MolNFT v1 · #15644 · protein
Crystal structure of stefin a in complex with cathepsin H: N-terminal residues of inhibitors can adapt to the active sites of endo-and exopeptidases
1NB3: “Crystal structure of stefin a in complex with cathepsin H: N-terminal residues of inhibitors can adapt to the…”. X-ray diffraction, 2 ligands (NAG, BMA), 9 pockets (best druggability 0.56). MolNFT v1 #15644 on GenesisL1: 3D…
- PDB
- 1NB3
- Type
- protein
- Length
- 1,304 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cathepsin H; Cathepsin H mini chain; Stefin a
- EC
- 3.4.22.16
- UniProt
- O46427, P01040
- Ligands
- NAG, BMA
- Pockets
- 9 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 26% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Cathepsin H (EC 3.4.22.16) | protein | 220 | 30% helix, 24% strand | O46427 |
| P, R, S, T | Cathepsin H mini chain (EC 3.4.22.16) | protein | 8 | 0% helix, 0% strand | O46427 |
| I, J, K, L | Stefin a | protein | 98 | 18% helix, 37% strand | P01040 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, P, B, R, C, S, D, T
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 191 | 0.56 | 0.79 | 30 | empty |
| 2 | 158 | 0.53 | 0.80 | 26 | empty |
| 3 | 210 | 0.52 | 0.77 | 34 | empty |
| 4 | 136 | 0.51 | 0.80 | 24 | empty |
| 5 | 68 | 0.33 | 0.76 | 19 | empty |
Interfaces
12 interfaces between chains.
- B–J · 844 Ų buried · 6 hydrogen bonds · protein-protein
- C–K · 835 Ų buried · 9 hydrogen bonds · protein-protein
- A–I · 814 Ų buried · 8 hydrogen bonds · protein-protein
- D–L · 803 Ų buried · 13 hydrogen bonds · protein-protein
- B–R · 365 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 1NB3 · Crystal structure of stefin A in complex with cathepsin H: N-terminal residues of… · the same entry in another collection · chain L against L, 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 O46427
- Every structure of UniProt P01040
- Elsewhere: RCSB PDB 1NB3 · PDBe 1NB3 · UniProt O46427 · UniProt P01040
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