6TDB

Neuropilin2-b1 domain in a complex with the C-terminal VEGFB167 peptide

• PDB DOI: https://doi.org/10.2210/pdb6TDB/pdb

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


• Deposited: 2019-11-08 Released: 2020-11-18 
• Deposition Author(s): Eldrid, C., Yu, L., Yelland, T., Fotinou, C., Djordjevic, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 0.250 
• R-Value Work: 0.183 
• R-Value Observed: 0.186 

Literature

NRP2-b1 domain in a complex with the C-terminal VEGFB167 peptide

Eldrid, C., Yu, L., Yelland, T., Fotinou, C., Djordjevic, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: surface plasmon resonance

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Biological Assembly Evidence: surface plasmon resonance

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 75.9 kDa 
• Atom Count: 5,451 
• Modelled Residue Count: 641 
• Deposited Residue Count: 663 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neuropilin-2	A, B, C, D	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
C-terminal VEGFB167 peptide	E [auth F], F [auth J], G [auth K]	5	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	H [auth A], I [auth B], J [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACE	K [auth F]	ACETYL GROUP C2 H4 O IKHGUXGNUITLKF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 0.250 
• R-Value Work: 0.183 
• R-Value Observed: 0.186 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.359	α = 90
b = 140.122	β = 132.972
c = 74.357	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-11-18 
Deposition Author(s): Eldrid, C., Yu, L., Yelland, T., Fotinou, C., Djordjevic, S.

Revision History  

• Version 1.0: 2020-11-18
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Advisory, Data collection, Database references, Other, Refinement description