7O1N | pdb_00007o1n

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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free: 
  0.209 (Depositor), 0.212 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

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

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

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

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

Macromolecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free:  0.209 (Depositor), 0.212 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

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

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-04-13 
Deposition Author(s): Djordjevic, S., Chandanani, J., Faleeva, M., Pinotsis, N.

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

Revision History  

• Version 1.0: 2022-04-13
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary