MolNFT v1 · #80393 · protein
Catalytic fragment of masp-2 in complex with its specific inhibitor developed by directed evolution on sgci scaffold
3TVJ · Mannan-binding lectin serine protease 2 a chain: “Catalytic fragment of masp-2 in complex with its specific inhibitor developed by directed evolution on sgci…”. X-ray diffraction, 1 ligand (SO4), 3 pockets (best druggability 0.44).…
- PDB
- 3TVJ
- Type
- protein
- Length
- 360 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mannan-binding lectin serine protease 2 a chain; Mannan-binding lectin serine protease 2…
- EC
- 3.4.21.104
- UniProt
- O00187, O46162
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.44
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mannan-binding lectin serine protease 2 a chain (EC 3.4.21.104) | protein | 83 | 0% helix, 31% strand | O00187 |
| B | Mannan-binding lectin serine protease 2 B chain (EC 3.4.21.104) | protein | 242 | 13% helix, 35% strand | O00187 |
| I | Protease inhibitor sgpi-2 | protein | 35 | 0% helix, 43% strand | O46162 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 83 | 0.44 | 0.80 | 27 | empty |
| 2 | 119 | 0.42 | 0.76 | 24 | empty |
| 3 | 58 | 0.25 | 0.72 | 16 | empty |
Interfaces
2 interfaces between chains.
- B–I · 1133 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 707 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3TVJ · Catalytic fragment of MASP-2 in complex with its specific inhibitor developed by directed… · the same entry in another collection · chain A against A, TM-score 1.00
- O00187 · AlphaFold monomer V2.0 prediction for mannan-binding lectin serine protease 2 (O00187) · a predicted model of the same protein · chain B against A, TM-score 0.97
- 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 0.79
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 O00187
- Every structure of UniProt O46162
- Elsewhere: RCSB PDB 3TVJ · PDBe 3TVJ · UniProt O00187 · UniProt O46162
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