MolNFT v1 · #96689 · protein
Human procaspase-7 bound to ac-devd-cmk
4JR1: “Human procaspase-7 bound to ac-devd-cmk”. X-ray diffraction, 3 ligands (ACE, 0QE, CL), 3 pockets (best druggability 0.74). MolNFT v1 #96689 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4JR1
- Type
- protein
- Length
- 459 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
- 3 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Procaspase-7 (EC 3.4.22.60) | protein | 223 | 29% helix, 22% strand | P55210 |
| B | Procaspase-7 (EC 3.4.22.60) | protein | 228 | 30% helix, 25% 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
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 419 | 0.74 | 0.83 | 45 | empty |
| 2 | 73 | 0.56 | 0.88 | 22 | empty |
| 3 | 96 | 0.38 | 0.76 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1623 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 460 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 413 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 disulfide, 2 modified (covalent ligand, disulfide, nonstandard).
Compared structures
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 4JR1 · PDBe 4JR1 · UniProt P55210
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