3HW8

ternary complex of DNA polymerase lambda of a two nucleotide gapped DNA substrate with a C in the scrunch site

PDB DOI: https://doi.org/10.2210/pdb3HW8/pdb
NAKB: 3HW8

Classification: TRANSFERASE/DNA
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2009-06-17 Released: 2009-08-25
Deposition Author(s): Garcia-Diaz, M., Bebenek, K., Larrea, A.A., Havener, J.M., Perera, L., Krahn, J.M., Pedersen, L.C., Ramsden, D.A., Kunkel, T.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.233
R-Value Work: 0.212
R-Value Observed: 0.212

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Scrunching Durning DNA Repair Synthesis

Garcia-Diaz, M., Bebenek, K., Larrea, A.A., Havener, J.M., Perera, L., Krahn, J.M., Pedersen, L.C., Ramsden, D.A., Kunkel, T.A.

To be published.

Macromolecule Content

Total Structure Weight: 44.74 kDa
Atom Count: 3,340
Modelled Residue Count: 349
Deposited Residue Count: 357
Unique protein chains: 1
Unique nucleic acid chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase lambda	A	335	Homo sapiens	Mutation(s): 1 Gene Names: POLL EC: 2.7.7.7 (PDB Primary Data), 4.2.99 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UGP5 (Homo sapiens) Explore Q9UGP5 Go to UniProtKB: Q9UGP5
PHAROS: Q9UGP5 GTEx: ENSG00000166169
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9UGP5
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(CPGPGPCPCPAPAPTPAPCPTPG)-3'	B	12	N/A
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Length	Organism	Image
5'-D(CPAPGPTPAPT)-3'	C	6	N/A
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Length	Organism	Image
5'-D(PGPCPCPG)-3'	D	4	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
D3T Query on D3T Download Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE C₁₀ H₁₇ N₂ O₁₃ P₃ URGJWIFLBWJRMF-JGVFFNPUSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A] mmCIF format, chain K [auth A]	K [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A]	F [auth A], G [auth A], H [auth A], I [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]