5SVH | pdb_00005svh

Crystal structure of the KIX domain of CBP in complex with a MLL/c-Myb chimera

• PDB DOI: https://doi.org/10.2210/pdb5SVH/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens, Gallus gallus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-08-06 Released: 2018-05-09 
• Deposition Author(s): Langelaan, D.N., Smith, S.P., Allingham, J.A.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.242 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Model: experimental

Literature

Design of a nanomolar affinity ligand to the KIX domain of CBP

Langelaan, D.N., Smith, S.P.

To be published.

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 2  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Hetero 12-mer - A6B6 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 17.17 kDa 
• Atom Count: 1,181 
• Modelled Residue Count: 127 
• Deposited Residue Count: 145 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CREB-binding protein	A	87	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MLL/c-Myb chimera	B	58	Homo sapiens, Gallus gallus This entity is chimeric	Mutation(s): 0  Gene Names: KMT2A, ALL1, CXXC7, HRX, HTRX, MLL, MLL1, TRX1, MYB EC: 2.1.1.43 (PDB Primary Data), 2.1.1.364 (UniProt), 2.1.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P01103 (Gallus gallus) Explore P01103  Go to UniProtKB:  P01103
Find proteins for Q03164 (Homo sapiens) Explore Q03164  Go to UniProtKB:  Q03164
PHAROS:  Q03164 GTEx:  ENSG00000118058
UniProt Groups	Q03164P01103

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], I [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], J [auth B], K [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.242 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.82	α = 90
b = 119.82	β = 90
c = 50.43	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-05-09 
Deposition Author(s): Langelaan, D.N., Smith, S.P., Allingham, J.A.

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Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	--

Revision History  

• Version 1.0: 2018-05-09
  Type: Initial release
  
• Version 1.1: 2018-10-17
  Changes: Data collection, Source and taxonomy, Structure summary
• Version 1.2: 2020-01-08
  Changes: Author supporting evidence
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Refinement description