MolNFT v1 · #45966 · protein
Crystal structure of cysteine protease inhibitor, chagasin, in complex with human cathepsin L
2NQD: “Crystal structure of cysteine protease inhibitor, chagasin, in complex with human cathepsin L”. X-ray diffraction, 3 ligands (NAG, NA, CL), 2 pockets (best druggability 0.41). MolNFT v1 #45966 on GenesisL1: 3D structure, binding…
- PDB
- 2NQD
- Type
- protein
- Length
- 330 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chagasin; Cathepsin L
- EC
- 3.4.22.15
- UniProt
- Q966X9, P07711
- Ligands
- NAG, NA, CL
- Pockets
- 2 · best druggability 0.41
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chagasin | protein | 109 | 6% helix, 50% strand | Q966X9 |
| B | Cathepsin L (EC 3.4.22.15) | protein | 221 | 29% helix, 22% strand | P07711 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B
- NA · Sodium ion · metal · chains A, B
- CL · Chloride ion · ion · 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 101 | 0.41 | 0.77 | 29 | NA |
| 2 | 50 | 0.31 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 957 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 2NQD · Crystal structure of cysteine protease inhibitor, chagasin, in complex with human… · the same entry in another collection · chain B against B, TM-score 1.00
- P07711 · AlphaFold monomer V2.0 prediction for procathepsin L (P07711) · a predicted model of the same protein · chain B against A, TM-score 0.99
- Q966X9 · AlphaFold monomer V2.0 prediction for chagasin (Q966X9) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q966X9
- Every structure of UniProt P07711
- Elsewhere: RCSB PDB 2NQD · PDBe 2NQD · UniProt Q966X9 · UniProt P07711
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