9EWD | pdb_00009ewd

DNA Polymerase Lambda I493K E529D, TMP:At Ca2+ Ground State Ternary Complex

PDB DOI: https://doi.org/10.2210/pdb9EWD/pdb

Classification: NUCLEAR PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2024-04-03 Released: 2025-07-23
Deposition Author(s): Nourisson, A., Haouz, A., Missoury, S., Delarue, M.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.12 Å
R-Value Free:
0.245 (Depositor), 0.242 (DCC)
R-Value Work:
0.202 (Depositor), 0.199 (DCC)
R-Value Observed:
0.204 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

DNA Polymerase Lambda I493K E529D, TTP:At Ca2+ Ground State Ternary Complex

Nourisson, A., Haouz, A., Missoury, S., Delarue, M.

To be published.

Macromolecule Content

Total Structure Weight: 43.92 kDa
Atom Count: 3,161
Modeled Residue Count: 341
Deposited Residue Count: 351
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	330	Homo sapiens	Mutation(s): 2 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
DNA primer strand downstream (5'P)	B [auth D]	4	Homo sapiens
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA primer strand upstream	C [auth P]	6	Homo sapiens
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA template strand	D [auth T]	11	Homo sapiens
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TMP (Subject of Investigation/LOI) Query on TMP 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]	THYMIDINE-5'-PHOSPHATE C₁₀ H₁₅ N₂ O₈ P GYOZYWVXFNDGLU-XLPZGREQSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
GOL Query on GOL 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]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-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 H [auth A] SDF format, chain I [auth A] SDF format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain G [auth A]	G [auth A], H [auth A], I [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A] mmCIF format, chain M [auth A]	M [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]
K Query on K Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A]	K [auth A], L [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Interactions & Density Focus chain K [auth A] Focus chain L [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain N [auth A] MOL2 format, chain F [auth A] MOL2 format, chain N [auth A] mmCIF format, chain F [auth A] mmCIF format, chain N [auth A]	F [auth A], N [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain N [auth A] Interactions & Density Focus chain F [auth A] Focus chain N [auth A]