MolNFT v1 · #112783 · protein

Caspase-7 variant 4 (V4) with reprogrammed substrate specificity due to Y230V/W232Y/S234V/Q276D substitutions bound to devd inhibitor.

4ZVR: “Caspase-7 variant 4 (V4) with reprogrammed substrate specificity due to Y230V/W232Y/S234V/Q276D substitutions…”. X-ray diffraction, 1 ligand (ACE), 2 pockets (best druggability 0.77). MolNFT v1 #112783 on GenesisL1: 3D structure…

PDB: 4ZVR
Type: protein
Length: 472 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Caspase-7; Peptide ACE-asp-glu-val-asj
EC: 3.4.22.60
UniProt: P55210
Ligands: ACE
Pockets: 2 · best druggability 0.77

Structure

x-ray diffraction · 3 distinct chains · 30% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Caspase-7 (EC 3.4.22.60)	protein	139	28% helix, 29% strand	P55210
B, D	Caspase-7 (EC 3.4.22.60)	protein	93	33% helix, 19% strand	P55210
E, F	Peptide ACE-asp-glu-val-asj	protein	4	0% helix, 50% strand	—

Ligands and binding sites

ACE · Acetyl group · ligand · 2 copies · chains B, E, D, F

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

Pockets

2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	535	0.77	0.84	42	empty
2	57	0.42	0.83	20	empty

Interfaces

10 interfaces between chains.

A–B · 2276 Å² buried · 34 hydrogen bonds · protein-protein
C–D · 2274 Å² buried · 36 hydrogen bonds · protein-protein
B–D · 1405 Å² buried · 22 hydrogen bonds · protein-protein
B–C · 428 Å² buried · 8 hydrogen bonds · protein-protein
A–D · 421 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent, 2 modified (covalent ligand, nonstandard).

Compared structures

4ZVR · Caspase-7 Variant 4 (V4) with reprogrammed substrate specificity due to… · the same entry in another collection · chain F against F, TM-score 1.00
P55210 · AlphaFold monomer V2.0 prediction for caspase-7 (P55210) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P55210
Elsewhere: RCSB PDB 4ZVR · PDBe 4ZVR · UniProt P55210

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