Research workbench
Human hepsin protease in complex with the Fab fragment of an inhibitory antibody
Analyse Human hepsin protease in complex with the Fab fragment of an inhibitory antibody in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3T2N
- Type
- protein
- Length
- 1,505 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine protease hepsin; Antibody, Fab fragment, light chain; Antibody, Fab fragment…
- EC
- 3.4.21.106
- UniProt
- P05981
- Pockets
- 18 · best druggability 0.70
Structure
x-ray diffraction · 6 distinct chains · 12% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serine protease hepsin (EC 3.4.21.106) | protein | 339 | 15% helix, 37% strand | P05981 |
| B | Serine protease hepsin (EC 3.4.21.106) | protein | 335 | 15% helix, 36% strand | P05981 |
| L | Antibody, Fab fragment, light chain | protein | 211 | 7% helix, 51% strand | — |
| H | Antibody, Fab fragment, heavy chain | protein | 203 | 10% helix, 51% strand | — |
| M | Antibody, Fab fragment, light chain | protein | 212 | 8% helix, 50% strand | — |
| I | Antibody, Fab fragment, heavy chain | protein | 205 | 10% helix, 52% strand | — |
Pockets
18 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 725 | 0.70 | 0.77 | 67 | empty |
| 2 | 683 | 0.64 | 0.74 | 64 | empty |
| 3 | 351 | 0.61 | 0.78 | 56 | empty |
| 4 | 570 | 0.61 | 0.74 | 59 | empty |
| 5 | 169 | 0.60 | 0.83 | 27 | empty |
Interfaces
7 interfaces between chains.
- M–I · 1532 Ų buried · 8 hydrogen bonds · protein-protein
- L–H · 1476 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 684 Ų buried · 9 hydrogen bonds · protein-protein
- A–L · 676 Ų buried · 4 hydrogen bonds · protein-protein
- B–M · 621 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 disulfide (disulfide).
Compared structures
- 3T2N · Human hepsin protease in complex with the Fab fragment of an inhibitory antibody · the same entry in another collection · chain I against I, TM-score 1.00
- P05981 · AlphaFold monomer V2.0 prediction for serine protease hepsin (P05981) · 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 P05981
- Elsewhere: RCSB PDB 3T2N · PDBe 3T2N · UniProt P05981
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