5MMV | pdb_00005mmv

Crystal structure of human Caspase-1 with 2-((2-naphthoyl)-L-valyl)-4-hydroxy-N-((3S)-2-hydroxy-5-oxotetrahydrofuran-3-yl)-2-azabicyclo[2.2.2]octane-3-carboxamide (Compound 1)

PDB DOI: https://doi.org/10.2210/pdb5MMV/pdb

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

Deposited: 2016-12-12 Released: 2017-12-20
Deposition Author(s): Brethon, A., Chantalat, L., Christin, O., Clary, L., Fournier, J.F., Gastreich, M., Harris, C., Pascau, J., Isabet, T., Rodeschin, V., Thoreau, E., Roche, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.249 (Depositor), 0.265 (DCC)
R-Value Work:
0.197 (Depositor), 0.210 (DCC)
R-Value Observed:
0.200 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Literature

Crystal structure of human Caspase-1 with 2-((2-naphthoyl)-L-valyl)-4-hydroxy-N-((3S)-2-hydroxy-5-oxotetrahydrofuran-3-yl)-2-azabicyclo[2.2.2]octane-3-carboxamide (Compound 1)

Brethon, A., Chantalat, L., Christin, O., Clary, L., Fournier, J.F., Gastreich, M., Harris, C., Pascau, J., Isabet, T., Rodeschin, V., Thoreau, E., Roche, D.

To be published.

Macromolecule Content

Total Structure Weight: 30.92 kDa
Atom Count: 2,176
Modeled Residue Count: 253
Deposited Residue Count: 268
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Caspase-1	A	179	Homo sapiens	Mutation(s): 0 Gene Names: CASP1, IL1BC, IL1BCE EC: 3.4.22.36
UniProt & NIH Common Fund Data Resources
Find proteins for P29466 (Homo sapiens) Explore P29466 Go to UniProtKB: P29466
PHAROS: P29466 GTEx: ENSG00000137752
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P29466
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Caspase-1	B	89	Homo sapiens	Mutation(s): 0 Gene Names: CASP1, IL1BC, IL1BCE EC: 3.4.22.36
UniProt & NIH Common Fund Data Resources
Find proteins for P29466 (Homo sapiens) Explore P29466 Go to UniProtKB: P29466
PHAROS: P29466 GTEx: ENSG00000137752
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P29466
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
WE0 Query on WE0 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	(3~{S})-3-[[(3~{S})-2-[(2~{S})-3-methyl-2-(naphthalen-2-ylcarbonylamino)butanoyl]-4-oxidanyl-2-azabicyclo[2.2.2]octan-3-yl]carbonylamino]-4-oxidanyl-butanoic acid C₂₈ H₃₅ N₃ O₇ UFOBHSQYOCPSRI-ACWQFCSSSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.249 (Depositor), 0.265 (DCC)
R-Value Work: 0.197 (Depositor), 0.210 (DCC)
R-Value Observed: 0.200 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.081	α = 90
b = 63.081	β = 90
c = 138.042	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
CNS	refinement
Coot	model building
MOLREP	phasing
XSCALE	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2017-12-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-12-20
Type: Initial release
Version 2.0: 2024-11-13
Changes: Atomic model, Data collection, Database references, Structure summary