7XIJ | pdb_00007xij

Crystal structure of CBP bromodomain liganded with Y08175

• PDB DOI: https://doi.org/10.2210/pdb7XIJ/pdb

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


• Deposited: 2022-04-13 Released: 2022-06-08 
• Deposition Author(s): Xiang, Q., Wang, C., Wu, T., Zhang, Y., Zhang, C., Luo, G., Wu, X., Shen, H., Xu, Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 
  0.221 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.201 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of CBP bromodomain liganded with Y08175

Xiang, Q., Wang, C., Wu, T., Zhang, Y., Zhang, C., Luo, G., Wu, X., Shen, H., Xu, Y.

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: 16.99 kDa 
• Atom Count: 1,245 
• Modeled Residue Count: 131 
• Deposited Residue Count: 136 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 2 of CREB-binding protein	A	136	Homo sapiens	Mutation(s): 0  Gene Names: CREBBP, CBP EC: 2.3.1.48 (PDB Primary Data), 2.3.1 (PDB Primary Data)
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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EJ3 (Subject of Investigation/LOI)	B [auth A]	3-[(1-ethanoyl-5-methoxy-indol-3-yl)carbonylamino]-4-fluoranyl-5-(1-methylpyrazol-4-yl)benzoic acid C23 H19 F N4 O5 RCPJEOKKJODBRQ-UHFFFAOYSA-N
GOL	D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS	C [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free:  0.221 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.201 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.89	α = 90
b = 56.89	β = 90
c = 80.62	γ = 120

Software Package:

Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-06-08 
Deposition Author(s): Xiang, Q., Wang, C., Wu, T., Zhang, Y., Zhang, C., Luo, G., Wu, X., Shen, H., Xu, Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	22007088

Revision History  

• Version 1.0: 2022-06-08
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description