7D3D | pdb_00007d3d

Crystal structure of SPOP bound with a peptide

• PDB DOI: https://doi.org/10.2210/pdb7D3D/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-09-18 Released: 2020-11-18 
• Deposition Author(s): Yang, C.-G., Gan, J.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.189 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.163 (Depositor), 0.162 (DCC) 
• R-Value Observed: 
  0.164 (Depositor) 

Starting Model: experimental

Literature

A peptide binder of E3 ligase adaptor SPOP disrupts oncogenic SPOP-protein interactions in kidney cancer cells.

Wang, Z., Zhang, H., Chen, B., Ouyang, T., Zheng, T., Zhou, R., Dong, Z., Huang, Y., Zhang, T., Jiang, H., Gan, J., Luo, C., Yang, C.-G.

(2021) Chin J Chem 39: 271-280

• DOI: https://doi.org/10.1002/cjoc.202000462

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 Evidence: gel filtration

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 34.82 kDa 
• Atom Count: 2,783 
• Modeled Residue Count: 301 
• Deposited Residue Count: 302 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Speckle-type POZ protein	A, C [auth B]	139	Homo sapiens	Mutation(s): 0  Gene Names: SPOP
UniProt & NIH Common Fund Data Resources
Find proteins for O43791 (Homo sapiens) Explore O43791  Go to UniProtKB:  O43791
PHAROS:  O43791 GTEx:  ENSG00000121067

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
GLU-VAL-SER-ILE-ILE-GLN-GLY-ALA-ASP-SER-THR-THR	B [auth a], D [auth b]	12	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL (Subject of Investigation/LOI)	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.189 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.163 (Depositor), 0.162 (DCC) 
• R-Value Observed: 0.164 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.196	α = 90
b = 58.555	β = 90
c = 94.18	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-11-18 
Deposition Author(s): Yang, C.-G., Gan, J.H.

Revision History  

• Version 1.0: 2020-11-18
  Type: Initial release
  
• Version 1.1: 2021-06-09
  Changes: Database references
• Version 1.2: 2023-11-29
  Changes: Data collection, Database references, Refinement description