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Structure of the clinically used myxomaviral serine protease inhibitor 1 (serp-1)
Analyse Structure of the clinically used myxomaviral serine protease inhibitor 1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BJ5
- Type
- protein
- Length
- 990 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine proteinase inhibitor 1
- UniProt
- P12393
- Ligands
- P15, NAG
- Pockets
- 10 · best druggability 0.72
Structure
x-ray diffraction · 6 distinct chains · 23% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Serine proteinase inhibitor 1 | protein | 293 | 26% helix, 35% strand | P12393 |
| F | Serine proteinase inhibitor 1 | protein | 38 | 0% helix, 58% strand | P12393 |
| A | Serine proteinase inhibitor 1 | protein | 292 | 26% helix, 38% strand | P12393 |
| G | Serine proteinase inhibitor 1 | protein | 39 | 0% helix, 54% strand | P12393 |
| C | Serine proteinase inhibitor 1 | protein | 288 | 27% helix, 36% strand | P12393 |
| H | Serine proteinase inhibitor 1 | protein | 40 | 0% helix, 53% strand | P12393 |
Ligands and binding sites
- P15 · 2,5,8,11,14,17-hexaoxanonadecan-19-ol · ligand · chains C, H
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains B, C, A, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 871 | 0.72 | 0.77 | 71 | empty |
| 2 | 771 | 0.69 | 0.76 | 49 | empty |
| 3 | 479 | 0.64 | 0.77 | 47 | empty |
| 4 | 346 | 0.64 | 0.79 | 52 | empty |
| 5 | 211 | 0.53 | 0.77 | 21 | empty |
Interfaces
9 interfaces between chains.
- C–H · 2399 Ų buried · 41 hydrogen bonds · protein-protein
- A–G · 2397 Ų buried · 32 hydrogen bonds · protein-protein
- B–F · 2372 Ų buried · 37 hydrogen bonds · protein-protein
- B–A · 518 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 385 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 glycan (N-glycosylation).
Compared structures
- 6BJ5 · Structure of the Clinically used Myxomaviral Serine Protease Inhibitor 1 (SERP-1) · the same entry in another collection · chain B against B, 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 P12393
- Elsewhere: RCSB PDB 6BJ5 · PDBe 6BJ5 · UniProt P12393
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