MolNFT v1 · #115092 · protein
Crystal structure of a retropepsin-like aspartic protease from rickettsia conorii
5C9B · Aprick protease: “Crystal structure of a retropepsin-like aspartic protease from rickettsia conorii”. X-ray diffraction, 3 pockets (best druggability 0.75). MolNFT v1 #115092 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5C9B
- Type
- protein
- Length
- 492 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aprick protease
- EC
- 3.-.-.-
- UniProt
- Q92FY8
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 10% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aprick protease (EC 3.-.-.-) | protein | 126 | 10% helix, 53% strand | Q92FY8 |
| B | Aprick protease (EC 3.-.-.-) | protein | 127 | 10% helix, 54% strand | Q92FY8 |
| C | Aprick protease (EC 3.-.-.-) | protein | 124 | 9% helix, 52% strand | Q92FY8 |
| D | Aprick protease (EC 3.-.-.-) | protein | 115 | 9% helix, 54% strand | Q92FY8 |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 716 | 0.75 | 0.80 | 70 | empty |
| 2 | 119 | 0.47 | 0.79 | 23 | empty |
| 3 | 98 | 0.39 | 0.76 | 19 | empty |
Interfaces
6 interfaces between chains.
- A–B · 733 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 716 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 459 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 454 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 222 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 5C9B · Crystal structure of a retropepsin-like aspartic protease from Rickettsia conorii · the same entry in another collection · chain A against A, 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 Q92FY8
- Elsewhere: RCSB PDB 5C9B · PDBe 5C9B · UniProt Q92FY8
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