5UHK | pdb_00005uhk

Crystal structure of the core catalytic domain of Human O-GlcNAcase

PDB DOI: https://doi.org/10.2210/pdb5UHK/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2017-01-11 Released: 2017-03-29
Deposition Author(s): Klein, D.J., Elsen, N.L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.97 Å
R-Value Free:
0.251 (Depositor), 0.264 (DCC)
R-Value Work:
0.194 (Depositor), 0.208 (DCC)
R-Value Observed:
0.197 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5UHK

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of the core catalytic domain of human O-GlcNAcase and molecular basis of activity and inhibition

Elsen, N.L., Patel, S.B., Ford, R.E., Hall, D.L., Hess, F., Kandula, H., Kornienko, M., Lumb, K.J., Reid, J., Selnick, H., Shipman, J.M., Sharma, S., Soisson, S.M., Klein, D.J.

To be published.

Macromolecule Content

Total Structure Weight: 117.82 kDa
Atom Count: 6,936
Modeled Residue Count: 846
Deposited Residue Count: 1,016
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
O-GlcNAcase TIM-barrel domain	A, C	345	Homo sapiens	Mutation(s): 0 Gene Names: MGEA5, HEXC, KIAA0679, MEA5 EC: 3.2.1.169 (PDB Primary Data), 3.2.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for O60502 (Homo sapiens) Explore O60502 Go to UniProtKB: O60502
PHAROS: O60502 GTEx: ENSG00000198408
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O60502
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
O-GlcNAcase stalk domain	B, D	163	Homo sapiens	Mutation(s): 0 Gene Names: MGEA5, HEXC, KIAA0679, MEA5 EC: 3.2.1.169 (PDB Primary Data), 3.2.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for O60502 (Homo sapiens) Explore O60502 Go to UniProtKB: O60502
PHAROS: O60502 GTEx: ENSG00000198408
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O60502
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth C] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain G [auth C] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain G [auth C] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], G [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.97 Å
R-Value Free: 0.251 (Depositor), 0.264 (DCC)
R-Value Work: 0.194 (Depositor), 0.208 (DCC)
R-Value Observed: 0.197 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.8	α = 90
b = 96.8	β = 90
c = 256.96	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2017-03-29

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-03-29
Type: Initial release
Version 1.1: 2024-03-06
Changes: Data collection, Database references

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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.