7O1N

Crystal Structure of Human Neuropilin-1 b1 Domain mutant - Y297A

PDB DOI: https://doi.org/10.2210/pdb7O1N/pdb

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

Deposited: 2021-03-29 Released: 2022-04-13
Deposition Author(s): Djordjevic, S., Chandanani, J., Faleeva, M., Pinotsis, N.
Funding Organization(s): Higher Education Funding Council for England

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.56 Å
R-Value Free: 0.209
R-Value Work: 0.180
R-Value Observed: 0.181

wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of Human Neuropilin-1 b1 Domain mutant - Y297A

Djordjevic, S., Chandanani, J., Faleeva, M., Siew, K., Pinotsis, N.

To be published.

Macromolecule Content

Total Structure Weight: 17.5 kDa
Atom Count: 1,382
Modelled Residue Count: 155
Deposited Residue Count: 155
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neuropilin-1	A	155	Homo sapiens	Mutation(s): 1 Gene Names: NRP1, NRP, VEGF165R
UniProt & NIH Common Fund Data Resources
Find proteins for O14786 (Homo sapiens) Explore O14786 Go to UniProtKB: O14786
PHAROS: O14786 GTEx: ENSG00000099250
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O14786
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.56 Å
R-Value Free: 0.209
R-Value Work: 0.180
R-Value Observed: 0.181
Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.076	α = 90
b = 80.076	β = 90
c = 62.198	γ = 120

Software Package:

Software Name	Purpose
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
Coot	model building
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2022-04-13

Deposition Author(s):

Funding Organization	Location	Grant Number
Higher Education Funding Council for England	United Kingdom	--

Revision History (Full details and data files)

Version 1.0: 2022-04-13
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Refinement description

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.