MolNFT v1 · #96690 · protein

Human procaspase-7/CASPASE-7 heterodimer bound to ac-devd-cmk

4JR2: “Human procaspase-7/CASPASE-7 heterodimer bound to ac-devd-cmk”. X-ray diffraction, 3 ligands (ACE, 0QE, CL), 2 pockets (best druggability 0.73). MolNFT v1 #96690 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4JR2
Type: protein
Length: 465 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Procaspase-7; Ac-devd-cmk
EC: 3.4.22.60
UniProt: P55210
Ligands: ACE, 0QE, CL
Pockets: 2 · best druggability 0.73

Structure

x-ray diffraction · 3 distinct chains · 31% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Procaspase-7 (EC 3.4.22.60)	protein	224	32% helix, 25% strand	P55210
B	Procaspase-7 (EC 3.4.22.60)	protein	233	31% helix, 27% strand	P55210
C, D	Ac-devd-cmk	protein	4	0% helix, 50% strand	—

Ligands and binding sites

ACE · Acetyl group · ligand · 2 copies · chains A, C, B, D
0QE · Chloromethane · ion · 2 copies · chains A, C, B, D
CL · Chloride ion · ion · 2 copies · chains A, B

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	543	0.73	0.81	53	empty
2	73	0.38	0.77	17	empty

Interfaces

3 interfaces between chains.

A–B · 1786 Å² buried · 22 hydrogen bonds · protein-protein
B–D · 465 Å² buried · 17 hydrogen bonds · protein-protein
A–C · 463 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

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

Compared structures

4JR2 · Human procaspase-7/caspase-7 heterodimer bound to Ac-DEVD-CMK · the same entry in another collection · chain A against A, 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 4JR2 · PDBe 4JR2 · UniProt P55210

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