6FKN
Drosophila Plexin A in complex with Semaphorin 1b
- PDB DOI: https://doi.org/10.2210/pdb6FKN/pdb
- Classification: SIGNALING PROTEIN
- Organism(s): Drosophila melanogaster
- Expression System: Homo sapiens
- Mutation(s): No 
- Deposited: 2018-01-24 Released: 2019-02-06 
- Funding Organization(s): Cancer Research UK
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 4.80 Å
- R-Value Free: 0.297 
- R-Value Work: 0.285 
- R-Value Observed: 0.285 
wwPDB Validation   3D Report Full Report
This is version 2.1 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Plexin A, isoform A | 715 | Drosophila melanogaster | Mutation(s): 0  Gene Names:  PlexA, BcDNA:GM05237, D-Plex A, Dmel\CG11081, DPlexA, lincRNA.927, plex, plex A, Plex1, plexA... | ||
UniProt | |||||
Find proteins for Q9V491 (Drosophila melanogaster) Explore Q9V491  Go to UniProtKB:  Q9V491 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q9V491 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
MIP07328p | 578 | Drosophila melanogaster | Mutation(s): 0  Gene Names: Sema1b, Sema-1b, Sema-1b-RB, semaphorin-like, CG6446, Dmel_CG6446 | ||
UniProt | |||||
Find proteins for Q7KK54 (Drosophila melanogaster) Explore Q7KK54  Go to UniProtKB:  Q7KK54 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q7KK54 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 3 | |||||
---|---|---|---|---|---|
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 | E | 4 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G81315DD GlyCosmos:  G81315DD GlyGen:  G81315DD |
Entity ID: 4 | |||||
---|---|---|---|---|---|
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 | F | 3 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE |
Entity ID: 5 | |||||
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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, H | 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 | I [auth A] J [auth A] K [auth A] L [auth C] M [auth C] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 4.80 Å
- R-Value Free: 0.297 
- R-Value Work: 0.285 
- R-Value Observed: 0.285 
- Space Group: P 65 2 2
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 153.63 | α = 90 |
b = 153.63 | β = 90 |
c = 425.37 | γ = 120 |
Software Name | Purpose |
---|---|
PHENIX | refinement |
xia2 | data reduction |
xia2 | data scaling |
PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2019-02-06  Deposition Author(s): Rozbesky, D., Harlos, K., Jones, E.Y.
Funding Organization | Location | Grant Number |
---|---|---|
Cancer Research UK | United Kingdom | B5R00120 |
Revision History (Full details and data files)
- Version 1.0: 2019-02-06
Type: Initial release - Version 1.1: 2020-06-17
Changes: Data collection, Database references - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary