4PQD | pdb_00004pqd

The longer crystal structure of the grow factor like domain from Beta amypoid precusor protein (APP22-126)

PDB DOI: https://doi.org/10.2210/pdb4PQD/pdb

Classification: PROTEIN BINDING
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-03-02 Released: 2015-04-08
Deposition Author(s): Tan, X., Li, W., Wang, Z.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.33 Å
R-Value Free:
0.186 (Depositor), 0.186 (DCC)
R-Value Work:
0.170 (Depositor), 0.170 (DCC)
R-Value Observed:
0.171 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4PQD

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

Literature

Mapping the interaction betwwen APP and DR6

Tan, X., Li, W., Wang, Z.

To be published.

Macromolecule Content

Total Structure Weight: 11.84 kDa
Atom Count: 986
Modeled Residue Count: 105
Deposited Residue Count: 105
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Amyloid beta A4 protein	A	105	Homo sapiens	Mutation(s): 0 Gene Names: APP, A4, AD1
UniProt & NIH Common Fund Data Resources
Find proteins for P05067 (Homo sapiens) Explore P05067 Go to UniProtKB: P05067
PHAROS: P05067 GTEx: ENSG00000142192
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P05067
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.33 Å
R-Value Free: 0.186 (Depositor), 0.186 (DCC)
R-Value Work: 0.170 (Depositor), 0.170 (DCC)
R-Value Observed: 0.171 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.755	α = 90
b = 49.025	β = 90
c = 65.141	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2015-04-08

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-04-08
Type: Initial release
Version 1.1: 2024-10-09
Changes: Data collection, Database references, Structure summary

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.