8CKG

Semaphorin-5A TSR 3-4 domains in complex with sulfate

• PDB DOI: https://doi.org/10.2210/pdb8CKG/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2023-02-15 Released: 2024-02-28 
• Deposition Author(s): Nagy, G.N., Duman, R., Harlos, K., El Omari, K., Wagner, A., Jones, E.Y.
• Funding Organization(s): Medical Research Council (MRC, United Kingdom)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free: 0.231 
• R-Value Work: 0.206 
• R-Value Observed: 0.207 

Literature

Semaphorin-5A TSR 3-4 domains in complex with sulfate

Nagy, G.N., Duman, R., Harlos, K., El Omari, K., Wagner, A., Jones, E.Y.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 29.02 kDa 
• Atom Count: 1,798 
• Modelled Residue Count: 209 
• Deposited Residue Count: 250 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Semaphorin-5A	A, B	125	Homo sapiens	Mutation(s): 2  Gene Names: SEMA5A, SEMAF
UniProt & NIH Common Fund Data Resources
Find proteins for Q13591 (Homo sapiens) Explore Q13591  Go to UniProtKB:  Q13591
PHAROS:  Q13591 GTEx:  ENSG00000112902

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MAN (Subject of Investigation/LOI)	D [auth A], E [auth A], G [auth B], H [auth B]	alpha-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
SO4 (Subject of Investigation/LOI)	C [auth A], F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free: 0.231 
• R-Value Work: 0.206 
• R-Value Observed: 0.207 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.081	α = 90
b = 29.286	β = 100.46
c = 90.429	γ = 90

Software Package:

Software Name	Purpose
autoPROC	data processing
CRANK2	phasing
PHENIX	refinement
Coot	model building
XDS	data reduction
Aimless	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-02-28 
Deposition Author(s): Nagy, G.N., Duman, R., Harlos, K., El Omari, K., Wagner, A., Jones, E.Y.

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Funding Organization	Location	Grant Number
Medical Research Council (MRC, United Kingdom)	United Kingdom	MR/T000503/1

Revision History  

• Version 1.0: 2024-02-28
  Type: Initial release