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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.05 Å
R-Value Free:
0.244 (Depositor), 0.256 (DCC)
R-Value Work:
0.213 (Depositor), 0.222 (DCC)
R-Value Observed:
0.214 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6YN8

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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

Macromolecule Content

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

Macromolecules

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9UDY8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
OZK (Subject of Investigation/LOI) Query on OZK Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	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		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.05 Å
R-Value Free: 0.244 (Depositor), 0.256 (DCC)
R-Value Work: 0.213 (Depositor), 0.222 (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

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2020-06-24

Deposition Author(s):

Revision History (Full details and data files)

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

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.