2QPT

Crystal structure of an EHD ATPase involved in membrane remodelling

PDB DOI: https://doi.org/10.2210/pdb2QPT/pdb

Classification: ENDOCYTOSIS
Organism(s): Mus musculus
Expression System: Escherichia coli
Mutation(s): Yes
Membrane Protein: Yes OPM

Deposited: 2007-07-25 Released: 2007-10-16
Deposition Author(s): Daumke, O.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free:
0.276 (Depositor), 0.270 (DCC)
R-Value Work:
0.234 (Depositor), 0.230 (DCC)
R-Value Observed:
0.236 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Architectural and mechanistic insights into an EHD ATPase involved in membrane remodelling.

Daumke, O., Lundmark, R., Vallis, Y., Martens, S., Butler, P.J., McMahon, H.T.

(2007) Nature 449: 923-927

PubMed: 17914359 Search on PubMed
DOI: https://doi.org/10.1038/nature06173
Primary Citation of Related Structures:
2QPT

Macromolecule Content

Total Structure Weight: 62.4 kDa
Atom Count: 3,834
Modelled Residue Count: 476
Deposited Residue Count: 550
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EH DOMAIN-CONTAINING PROTEIN-2	A	550	Mus musculus	Mutation(s): 1 Gene Names: Ehd2 Membrane Entity: Yes
UniProt
Find proteins for Q8BH64 (Mus musculus) Explore Q8BH64 Go to UniProtKB: Q8BH64
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8BH64
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ANP Query on ANP 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]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.276 (Depositor), 0.270 (DCC)
R-Value Work: 0.234 (Depositor), 0.230 (DCC)
R-Value Observed: 0.236 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.851	α = 90
b = 134.653	β = 106.05
c = 56.068	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
SHARP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2007-10-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-10-16
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2021-10-20
Changes: Database references, Derived calculations
Version 1.3: 2024-02-21
Changes: Data collection

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.