/dna
Title : Human DNA polymerase eta-DNA ternary complex with Sp-dATP-alpha-S: reaction with 20 mM Mg2+ for 600s
Release Data : 2016-06-22
Compound :
mol_id molecule chains synonym
1 DNA polymerase eta A RAD30 homolog A,Xeroderma pigmentosum variant type protein
ec: 2.7.7.7
mol_id molecule chains
2 DNA (5'-D(*CP*AP*TP*TP*AP*TP*GP*AP*CP*GP*CP*T)-3') T
mol_id molecule chains
3 DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*TP*(DS))-3') P
Source :
mol_id organism_scientific organism_common expression_system
1 Homo sapiens  (taxid:9606) Human Escherichia coli  (taxid:469008)
gene: POLH, RAD30, RAD30A, XPV
expression_system_strain: BL21(DE3)
expression_system_vector_type: plasmid
expression_system_plasmid: pET28
mol_id organism_scientific
2 Homo sapiens  (taxid:9606)
synthetic: yes
mol_id organism_scientific
3 Homo sapiens  (taxid:9606)
synthetic: yes
Authors : Gao, Y., Yang, W.
Keywords : in crystallo reaction, DNA polymerase, metal ion dependent catalysis, replication, transferase-dna complex
Exp. method : X-RAY DIFFRACTION ( 1.7000 Å )
Citation :

Capture of a third Mg2+ is essential for catalyzing DNA synthesis.

Gao, Y.,Yang, W.
(2016)  Science  352 : 1334 - 1337

PubMed: 27284197
DOI: 10.1126/science.aad9633

Reaction

Chain : A
UniProt : Q9Y253 (POLH_HUMAN)
Reaction : Reaction=a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) = diphosphate + DNA(n+1); Xref=Rhea:RHEA:22508, Rhea:RHEA-COMP:11130, Rhea:RHEA-COMP:11131, ChEBI:CHEBI:33019, ChEBI:CHEBI:61560, ChEBI:CHEBI:83828; EC=2.7.7.7; Evidence={ECO:0000269|PubMed:27284197};