4TS8 | pdb_00004ts8

Crystal structure of the bromodomain of human CREBBP in complex with XZ08

• PDB DOI: https://doi.org/10.2210/pdb4TS8/pdb

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


• Deposited: 2014-06-18 Released: 2015-07-01 
• Deposition Author(s): Dong, J., Gartenmann, L., Spiliotopoulos, D., Caflisch, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.254 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the bromodomain of human CREBBP in complex with XZ08

Dong, J., Gartenmann, L., Spiliotopoulos, D., Caflisch, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 14.6 kDa 
• Atom Count: 1,010 
• Modeled Residue Count: 112 
• Deposited Residue Count: 119 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CREB-binding protein	A	119	Homo sapiens	Mutation(s): 0  Gene Names: CREBBP, CBP EC: 2.3.1.48 (PDB Primary Data), 2.3.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q92793 (Homo sapiens) Explore Q92793  Go to UniProtKB:  Q92793
PHAROS:  Q92793 GTEx:  ENSG00000005339

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XZ8	D [auth A]	4-(1-acetyl-1H-indol-3-yl)-5-methyl-1,2-dihydro-3H-pyrazol-3-one C14 H13 N3 O2 HCHHWOYUIPSLJH-UHFFFAOYSA-N
EDO	B [auth A], C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
XZ8	BindingDB:  4TS8	Kd: 2.00e+4 (nM) from 1 assay(s)
		IC50: 2.00e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.254 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 24.73	α = 90
b = 46.16	β = 93.51
c = 56.959	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
XDS	data reduction
Coot	model building
PDB_EXTRACT	data extraction
PHASER	phasing
PHENIX	refinement
XSCALE	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-07-01 
Deposition Author(s): Dong, J., Gartenmann, L., Spiliotopoulos, D., Caflisch, A.

Revision History  

• Version 1.0: 2015-07-01
  Type: Initial release
  
• Version 1.1: 2023-12-20
  Changes: Data collection, Database references, Refinement description