4FMF

Crystal structure of human nectin-1 full ectodomain (D1-D3)

• PDB DOI: https://doi.org/10.2210/pdb4FMF/pdb

• Classification: CELL ADHESION
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2012-06-16 Released: 2012-08-22 
• Deposition Author(s): Harrison, O.J., Brasch, J., Shapiro, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.258 
• R-Value Work: 0.233 
• R-Value Observed: 0.234 

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 142.64 kDa 
• Atom Count: 9,598 
• Modelled Residue Count: 1,204 
• Deposited Residue Count: 1,252 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Poliovirus receptor-related protein 1	A, B, C, D	313	Homo sapiens	Mutation(s): 0  Gene Names: PVRL1, HVEC, PRR1
UniProt & NIH Common Fund Data Resources
Find proteins for Q15223 (Homo sapiens) Explore Q15223  Go to UniProtKB:  Q15223
PHAROS:  Q15223 GTEx:  ENSG00000110400

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, F, G, H	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMT	I [auth A], J [auth B], K [auth C], L [auth D]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.258 
• R-Value Work: 0.233 
• R-Value Observed: 0.234 
• Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.288	α = 90
b = 106.288	β = 90
c = 334.622	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-22 
Deposition Author(s): Harrison, O.J., Brasch, J., Shapiro, L.

Revision History  

• Version 1.0: 2012-08-22
  Type: Initial release
  
• Version 1.1: 2012-09-05
  Changes: Database references
• Version 1.2: 2012-09-26
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2023-09-13
  Changes: Data collection, Database references, Refinement description, Structure summary