5QP9 | pdb_00005qp9

PanDDA analysis group deposition -- Crystal Structure of DCP2 (NUDT20) in complex with Z100435060

PDB DOI: https://doi.org/10.2210/pdb5QP9/pdb
Deposition Group: G_1002061 (changed state) | Explore G_1002061

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

Deposited: 2019-02-22 Released: 2019-05-08
Deposition Author(s): Nelson, E.R., Velupillai, S., Talon, R., Collins, P.M., Krojer, T., Wang, D., Brandao-Neto, J., Douangamath, A., Burgess-Brown, N., Arrowsmith, C.H., Bountra, C., Huber, K., von Delft, F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.72 Å
R-Value Free:
0.253 (Depositor), 0.257 (DCC)
R-Value Work:
0.202 (Depositor), 0.224 (DCC)
R-Value Observed:
0.204 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

PanDDA analysis group deposition

Nelson, E.R., Velupillai, S., Talon, R., Collins, P.M., Krojer, T., Wang, D., Brandao-Neto, J., Douangamath, A., Burgess-Brown, N., Arrowsmith, C.H., Bountra, C., Huber, K., von Delft, F.

To be published.

Macromolecule Content

Total Structure Weight: 19.64 kDa
Atom Count: 1,328
Modeled Residue Count: 149
Deposited Residue Count: 167
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DCP2 (NUDT20)	A	167	Homo sapiens	Mutation(s): 0 Gene Names: DCP2, NUDT20 EC: 3.6.1.62
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IU60 (Homo sapiens) Explore Q8IU60 Go to UniProtKB: Q8IU60
PHAROS: Q8IU60 GTEx: ENSG00000172795
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8IU60
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LJD Query on LJD 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]	N-[(4-chlorophenyl)methyl]-1-methyl-1H-pyrazole-4-carboxamide C₁₂ H₁₂ Cl N₃ O LBSYJSKGYMMGBC-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
EDO Query on EDO 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]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A]	E [auth A], F [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A]