5QIX

Covalent fragment group deposition -- Crystal Structure of OUTB2 in complex with PCM-0103007

PDB DOI: https://doi.org/10.2210/pdb5QIX/pdb
Deposition Group: G_1002053 (changed state) ExploreG_1002053

Classification: hydrolase/hydrolase inhibitor
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-08-10 Released: 2019-12-18
Deposition Author(s): Sethi, R., Douangamath, A., Resnick, E., Bradley, A.R., Collins, P., Brandao-Neto, J., Talon, R., Krojer, T., Bountra, C., Arrowsmith, C.H., Edwards, A., London, N., von Delft, F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.39 Å
R-Value Free: 0.198
R-Value Work: 0.147
R-Value Observed: 0.149

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Covalent fragment group deposition

Sethi, R., Douangamath, A., Resnick, E., Bradley, A.R., Collins, P., Brandao-Neto, J., Talon, R., Krojer, T., Bountra, C., Arrowsmith, C.H., Edwards, A., London, N., von Delft, F.

To be published.

Macromolecule Content

Total Structure Weight: 26.97 kDa
Atom Count: 2,146
Modelled Residue Count: 223
Deposited Residue Count: 225
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin thioesterase OTUB2	A	225	Homo sapiens	Mutation(s): 0 Gene Names: OTUB2, C14orf137, OTB2, OTU2 EC: 3.4.19.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q96DC9 (Homo sapiens) Explore Q96DC9 Go to UniProtKB: Q96DC9
PHAROS: Q96DC9 GTEx: ENSG00000089723
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q96DC9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
J5V Query on J5V Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	N-(3-phenylprop-2-yn-1-yl)acetamide C₁₁ H₁₁ N O MEDMJWLHQZDCBX-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] 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 C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [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]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]
UNL Query on UNL Download Ideal Coordinates CCD File	J [auth A], K [auth A], L [auth A]	Unknown ligand LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A]