5QXM | pdb_00005qxm

PanDDA analysis group deposition -- Crystal Structure of ATAD2 in complex with DF789

PDB DOI: https://doi.org/10.2210/pdb5QXM/pdb
Deposition Group: G_1002118 (changed state) ExploreG_1002118

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

Deposited: 2020-02-11 Released: 2020-04-08
Deposition Author(s): Snee, M., Talon, R., Fowley, D., Collins, P., Nelson, A., Arrowsmith, C.H., Bountra, C., Edwards, A., Von-Delft, F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.179 (Depositor), 0.200 (DCC)
R-Value Work:
0.164 (Depositor), 0.200 (DCC)
R-Value Observed:
0.165 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

PanDDA analysis group deposition - Bromodomain of human ATAD2 fragment screening

Snee, M., Talon, R., Fowley, D., Collins, P., Nelson, A., Arrowsmith, C.H., Bountra, C., Edwards, A., Von-Delft, F.

To be published.

Macromolecule Content

Total Structure Weight: 16.34 kDa
Atom Count: 1,494
Modeled Residue Count: 130
Deposited Residue Count: 130
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATPase family AAA domain-containing protein 2	A	130	Homo sapiens	Mutation(s): 0 Gene Names: ATAD2, L16, PRO2000 EC: 3.6.1.3 (PDB Primary Data), 3.6.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q6PL18 (Homo sapiens) Explore Q6PL18 Go to UniProtKB: Q6PL18
PHAROS: Q6PL18 GTEx: ENSG00000156802
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6PL18
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RHJ (Subject of Investigation/LOI) Query on RHJ Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	cyclobutyl[(3aS,4R,5R,7S,8aS)-4,5-dihydroxyhexahydro-1H-3a,7-epoxycyclohepta[c]pyrrol-2(3H)-yl]methanone C₁₄ H₂₁ N O₄ BYVLFJJVWOHEND-JCCXBDGPSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A]	D [auth A] E [auth A] F [auth A] H [auth A] I [auth A] D [auth A], E [auth A], F [auth A], H [auth A], I [auth A], J [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.179 (Depositor), 0.200 (DCC)
R-Value Work: 0.164 (Depositor), 0.200 (DCC)
R-Value Observed: 0.165 (Depositor)

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.769	α = 90
b = 80.769	β = 90
c = 140.797	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2020-04-08

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-04-08
Type: Initial release
Version 2.0: 2023-05-31
Changes: Database references, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2024-05-22
Changes: Data collection

Prepare Data

Validate Data

Deposit Data

Help and Resources

.id_divider{ color: #ccc; padding: 0 10px 0 10px; } .extended_id_info{ color: #ccc; font-size: 18px; position: relative; top: -10px; left: 4px; } 5QXM | pdb_00005qxm

PanDDA analysis group deposition -- Crystal Structure of ATAD2 in complex with DF789

PanDDA analysis group deposition - Bromodomain of human ATAD2 fragment screening

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations