MolNFT v1 · #15646 · protein
Crystal structure of stefin a in complex with cathepsin H
1NB5: “Crystal structure of stefin a in complex with cathepsin H”. X-ray diffraction, 2 ligands (NAG, BMA), 6 pockets (best druggability 0.69). MolNFT v1 #15646 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1NB5
- 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
- 6 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 24% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Cathepsin H (EC 3.4.22.16) | protein | 220 | 28% 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, 39% 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
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 688 | 0.69 | 0.77 | 63 | empty |
| 2 | 163 | 0.47 | 0.76 | 27 | empty |
| 3 | 135 | 0.46 | 0.78 | 19 | empty |
| 4 | 59 | 0.33 | 0.77 | 16 | empty |
| 5 | 70 | 0.30 | 0.74 | 15 | empty |
Interfaces
17 interfaces between chains.
- D–L · 954 Ų buried · 11 hydrogen bonds · protein-protein
- C–K · 902 Ų buried · 14 hydrogen bonds · protein-protein
- A–I · 871 Ų buried · 7 hydrogen bonds · protein-protein
- B–J · 838 Ų buried · 8 hydrogen bonds · protein-protein
- A–P · 415 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 1NB5 · Crystal structure of stefin A in complex with cathepsin H · 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 1NB5 · PDBe 1NB5 · UniProt O46427 · UniProt P01040
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