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.

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
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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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

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

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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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O43791
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

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	3D Interactions
GOL (Subject of Investigation/LOI) Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

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

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2020-11-18

Deposition Author(s):

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.