1KEX

Crystal Structure of the b1 Domain of Human Neuropilin-1

• PDB DOI: https://doi.org/10.2210/pdb1KEX/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2001-11-18 Released: 2003-01-28 
• Deposition Author(s): Lee, C.C., Kreusch, A., McMullan, D., Ng, K., Spraggon, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.266 
• R-Value Work: 0.189 

Starting Model: experimental

Literature

Crystal Structure of the Human Neuropilin-1 b1 Domain

Lee, C.C., Kreusch, A., McMullan, D., Ng, K., Spraggon, G.

(2003) Structure 11: 99-108

• PubMed: 12517344 
• DOI: https://doi.org/10.1016/s0969-2126(02)00941-3
• Primary Citation of Related Structures:  
  1KEX


• PubMed Abstract: 
  

  Neuropilin-1 (Npn-1) is a type I cell surface receptor involved in a broad range of developmental processes, including axon guidance, angiogenesis, and heterophilic cell adhesion. We have determined the crystal structure of the human Npn-1 b1 domain to 1.9 A. The overall structure resembles coagulation factor V and VIII (F5/8) C1 and C2 domains, exhibiting a distorted jellyroll fold. Details of the structure provide insight to b1 domain regions responsible for ligand binding and facilitate rationalization of existing biochemical binding data. A polar cleft formed by adjacent loops at one end of the molecule in conjunction with flanking electronegative surfaces may represent the binding site for the positively charged tails of semaphorins and VEGF(165). The nature of the cell adhesion binding site of the b1 domain can be visualized in context of the structure.

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Organizational Affiliation: 

The Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, CA 92121, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 17.59 kDa 
• Atom Count: 1,440 
• Modelled Residue Count: 155 
• Deposited Residue Count: 155 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neuropilin-1	A	155	Homo sapiens	Mutation(s): 0  Gene Names: nrp1
UniProt & NIH Common Fund Data Resources
Find proteins for O14786 (Homo sapiens) Explore O14786  Go to UniProtKB:  O14786
PHAROS:  O14786 GTEx:  ENSG00000099250

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.266 
• R-Value Work: 0.189 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.827	α = 90
b = 62.827	β = 90
c = 88.375	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-01-28 
Deposition Author(s): Lee, C.C., Kreusch, A., McMullan, D., Ng, K., Spraggon, G.

Revision History  

• Version 1.0: 2003-01-28
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-16
  Changes: Data collection, Database references, Refinement description