5L56
Plexin A1 full extracellular region, domains 1 to 10, to 4 angstrom
- PDB DOI: https://doi.org/10.2210/pdb5L56/pdb
- Classification: SIGNALING PROTEIN
- Organism(s): Mus musculus
- Expression System: Homo sapiens
- Mutation(s): No 
- Deposited: 2016-05-28 Released: 2016-07-06 
- Funding Organization(s): HFSP, Cancer Research UK, Medical Research Council (United Kingdom), Wellcome Trust
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 4.00 Å
- R-Value Free: 0.308 
- R-Value Work: 0.257 
- R-Value Observed: 0.259 
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 |
Plexin-A1 | 1,212 | Mus musculus | Mutation(s): 0  Gene Names: Plxna1, Kiaa4053 | ||
UniProt | |||||
Find proteins for P70206 (Mus musculus) Explore P70206  Go to UniProtKB:  P70206 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P70206 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | B, D | 4 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G81315DD GlyCosmos:  G81315DD GlyGen:  G81315DD |
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | C, I | 6 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G09724ZC GlyCosmos:  G09724ZC GlyGen:  G09724ZC |
Entity ID: 4 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | E, F, J | 7 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G55220VL GlyCosmos:  G55220VL GlyGen:  G55220VL |
Entity ID: 5 | |||||
---|---|---|---|---|---|
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 | G | 5 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G22768VO GlyCosmos:  G22768VO GlyGen:  G22768VO |
Small Molecules
Ligands 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | K [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: 4.00 Å
- R-Value Free: 0.308 
- R-Value Work: 0.257 
- R-Value Observed: 0.259 
- Space Group: P 43 21 2
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 195.343 | α = 90 |
b = 195.343 | β = 90 |
c = 176.18 | γ = 90 |
Software Name | Purpose |
---|---|
REFMAC | refinement |
iMOSFLM | data reduction |
Aimless | data scaling |
PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2016-07-06  Deposition Author(s): Janssen, B.J.C., Kong, Y., Malinauskas, T., Vangoor, V.R., Coles, C.H., Kaufmann, R., Ni, T., Gilbert, R.J.C., Padilla-Parra, S., Pasterkamp, R.J., Jones, E.Y.
Funding Organization | Location | Grant Number |
---|---|---|
HFSP | United Kingdom | LT000340 |
Cancer Research UK | United Kingdom | A10976 |
Medical Research Council (United Kingdom) | United Kingdom | G9900061 |
Wellcome Trust | United Kingdom | 090532/Z/09/Z |
Revision History (Full details and data files)
- Version 1.0: 2016-07-06
Type: Initial release - Version 1.1: 2016-08-17
Changes: Database references - Version 1.2: 2017-08-30
Changes: Author supporting evidence - Version 1.3: 2018-09-19
Changes: Data collection - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary