5B4W

Crystal structure of Plexin inhibitor complex

• PDB DOI: https://doi.org/10.2210/pdb5B4W/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens, unidentified
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2016-04-19 Released: 2016-12-28 
• Deposition Author(s): Matsunaga, Y., Kitago, Y., Arimori, T., Takagi, J.
• Funding Organization(s): AMED

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.265 
• R-Value Work: 0.225 
• R-Value Observed: 0.227 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Biological Assembly 5  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 5 assigned by authors and generated by PISA (software)

Biological Assembly 6  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 6 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 385.27 kDa 
• Atom Count: 21,235 
• Modelled Residue Count: 2,770 
• Deposited Residue Count: 3,582 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Plexin-B1	A, B, C, D, E, F	579	Homo sapiens	Mutation(s): 0  Gene Names: PLXNB1, KIAA0407, PLXN5, SEP
UniProt & NIH Common Fund Data Resources
Find proteins for O43157 (Homo sapiens) Explore O43157  Go to UniProtKB:  O43157
PHAROS:  O43157 GTEx:  ENSG00000164050

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Synthesized cyclic peptide	G, H, I, J, K, L	18	unidentified	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	M [auth A], N [auth B], O [auth B], P [auth C], Q [auth D], R [auth E], S [auth F]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.265 
• R-Value Work: 0.225 
• R-Value Observed: 0.227 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.426	α = 90
b = 217.924	β = 115.3
c = 106.475	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data collection
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-12-28 
Deposition Author(s): Matsunaga, Y., Kitago, Y., Arimori, T., Takagi, J.

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Funding Organization	Location	Grant Number
AMED	Japan	--

Revision History  

• Version 1.0: 2016-12-28
  Type: Initial release
  
• Version 1.1: 2020-02-26
  Changes: Data collection
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.3: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.4: 2023-11-15
  Changes: Data collection