5EPJ | pdb_00005epj

Crystal Structure of chromodomain of CBX7 in complex with inhibitor UNC3866

• PDB DOI: https://doi.org/10.2210/pdb5EPJ/pdb

• Classification: TRANSCRIPTION/TRANSCRIPTION INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-11-11 Released: 2015-12-16 
• Deposition Author(s): Liu, Y., Tempel, W., Walker, J.R., Stuckey, J.I., Dickson, B.M., James, L.I., Frye, S.V., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Min, J., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.260 (Depositor), 0.269 (DCC) 
• R-Value Work: 
  0.237 (Depositor), 0.249 (DCC) 
• R-Value Observed: 
  0.238 (Depositor) 

Literature

Crystal Structure of chromodomain of CBX7 in complex with inhibitor UNC3866

Liu, Y., Tempel, W., Walker, J.R., Stuckey, J.I., Dickson, B.M., James, L.I., Frye, S.V., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Min, J.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 7.61 kDa 
• Atom Count: 572 
• Modeled Residue Count: 58 
• Deposited Residue Count: 62 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chromobox protein homolog 7	A	56	Homo sapiens	Mutation(s): 0  Gene Names: CBX7
UniProt & NIH Common Fund Data Resources
Find proteins for O95931 (Homo sapiens) Explore O95931  Go to UniProtKB:  O95931
PHAROS:  O95931 GTEx:  ENSG00000100307

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
peptide-like inhibitor UNC3866	B	6	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UNX	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A]	UNKNOWN ATOM OR ION X

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
5R5	B	L-PEPTIDE LINKING	C4 H9 N O3		SER
ELY	B	L-PEPTIDE LINKING	C10 H22 N2 O2		LYS

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002208	B	UNC3866	Oligopeptide / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.260 (Depositor), 0.269 (DCC) 
• R-Value Work:  0.237 (Depositor), 0.249 (DCC) 
• R-Value Observed: 0.238 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m35epj

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.286	α = 90
b = 40.286	β = 90
c = 82.092	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-12-16 
Deposition Author(s): Liu, Y., Tempel, W., Walker, J.R., Stuckey, J.I., Dickson, B.M., James, L.I., Frye, S.V., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Min, J., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2015-12-16
  Type: Initial release
  
• Version 1.1: 2015-12-30
  Changes: Refinement description
• Version 2.0: 2019-11-27
  Changes: Atomic model, Derived calculations, Structure summary
• Version 2.1: 2025-04-02
  Changes: Data collection, Database references, Derived calculations, Structure summary