5GNH | pdb_00005gnh

Myotubularin-related protein 2

PDB DOI: https://doi.org/10.2210/pdb5GNH/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2016-07-21 Released: 2017-07-26
Deposition Author(s): Lee, B.I., Bong, S.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.258 (Depositor), 0.228 (DCC)
R-Value Work:
0.203 (Depositor)
R-Value Observed:
0.206 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5GNH

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

Literature

Crystal structure of MTMR2

Lee, B.I., Bong, S.M.

To be published.

Macromolecule Content

Total Structure Weight: 132.35 kDa
Atom Count: 8,330
Modeled Residue Count: 1,012
Deposited Residue Count: 1,142
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Myotubularin-related protein 2	A, B	571	Homo sapiens	Mutation(s): 1 Gene Names: MTMR2, KIAA1073 EC: 3.1.3.95 (PDB Primary Data), 3.1.3.64 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q13614 (Homo sapiens) Explore Q13614 Go to UniProtKB: Q13614
PHAROS: Q13614 GTEx: ENSG00000087053
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q13614
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B], E [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Focus chain D [auth B] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.258 (Depositor), 0.228 (DCC)
R-Value Work: 0.203 (Depositor)
R-Value Observed: 0.206 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 158.344	α = 90
b = 82.82	β = 117.59
c = 99.972	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data processing
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2017-07-26

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-07-26
Type: Initial release
Version 1.1: 2024-03-20
Changes: Data collection, Database references, Refinement description

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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.