MolNFT v1 · #38651 · protein

Crystal structure of human caspase-1 (GLU390->asp) in complex with 3- [2-(2-benzyloxycarbonylamino-3-methyl-butyrylamino)-propionylamino]- 4-oxo-pentanoic acid (Z-vad-fmk)

2H4W: “Crystal structure of human caspase-1 (GLU390->asp) in complex with 3…”. X-ray diffraction, 2 ligands (PHQ, CF0), 1 pocket (best druggability 0.49). MolNFT v1 #38651 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2H4W
Type: protein
Length: 259 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Caspase-1; N-[(BENZYLOXY)CARBONYL]-L-valyl-N-[(2S)-1-carboxy-4-fluoro…
EC: 3.4.22.36
UniProt: P29466
Ligands: PHQ, CF0
Pockets: 1 · best druggability 0.49

Structure

x-ray diffraction · 3 distinct chains · 28% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Caspase-1 (EC 3.4.22.36)	protein	168	29% helix, 18% strand	P29466
B	Caspase-1 (EC 3.4.22.36)	protein	88	27% helix, 17% strand	P29466
C	N-[(BENZYLOXY)CARBONYL]-L-valyl-N-[(2S)-1-carboxy-4-fluoro- 3-oxobutan-2-yl]-L-alaninamide	protein	3	0% helix, 33% strand	—

Ligands and binding sites

PHQ · benzyl chlorocarbonate · ligand · chains B, C
CF0 · Fluoromethane · ion · chains A, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	63	0.49	0.85	17	empty

Interfaces

3 interfaces between chains.

A–B · 2693 Å² buried · 45 hydrogen bonds · protein-protein
B–C · 229 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 165 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

2H4W · Crystal structure of human caspase-1 (Glu390->Asp) in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
P29466 · AlphaFold monomer V2.0 prediction for caspase-1 (P29466) · a predicted model of the same protein · chain B against A, TM-score 0.96

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P29466
Elsewhere: RCSB PDB 2H4W · PDBe 2H4W · UniProt P29466

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