5QPC | pdb_00005qpc

Crystal Structure of DCP2 (NUDT20) after initial refinement with no ligand modelled (structure $n)

PDB DOI: https://doi.org/10.2210/pdb5QPC/pdb
Deposition Group: G_1002062 (ground state) | Explore G_1002062

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: 1.66 Å
R-Value Free:
0.236 (Depositor), 0.236 (DCC)
R-Value Work:
0.197 (Depositor), 0.197 (DCC)
R-Value Observed:
0.199 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5QPC

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

Literature

PanDDA analysis group deposition of ground-state model

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: 19.5 kDa
Atom Count: 1,368
Modeled Residue Count: 149
Deposited Residue Count: 167
Unique protein chains: 1

Macromolecules

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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
PEG Query on PEG 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]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-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 F [auth A] SDF format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [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]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.66 Å
R-Value Free: 0.236 (Depositor), 0.236 (DCC)
R-Value Work: 0.197 (Depositor), 0.197 (DCC)
R-Value Observed: 0.199 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.23	α = 90
b = 61.198	β = 90
c = 66.037	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2019-05-08

Deposition Author(s):

Brandao-Neto, J.

Douangamath, A.

Burgess-Brown, N.

Arrowsmith, C.H.

Revision History (Full details and data files)

Version 1.0: 2019-05-08
Type: Initial release
Version 1.1: 2019-11-20
Changes: Data collection
Version 1.2: 2024-03-06
Changes: Data collection, Database references
Version 1.3: 2026-02-18
Changes: Refinement description, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.