Research workbench
Crystal structure of a retropepsin-like aspartic protease from rickettsia conorii
Analyse Crystal structure of a retropepsin-like aspartic protease from rickettsia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5C9F
- Type
- protein
- Length
- 514 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aprick protease
- EC
- 3.-.-.-
- UniProt
- Q92FY8
- Ligands
- NA, CL
- Pockets
- 2 · best druggability 0.48
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Aprick protease (EC 3.-.-.-) | protein | 132 | 8% helix, 57% strand | Q92FY8 |
| B | Aprick protease (EC 3.-.-.-) | protein | 124 | 8% helix, 53% strand | Q92FY8 |
| D | Aprick protease (EC 3.-.-.-) | protein | 126 | 8% helix, 53% strand | Q92FY8 |
Ligands and binding sites
- NA · Sodium ion · metal · 3 copies · chains B, D
- CL · Chloride ion · ion · 12 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 127 | 0.48 | 0.79 | 25 | empty |
| 2 | 80 | 0.32 | 0.74 | 23 | empty |
Interfaces
6 interfaces between chains.
- C–D · 764 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 757 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 638 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 614 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 310 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5C9F · 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 5C9F · PDBe 5C9F · UniProt Q92FY8
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