1XSN

Crystal Structure of human DNA polymerase lambda in complex with a one nucleotide DNA gap and ddTTP

PDB DOI: https://doi.org/10.2210/pdb1XSN/pdb
NAKB: 1XSN

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

Deposited: 2004-10-19 Released: 2005-01-18
Deposition Author(s): Garcia-Diaz, M., Bebenek, K., Krahn, J.M., Kunkel, T.A., Pedersen, L.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.255
R-Value Work: 0.213
R-Value Observed: 0.213

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

A closed conformation for the Pol lambda catalytic cycle.

Garcia-Diaz, M., Bebenek, K., Krahn, J.M., Kunkel, T.A., Pedersen, L.C.

(2005) Nat Struct Mol Biol 12: 97-98

PubMed: 15608652 Search on PubMed
DOI: https://doi.org/10.1038/nsmb876
Primary Citation of Related Structures:
1XSL, 1XSN, 1XSP

PubMed Abstract:
Pol lambda is a family X member believed to fill short gaps during DNA repair. Here we report crystal structures of Pol lambda representing three steps in filling a single-nucleotide gap. These structures indicate that, unlike other DNA polymerases, Pol lambda does not undergo large subdomain movements during catalysis, and they provide a clear characterization of the geometry and stereochemistry of the in-line nucleotidyl transfer reaction.

Organizational Affiliation

Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina 27709, USA.

Macromolecule Content

Total Structure Weight: 44.57 kDa
Atom Count: 3,305
Modelled Residue Count: 345
Deposited Residue Count: 356
Unique protein chains: 1
Unique nucleic acid chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase lambda	D [auth A]	335	Homo sapiens	Mutation(s): 1 Gene Names: POLL EC: 2.7.7.7 (PDB Primary Data), 4.2.99 (UniProt)
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: 1
Molecule	Chains	Length	Organism	Image
5'-D(CPGPGPCPAPAPTPAPCPTP*G)-3'	A [auth T]	11	N/A
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(CPAPGPTPAP(2DT))-3'	B [auth P]	6	N/A
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Length	Organism	Image
5'-D(PGPCPCPG)-3'	C [auth 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 L [auth A] MOL2 format, chain L [auth A] mmCIF format, chain L [auth A]	L [auth A]	2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE C₁₀ H₁₇ N₂ O₁₃ P₃ URGJWIFLBWJRMF-JGVFFNPUSA-N		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain E [auth T] SDF format, chain F [auth P] SDF format, chain G [auth P] SDF format, chain H [auth P] MOL2 format, chain E [auth T] MOL2 format, chain F [auth P] MOL2 format, chain G [auth P] MOL2 format, chain H [auth P] mmCIF format, chain E [auth T] mmCIF format, chain F [auth P] mmCIF format, chain G [auth P] mmCIF format, chain H [auth P]	E [auth T], F [auth P], G [auth P], H [auth P]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth T] Focus chain F [auth P] Focus chain G [auth P] Focus chain H [auth P] Interactions & Density Focus chain E [auth T] Focus chain F [auth P] Focus chain G [auth P] Focus chain H [auth P]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A]	J [auth A], K [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain J [auth A] Focus chain K [auth A]