5LUG | pdb_00005lug

Crystal structure of human Spindlin-2B protein in complex with ART(M3L)QTA(2MR)KS peptide

• PDB DOI: https://doi.org/10.2210/pdb5LUG/pdb

• Classification: CELL CYCLE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3), Escherichia coli #1/H766
• Mutation(s): No 


• Deposited: 2016-09-08 Released: 2017-09-20 
• Deposition Author(s): Srikannathasan, V., Gileadi, C., Talon, R., Shrestha, L., Kopec, J., Szykowska, A., Burgess-Brown, N., Arrowsmith, C.H., Edwards, A.M., Bountra, C., von Delft, F., Oppermann, U., Huber, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.221 (Depositor), 0.213 (DCC) 
• R-Value Work: 
  0.194 (Depositor) 
• R-Value Observed: 
  0.196 (Depositor) 

Literature

Crystal structure of human Spindlin-2B protein in complex with ART(M3L)QTA(2MR)KS peptide

Srikannathasan, V.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 107.48 kDa 
• Atom Count: 7,746 
• Modeled Residue Count: 854 
• Deposited Residue Count: 928 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spindlin-like protein 2, isoform CRA_a	A, B, C, D	222	Homo sapiens	Mutation(s): 0  Gene Names: SPIN-2, hCG_1642309
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BPZ2 (Homo sapiens) Explore Q9BPZ2  Go to UniProtKB:  Q9BPZ2
GTEx:  ENSG00000186787

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ALA-ARG-THR-M3L-GLN-THR-ALA-2MR-LYS-SER	E [auth F], F [auth G], G [auth H], H [auth E]	10	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens) Explore P68431  Go to UniProtKB:  P68431
PHAROS:  P68431 GTEx:  ENSG00000197409 ENSG00000197153 ENSG00000278828 ENSG00000275714 ENSG00000273983 ENSG00000274750 ENSG00000275379 ENSG00000277775

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2MR	K [auth B]	N3, N4-DIMETHYLARGININE C8 H18 N4 O2 HVPFXCBJHIIJGS-LURJTMIESA-N
EDO	I [auth A], J [auth A], L [auth B], M [auth B], N [auth B], O [auth D]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
2MR	E [auth F], F [auth G], G [auth H], H [auth E]	L-PEPTIDE LINKING	C8 H18 N4 O2		ARG
M3L	E [auth F], F [auth G], G [auth H], H [auth E]	L-PEPTIDE LINKING	C9 H21 N2 O2		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.221 (Depositor), 0.213 (DCC) 
• R-Value Work:  0.194 (Depositor) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.533	α = 90
b = 81.225	β = 99.86
c = 93.967	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-09-20 
Deposition Author(s): Srikannathasan, V., Gileadi, C., Talon, R., Shrestha, L., Kopec, J., Szykowska, A., Burgess-Brown, N., Arrowsmith, C.H., Edwards, A.M., Bountra, C., von Delft, F., Oppermann, U., Huber, K.

Revision History  

• Version 1.0: 2017-09-20
  Type: Initial release
  
• Version 1.1: 2018-01-31
  Changes: Database references
• Version 1.2: 2025-04-09
  Changes: Data collection, Database references, Structure summary