Research workbench
Catalytic fragment of masp-1 in complex with its specific inhibitor developed by directed evolution on sgci scaffold
Analyse Catalytic fragment of masp-1 in complex with its specific inhibitor developed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DJZ
- Type
- protein
- Length
- 865 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mannan-binding lectin serine protease 1 heavy chain; Mannan-binding lectin serine…
- EC
- 3.4.21.-
- UniProt
- P48740, O46162
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Mannan-binding lectin serine protease 1 heavy chain (EC 3.4.21.-) | protein | 148 | 2% helix, 40% strand | P48740 |
| B, D | Mannan-binding lectin serine protease 1 light chain (EC 3.4.21.-) | protein | 251 | 13% helix, 33% strand | P48740 |
| H | Protease inhibitor sgpi-2 | protein | 34 | 0% helix, 38% strand | O46162 |
| I | Protease inhibitor sgpi-2 | protein | 33 | 0% helix, 39% strand | O46162 |
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 | 877 | 0.73 | 0.77 | 92 | empty |
| 2 | 110 | 0.53 | 0.83 | 29 | empty |
| 3 | 191 | 0.49 | 0.76 | 30 | empty |
| 4 | 65 | 0.39 | 0.79 | 20 | empty |
| 5 | 58 | 0.30 | 0.75 | 15 | empty |
Interfaces
6 interfaces between chains.
- D–I · 1098 Ų buried · 25 hydrogen bonds · protein-protein
- B–H · 1064 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 865 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 830 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 330 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 disulfide (disulfide).
Compared structures
- 4DJZ · Catalytic fragment of masp-1 in complex with its specific inhibitor developed by directed… · the same entry in another collection · chain D against D, TM-score 1.00
- P48740 · AlphaFold monomer V2.0 prediction for mannan-binding lectin serine protease 1 (P48740) · a predicted model of the same protein · chain B against A, TM-score 0.96
- O46162 · AlphaFold monomer V2.0 prediction for serine protease inhibitor I/II (O46162) · a predicted model of the same protein · chain I against A, TM-score 0.84
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 P48740
- Every structure of UniProt O46162
- Elsewhere: RCSB PDB 4DJZ · PDBe 4DJZ · UniProt P48740 · UniProt O46162
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.