MolNFT v1 · #186720 · protein

Crystal structure of caspase-3 with inhibitor ac-vdrvd-cho

7RNB · Caspase-3 subunit P17: “Crystal structure of caspase-3 with inhibitor ac-vdrvd-cho”. X-ray diffraction, 1 ligand (ACE), 2 pockets (best druggability 0.67). MolNFT v1 #186720 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 7RNB
Type: protein
Length: 478 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Caspase-3 subunit P17; Caspase-3 subunit P12; Ac-vdrvd-cho
UniProt: P42574
Ligands: ACE
Pockets: 2 · best druggability 0.67

Structure

x-ray diffraction · 4 distinct chains · 30% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Caspase-3 subunit P17	protein	141	27% helix, 32% strand	P42574
B	Caspase-3 subunit P12	protein	92	34% helix, 21% strand	P42574
D	Caspase-3 subunit P12	protein	94	33% helix, 20% strand	P42574
F, G	Ac-vdrvd-cho	protein	5	0% helix, 60% strand	—

Ligands and binding sites

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

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	339	0.67	0.81	39	empty
2	52	0.25	0.73	22	empty

Interfaces

10 interfaces between chains.

C–D · 2172 Å² buried · 32 hydrogen bonds · protein-protein
A–B · 2166 Å² buried · 34 hydrogen bonds · protein-protein
B–D · 1416 Å² buried · 19 hydrogen bonds · protein-protein
A–D · 447 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 431 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

7RNB · Crystal structure of caspase-3 with inhibitor Ac-VDRVD-CHO · the same entry in another collection · chain G against G, TM-score 1.00
P42574 · AlphaFold monomer V2.0 prediction for caspase-3 (P42574) · a predicted model of the same protein · chain C 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 P42574
Elsewhere: RCSB PDB 7RNB · PDBe 7RNB · UniProt P42574

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.