Research workbench
Crystal structure of falcipain-2 with its inhibitor, E64
Analyse Crystal structure of falcipain-2 with its inhibitor, E64 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BPF
- Type
- protein
- Length
- 925 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cysteine protease falcipain-2
- EC
- 3.4.22.-
- UniProt
- Q9NBD4
- Ligands
- E64
- Pockets
- 7 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 26% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cysteine protease falcipain-2 (EC 3.4.22.-) | protein | 236 | 25% helix, 22% strand | Q9NBD4 |
| B | Cysteine protease falcipain-2 (EC 3.4.22.-) | protein | 240 | 27% helix, 20% strand | Q9NBD4 |
| C | Cysteine protease falcipain-2 (EC 3.4.22.-) | protein | 234 | 26% helix, 24% strand | Q9NBD4 |
| D | Cysteine protease falcipain-2 (EC 3.4.22.-) | protein | 215 | 27% helix, 20% strand | Q9NBD4 |
Ligands and binding sites
- E64 · N-[N-[1-hydroxycarboxyethyl-carbonyl]leucylamino-butyl]-guanidine · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 631 | 0.68 | 0.77 | 65 | E64 |
| 2 | 212 | 0.62 | 0.82 | 28 | empty |
| 3 | 214 | 0.61 | 0.82 | 28 | empty |
| 4 | 262 | 0.57 | 0.78 | 33 | empty |
| 5 | 186 | 0.57 | 0.80 | 26 | empty |
Interfaces
4 interfaces between chains.
- A–D · 729 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 632 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 344 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 285 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide, 4 covalent (disulfide, covalent ligand).
Compared structures
- 3BPF · Crystal Structure of Falcipain-2 with Its inhibitor, E64 · the same entry in another collection · chain B against B, TM-score 1.00
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 Q9NBD4
- Elsewhere: RCSB PDB 3BPF · PDBe 3BPF · UniProt Q9NBD4
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