5T3P

Crystal structure of Human Peroxisomal coenzyme A diphosphatase NUDT7

PDB DOI: https://doi.org/10.2210/pdb5T3P/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-08-26 Released: 2017-09-13
Deposition Author(s): Srikannathasan, V., Nunez, C.A., Tallant, C., Siejka, P., Mathea, S., Kopec, J., Elkins, J.M., Burgess-Brown, N., Arrowsmith, C.H., Edwards, A.M., Bountra, C., von Delft, F., Huber, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.03 Å
R-Value Free: 0.225
R-Value Work: 0.177
R-Value Observed: 0.180

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of Human Peroxisomal coenzyme A diphosphatase NUDT7

Srikannathasan, V.

To be published.

Macromolecule Content

Total Structure Weight: 80.75 kDa
Atom Count: 5,567
Modelled Residue Count: 660
Deposited Residue Count: 708
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisomal coenzyme A diphosphatase NUDT7	A, B, C	236	Homo sapiens	Mutation(s): 0 Gene Names: NUDT7 EC: 3.6.1 (PDB Primary Data), 3.6.1.77 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P0C024 (Homo sapiens) Explore P0C024 Go to UniProtKB: P0C024
PHAROS: P0C024 GTEx: ENSG00000140876
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0C024
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
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 G [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth C] SDF format, chain L [auth C] SDF format, chain M [auth C] 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 B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth C] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth C] mmCIF format, chain L [auth C] mmCIF format, chain M [auth C]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth B] D [auth A], E [auth A], F [auth A], G [auth A], H [auth B], I [auth B], J [auth B], K [auth C], L [auth C], M [auth C]	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 G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.03 Å
R-Value Free: 0.225
R-Value Work: 0.177
R-Value Observed: 0.180
Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.73	α = 90
b = 113.73	β = 90
c = 108.2	γ = 120

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2017-09-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-09-13
Type: Initial release
Version 1.1: 2018-02-07
Changes: Data collection
Version 1.2: 2024-01-17
Changes: Data collection, Database references, Refinement description