4RN5 | pdb_00004rn5

B1 domain of human Neuropilin-1 with acetate ion in a ligand-binding site

• PDB DOI: https://doi.org/10.2210/pdb4RN5/pdb

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


• Deposited: 2014-10-23 Released: 2015-10-28 
• Deposition Author(s): Allerston, C.K., Yelland, T.S., Jarvis, A., Jenkins, K., Winfield, N., Cheng, L., Jia, H., Zachary, I., Selwood, D.L., Djordjevic, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free: 
  0.201 (Depositor), 0.196 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Literature

Conserved water molecules in a ligand-binding site of neuropilin-1

Allerston, C.K., Yelland, T.S., Jarvis, A., Jenkins, K., Winfield, N., Cheng, L., Jia, H., Zachary, I., Selwood, D.L., Djordjevic, S.

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: 18.2 kDa 
• Atom Count: 1,432 
• Modelled Residue Count: 158 
• Deposited Residue Count: 158 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neuropilin-1	A	158	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT	B [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free:  0.201 (Depositor), 0.196 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.839	α = 90
b = 62.839	β = 90
c = 87.918	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
PHASER	phasing
PHENIX	refinement
d*TREK	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-10-28 
Deposition Author(s): Allerston, C.K., Yelland, T.S., Jarvis, A., Jenkins, K., Winfield, N., Cheng, L., Jia, H., Zachary, I., Selwood, D.L., Djordjevic, S.

Revision History  

• Version 1.0: 2015-10-28
  Type: Initial release
  
• Version 1.1: 2024-11-27
  Changes: Data collection, Database references, Derived calculations, Structure summary