4FOM
Crystal structure of human nectin-3 full ectodomain (D1-D3)
- PDB DOI: https://doi.org/10.2210/pdb4FOM/pdb
- Classification: CELL ADHESION
- Organism(s): Homo sapiens
- Expression System: Homo sapiens
- Mutation(s): No 
- Deposited: 2012-06-20 Released: 2012-08-22 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 3.93 Å
- R-Value Free: 0.279 
- R-Value Work: 0.247 
- R-Value Observed: 0.248 
This is version 2.1 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Poliovirus receptor-related protein 3 | 308 | Homo sapiens | Mutation(s): 0  Gene Names: PVRL3, PRR3 | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q9NQS3 (Homo sapiens) Explore Q9NQS3  Go to UniProtKB:  Q9NQS3 | |||||
PHAROS:  Q9NQS3 GTEx:  ENSG00000177707  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q9NQS3 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | B, E | 5 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G22768VO GlyCosmos:  G22768VO GlyGen:  G22768VO |
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | C | 3 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE |
Entity ID: 4 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | D | 6 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G82348BZ GlyCosmos:  G82348BZ GlyGen:  G82348BZ |
Small Molecules
Ligands 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | F [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 3.93 Å
- R-Value Free: 0.279 
- R-Value Work: 0.247 
- R-Value Observed: 0.248 
- Space Group: P 65 2 2
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 131.867 | α = 90 |
b = 131.867 | β = 90 |
c = 247.543 | γ = 120 |
Software Name | Purpose |
---|---|
ADSC | data collection |
PHASER | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
Entry History 
Deposition Data
- Released Date: 2012-08-22  Deposition Author(s): Harrison, O.J., Jin, X., Brasch, J., Shapiro, L.
Revision History (Full details and data files)
- 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