MolNFT v1 · #59389 · protein
Crystal structure of falcipain-3 with its inhibitor, K11017
3BWK · Cysteine protease falcipain-3: “Crystal structure of falcipain-3 with its inhibitor, K11017”. X-ray diffraction, 2 ligands (C1P, SO4), 13 pockets (best druggability 0.81). MolNFT v1 #59389 on GenesisL1: 3D structure, binding sites…
- PDB
- 3BWK
- Type
- protein
- Length
- 949 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cysteine protease falcipain-3
- EC
- 3.4.22.-
- UniProt
- Q9NBA7
- Ligands
- C1P, SO4
- Pockets
- 13 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 26% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cysteine protease falcipain-3 (EC 3.4.22.-) | protein | 242 | 26% helix, 23% strand | Q9NBA7 |
| C | Cysteine protease falcipain-3 (EC 3.4.22.-) | protein | 234 | 26% helix, 22% strand | Q9NBA7 |
| D | Cysteine protease falcipain-3 (EC 3.4.22.-) | protein | 231 | 26% helix, 20% strand | Q9NBA7 |
Ligands and binding sites
- C1P · N~2~-(morpholin-4-ylcarbonyl)-N-[(3S)-1-phenyl-5-(phenylsulfonyl)pentan-3-yl]-L-leucinamide · ligand · 4 copies · chains A, C, B, D
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 563 | 0.81 | 0.87 | 74 | empty |
| 2 | 463 | 0.79 | 0.87 | 49 | empty |
| 3 | 343 | 0.64 | 0.79 | 47 | empty |
| 4 | 301 | 0.62 | 0.79 | 46 | C1P |
| 5 | 108 | 0.53 | 0.83 | 21 | empty |
Interfaces
6 interfaces between chains.
- B–D · 702 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 692 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 576 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 546 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 88 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide, 4 covalent (disulfide, covalent ligand).
Compared structures
- 3BWK · Crystal Structure of Falcipain-3 with Its inhibitor, K11017 · the same entry in another collection · chain C against C, 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 3BWK · PDBe 3BWK · UniProt Q9NBA7
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