6YN8 | pdb_00006yn8

Human MALT1(334-719) in complex with a tetrazole containing compound

• PDB DOI: https://doi.org/10.2210/pdb6YN8/pdb

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


• Deposited: 2020-04-11 Released: 2020-06-24 
• Deposition Author(s): Renatus, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.05 Å
• R-Value Free: 
  0.244 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.213 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Starting Model: experimental

Literature

Stabilizing Inactive Conformations of MALT1 as an Effective Approach to Inhibit Its Protease Activity

Hughes, N., Erbel, P., Bornancin, F., Wiesmann, C., Schiering, N., Villard, F., Decock, A., Rubi, B., Melkko, S., Spanka, C., Buschmann, N., Pissot-Soldermann, C., Simic, O., Beerli, R., Sorge, M., Tintelnot-Blomley, M., Beltz, K., Regnier, C.H., Quancard, J., Schlapbach, A., Langlois, J., Renatus, M.

(2020) Adv Ther (Weinh) 3

• DOI: https://doi.org/10.1002/adtp.202000078

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 44.5 kDa 
• Atom Count: 2,933 
• Modelled Residue Count: 365 
• Deposited Residue Count: 389 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mucosa-associated lymphoid tissue lymphoma translocation protein 1	A	389	Homo sapiens	Mutation(s): 0  Gene Names: MALT1, MLT EC: 3.4.22
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UDY8 (Homo sapiens) Explore Q9UDY8  Go to UniProtKB:  Q9UDY8
PHAROS:  Q9UDY8 GTEx:  ENSG00000172175

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OZK (Subject of Investigation/LOI)	B [auth A]	3-azanyl-3-methyl-~{N}-[(3~{R})-4-oxidanylidene-5-[[4-[2-(1~{H}-1,2,3,4-tetrazol-5-yl)phenyl]phenyl]methyl]-2,3-dihydro-1,5-benzoxazepin-3-yl]butanamide C28 H29 N7 O3 PJFIRCYASUNIFO-JOCHJYFZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.05 Å
• R-Value Free:  0.244 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.213 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: C 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.293	α = 90
b = 106.356	β = 90
c = 106.455	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-06-24 
Deposition Author(s): Renatus, M.

Revision History  

• Version 1.0: 2020-06-24
  Type: Initial release
  
• Version 1.1: 2021-01-13
  Changes: Database references
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Refinement description