6TJT

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

• PDB DOI: https://doi.org/10.2210/pdb6TJT/pdb

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


• Deposited: 2019-11-26 Released: 2020-12-16 
• 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: 1.31 Å
• R-Value Free: 0.179 
• R-Value Work: 0.153 
• R-Value Observed: 0.154 

Starting Model: experimental

Literature

NRP2-b1 domain in a complex with the C-terminal VEGFC 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

Macromolecule Content

• Total Structure Weight: 38.84 kDa 
• Atom Count: 2,955 
• Modelled Residue Count: 323 
• Deposited Residue Count: 336 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neuropilin-2	A, B	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
VEGFC C terminal peptide	C [auth D], D [auth F]	6	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P49767 (Homo sapiens) Explore P49767  Go to UniProtKB:  P49767
PHAROS:  P49767 GTEx:  ENSG00000150630

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], F [auth A], H [auth B], I [auth B], J [auth B], K [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	G [auth A], L [auth B], M [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.31 Å
• R-Value Free: 0.179 
• R-Value Work: 0.153 
• R-Value Observed: 0.154 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.24	α = 90
b = 76.544	β = 96.059
c = 63.357	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: 2020-12-16 
Deposition Author(s): Eldrid, C., Yu, L., Yelland, T., Fotinou, C., Djordjevic, S.

Revision History  

• Version 1.0: 2020-12-16
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary