4I1R | pdb_00004i1r

Human MALT1 (caspase-IG3) in complex with thioridazine

PDB DOI: https://doi.org/10.2210/pdb4I1R/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-11-21 Released: 2013-08-28
Deposition Author(s): Schlauderer, F., Lammens, K., Hopfner, K.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.249 (Depositor), 0.266 (DCC)
R-Value Work:
0.201 (Depositor), 0.212 (DCC)
R-Value Observed:
0.205 (Depositor)

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Ligand Structure Quality Assessment

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

Literature

Structural Analysis of Phenothiazine Derivatives as Allosteric Inhibitors of the MALT1 Paracaspase.

Schlauderer, F., Lammens, K., Nagel, D., Vincendeau, M., Eitelhuber, A.C., Verhelst, S.H., Kling, D., Chrusciel, A., Ruland, J., Krappmann, D., Hopfner, K.P.

(2013) Angew Chem Int Ed Engl 52: 10384-10387

PubMed: 23946259 Search on PubMed
DOI: https://doi.org/10.1002/anie.201304290
Primary Citation Related Structures:
4I1R

Organizational Affiliation

Gene Center, Department of Biochemistry, Ludwig-Maximilians University Munich, Feodor-Lynen-Strasse 25, 80377 Munich (Germany).

Macromolecule Content

Total Structure Weight: 44.56 kDa
Atom Count: 2,857
Modeled Residue Count: 353
Deposited Residue Count: 388
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mucosa-associated lymphoid tissue lymphoma translocation protein 1	A	388	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
LZU Query on LZU 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]	10-{2-[(2S)-1-methylpiperidin-2-yl]ethyl}-2-(methylsulfanyl)-10H-phenothiazine C₂₁ H₂₆ N₂ S₂ KLBQZWRITKRQQV-INIZCTEOSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
LZU	BindingDB: 4I1R	IC50: min: 3430, max: 4100 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.249 (Depositor), 0.266 (DCC)
R-Value Work: 0.201 (Depositor), 0.212 (DCC)
R-Value Observed: 0.205 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.838	α = 90
b = 70.608	β = 93.63
c = 57.525	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
PHASER	phasing
BUSTER	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-08-28

Deposition Author(s):

Schlauderer, F.

Revision History (Full details and data files)

Version 1.0: 2013-08-28
Type: Initial release
Version 1.1: 2013-10-16
Changes: Database references
Version 1.2: 2024-02-28
Changes: Data collection, Database references, Derived calculations

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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.