MolNFT v1 · #59158 · protein
Crystal structure of falcipain-3 with its inhibitor, leupeptin
3BPM · Cysteine protease falcipain-3: “Crystal structure of falcipain-3 with its inhibitor, leupeptin”. X-ray diffraction, 2 ligands (ACE, SO4), 4 pockets (best druggability 0.73). MolNFT v1 #59158 on GenesisL1: 3D structure, binding sites…
- PDB
- 3BPM
- Type
- protein
- Length
- 481 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cysteine protease falcipain-3; Leupeptin
- EC
- 3.4.22.-
- UniProt
- Q9NBA7
- Ligands
- ACE, SO4
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 27% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cysteine protease falcipain-3 (EC 3.4.22.-) | protein | 243 | 26% helix, 25% strand | Q9NBA7 |
| B | Cysteine protease falcipain-3 (EC 3.4.22.-) | protein | 232 | 29% helix, 23% strand | Q9NBA7 |
| C, D | Leupeptin | protein | 3 | 0% helix, 33% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains B, C, A, D
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 77 | 0.73 | 0.97 | 21 | empty |
| 2 | 414 | 0.62 | 0.77 | 47 | empty |
| 3 | 264 | 0.61 | 0.79 | 39 | empty |
| 4 | 188 | 0.58 | 0.81 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–B · 826 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 349 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 343 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 covalent, 2 modified (disulfide, covalent ligand, nonstandard).
Compared structures
- 3BPM · Crystal Structure of Falcipain-3 with Its inhibitor, Leupeptin · the same entry in another collection · chain A against A, 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 Q9NBA7
- Elsewhere: RCSB PDB 3BPM · PDBe 3BPM · UniProt Q9NBA7
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