5LBA | pdb_00005lba

Crystal structure of human RECQL5 helicase in complex with DSPL fragment(1-cyclohexyl-3-(oxolan-2-ylmethyl)urea, SGC - Diamond XChem I04-1 fragment screening.

PDB DOI: https://doi.org/10.2210/pdb5LBA/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2016-06-15 Released: 2016-07-06
Deposition Author(s): Newman, J.A., Aitkenhead, H., Talon, R., Savitsky, P., Krojer, T., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Gileadi, O., Structural Genomics Consortium (SGC)
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.303 (Depositor), 0.331 (DCC)
R-Value Work:
0.237 (Depositor), 0.271 (DCC)
R-Value Observed:
0.240 (Depositor)

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

Crystal structure of human RECQL5 helicase in complex with 3D fragment (1-cyclohexyl-3-(oxolan-2-ylmethyl)urea)

Newman, J.A., Talon, R., Aitkenhead, H., Savitsky, P., Krojer, T., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Gileadi, O.

To be published.

Macromolecule Content

Total Structure Weight: 200.68 kDa
Atom Count: 13,954
Modeled Residue Count: 1,733
Deposited Residue Count: 1,780
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent DNA helicase Q5	A [auth B], B [auth A], C, D	445	Homo sapiens	Mutation(s): 0 Gene Names: RECQL5, RECQ5 EC: 3.6.4.12 (PDB Primary Data), 5.6.2.4 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O94762 (Homo sapiens) Explore O94762 Go to UniProtKB: O94762
PHAROS: O94762 GTEx: ENSG00000108469
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O94762
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain S [auth D] SDF format, chain P [auth C] SDF format, chain K [auth A] SDF format, chain G [auth B] MOL2 format, chain S [auth D] MOL2 format, chain P [auth C] MOL2 format, chain K [auth A] MOL2 format, chain G [auth B] mmCIF format, chain S [auth D] mmCIF format, chain P [auth C] mmCIF format, chain K [auth A] mmCIF format, chain G [auth B]	G [auth B], K [auth A], P [auth C], S [auth D]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain G [auth B] Focus chain K [auth A] Focus chain P [auth C] Focus chain S [auth D] Interactions & Density Focus chain G [auth B] Focus chain K [auth A] Focus chain P [auth C] Focus chain S [auth D]
6SV Query on 6SV Download:Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	1-cyclohexyl-3-[[(2~{R})-oxolan-2-yl]methyl]urea C₁₂ H₂₂ N₂ O₂ RYUZWZOTJULRNS-LLVKDONJSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain T [auth D] SDF format, chain M [auth A] MOL2 format, chain H [auth B] MOL2 format, chain T [auth D] MOL2 format, chain M [auth A] mmCIF format, chain H [auth B] mmCIF format, chain T [auth D] mmCIF format, chain M [auth A]	H [auth B], M [auth A], T [auth D]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Focus chain M [auth A] Focus chain T [auth D] Interactions & Density Focus chain H [auth B] Focus chain M [auth A] Focus chain T [auth D]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain R [auth D] SDF format, chain O [auth C] SDF format, chain L [auth A] SDF format, chain F [auth B] MOL2 format, chain R [auth D] MOL2 format, chain O [auth C] MOL2 format, chain L [auth A] MOL2 format, chain F [auth B] mmCIF format, chain R [auth D] mmCIF format, chain O [auth C] mmCIF format, chain L [auth A] mmCIF format, chain F [auth B]	F [auth B], L [auth A], O [auth C], R [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Focus chain L [auth A] Focus chain O [auth C] Focus chain R [auth D] Interactions & Density Focus chain F [auth B] Focus chain L [auth A] Focus chain O [auth C] Focus chain R [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain N [auth C] SDF format, chain Q [auth D] SDF format, chain J [auth A] SDF format, chain E [auth B] MOL2 format, chain N [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain J [auth A] MOL2 format, chain E [auth B] mmCIF format, chain N [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain J [auth A] mmCIF format, chain E [auth B]	E [auth B], J [auth A], N [auth C], Q [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Focus chain J [auth A] Focus chain N [auth C] Focus chain Q [auth D] Interactions & Density Focus chain E [auth B] Focus chain J [auth A] Focus chain N [auth C] Focus chain Q [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.303 (Depositor), 0.331 (DCC)
R-Value Work: 0.237 (Depositor), 0.271 (DCC)
R-Value Observed: 0.240 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.926	α = 109.9
b = 85.261	β = 90.02
c = 105.915	γ = 97.01

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
REFMAC	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2016-07-06

Deposition Author(s):

Structural Genomics Consortium (SGC)

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	--

Revision History (Full details and data files)

Version 1.0: 2016-07-06
Type: Initial release
Version 1.1: 2018-01-24
Changes: Database references, Structure summary
Version 1.2: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-10-16
Changes: Structure summary