5C7G

Crystal Structure of the b1 Domain of Human Neuropilin-1 in complex with a bicine molecule

• PDB DOI: https://doi.org/10.2210/pdb5C7G/pdb

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


• Deposited: 2015-06-24 Released: 2016-07-06 
• Deposition Author(s): Didierjean, C., Jelsch, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.172 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.141 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.143 (Depositor) 

Starting Model: experimental

Literature

Design, synthesis and biological evaluation of new peptidomimetic compounds targeting NRP-1 receptor TO BE PUBLISHED

Richard, M., Pelligrini Moise, N., Jelsch, C., Maigret, B., Didierjean, C., Manival, X., Charron, C.

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: 18.61 kDa 
• Atom Count: 1,528 
• Modelled Residue Count: 155 
• Deposited Residue Count: 161 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neuropilin-1	A	161	Homo sapiens	Mutation(s): 0  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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BCN	B [auth A]	BICINE C6 H13 N O4 FSVCELGFZIQNCK-UHFFFAOYSA-N
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.172 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.141 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.143 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.28	α = 90
b = 62.28	β = 90
c = 85.96	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-07-06 
Deposition Author(s): Didierjean, C., Jelsch, C.

Revision History  

• Version 1.0: 2016-07-06
  Type: Initial release
  
• Version 2.0: 2024-01-10
  Changes: Atomic model, Data collection, Database references, Derived calculations, Refinement description
• Version 2.1: 2024-10-09
  Changes: Structure summary