5DQ0

Structure of human neuropilin-2 b1 domain with novel and unique zinc binding site

• PDB DOI: https://doi.org/10.2210/pdb5DQ0/pdb

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


• Deposited: 2015-09-14 Released: 2016-09-28 
• Deposition Author(s): Tsai, Y.I., Rana, R.R., Zachary, I., Djordjevic, S.
• Funding Organization(s): British Heart Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.217 
• R-Value Work: 0.177 
• R-Value Observed: 0.179 

Literature

Structure of human neuropilin-2 b1 domain with novel and unique zinc binding site

Tsai, Y.I., Frankel, P., Rana, R.R., Fotinou, C., Yelland, T.S., Zachary, I., 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: 18.96 kDa 
• Atom Count: 1,467 
• Modelled Residue Count: 157 
• Deposited Residue Count: 162 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neuropilin-2	A	162	Homo sapiens	Mutation(s): 0  Gene Names: NRP2, VEGF165R2
UniProt & NIH Common Fund Data Resources
Find proteins for O60462 (Homo sapiens) Explore O60462  Go to UniProtKB:  O60462
PHAROS:  O60462 GTEx:  ENSG00000118257

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES	I [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
ZN	B [auth A], C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	G [auth A], H [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	E [auth A], F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.217 
• R-Value Work: 0.177 
• R-Value Observed: 0.179 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.39	α = 90
b = 105.27	β = 90
c = 45.75	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Coot	model building
SCALA	data scaling
MOSFLM	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-09-28 
Deposition Author(s): Tsai, Y.I., Rana, R.R., Zachary, I., Djordjevic, S.

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Funding Organization	Location	Grant Number
British Heart Foundation	United Kingdom	PG/10/52/28448

Revision History  

• Version 1.0: 2016-09-28
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description