MolNFT v1 · #9960 · protein
Crystal structure of MHC class II associated P41 II fragment in complex with cathepsin L
1ICF · Protein (cathepsin L: heavy chain): “Crystal structure of MHC class II associated P41 II fragment in complex with cathepsin L”. X-ray diffraction, 1 ligand (NAG), 5 pockets (best druggability 0.60). MolNFT v1 #9960 on GenesisL1: 3D…
- PDB
- 1ICF
- Type
- protein
- Length
- 564 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (cathepsin L: heavy chain); Protein (cathepsin L: light chain); Protein…
- EC
- 3.4.22.15
- UniProt
- P07711, P04233
- Ligands
- NAG
- Pockets
- 5 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 23% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Protein (cathepsin L: heavy chain) (EC 3.4.22.15) | protein | 175 | 32% helix, 19% strand | P07711 |
| B, D | Protein (cathepsin L: light chain) (EC 3.4.22.15) | protein | 42 | 7% helix, 40% strand | P07711 |
| I, J | Protein (invariant chain) | protein | 65 | 9% helix, 22% strand | P04233 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains I, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 283 | 0.60 | 0.79 | 37 | empty |
| 2 | 305 | 0.55 | 0.76 | 35 | empty |
| 3 | 68 | 0.45 | 0.83 | 18 | empty |
| 4 | 79 | 0.43 | 0.80 | 21 | empty |
| 5 | 85 | 0.38 | 0.77 | 18 | empty |
Interfaces
9 interfaces between chains.
- C–D · 2495 Ų buried · 45 hydrogen bonds · protein-protein
- A–B · 2460 Ų buried · 42 hydrogen bonds · protein-protein
- A–I · 926 Ų buried · 17 hydrogen bonds · protein-protein
- C–J · 915 Ų buried · 18 hydrogen bonds · protein-protein
- A–J · 299 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 1ICF · Crystal structure of MHC class II associated P41 II fragment in complex with cathepsin L · the same entry in another collection · chain J against J, TM-score 1.00
- P07711 · AlphaFold monomer V2.0 prediction for procathepsin L (P07711) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P04233 · AlphaFold monomer V2.0 prediction for HLA class II histocompatibility antigen gamma chain… · a predicted model of the same protein · chain I against A, TM-score 0.95
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 P07711
- Every structure of UniProt P04233
- Elsewhere: RCSB PDB 1ICF · PDBe 1ICF · UniProt P07711 · UniProt P04233
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