7O9Z

Crystal structure of Human Menin in complex with BD-08

• PDB DOI: https://doi.org/10.2210/pdb7O9Z/pdb

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


• Deposited: 2021-04-18 Released: 2022-07-27 
• Deposition Author(s): Groves, M.R., Gao, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.243 
• R-Value Work: 0.211 
• R-Value Observed: 0.213 

Starting Model: experimental

Literature

Crystal structure of Human Menin in complex with BD-08

Groves, M.R., Gao, K.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 55.53 kDa 
• Atom Count: 3,875 
• Modelled Residue Count: 462 
• Deposited Residue Count: 494 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Menin	A	494	Homo sapiens	Mutation(s): 0  Gene Names: MEN1, hCG_2017452
UniProt & NIH Common Fund Data Resources
Find proteins for O00255 (Homo sapiens) Explore O00255  Go to UniProtKB:  O00255
PHAROS:  O00255 GTEx:  ENSG00000133895

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
V6N (Subject of Investigation/LOI)	B [auth A]	(~{E})-2-cyano-3-(2~{H}-indazol-6-yl)-~{N}-(2-morpholin-4-ylethyl)prop-2-enamide C17 H19 N5 O2 DCPLXQDYVXXNNX-OQLLNIDSSA-N
GOL	D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	C [auth A], F [auth A], G [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.243 
• R-Value Work: 0.211 
• R-Value Observed: 0.213 
• Space Group: P 4₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.193	α = 90
b = 107.193	β = 90
c = 107.443	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2022-07-27 
Deposition Author(s): Groves, M.R., Gao, K.

Revision History  

• Version 1.0: 2022-07-27
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description