MolNFT v1 · #53895 · protein
Intracellular subtilisin precursor from B. clausii
2X8J · Intracellular subtilisin protease: “Intracellular subtilisin precursor from B. clausii”. X-ray diffraction, 1 ligand (NA), 12 pockets (best druggability 0.57). MolNFT v1 #53895 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 2X8J
- Type
- protein
- Length
- 1,836 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Intracellular subtilisin protease
- EC
- 3.4.21.62
- UniProt
- D0AB41
- Ligands
- NA
- Pockets
- 12 · best druggability 0.57
Structure
x-ray diffraction · 5 distinct chains · 31% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Intracellular subtilisin protease (EC 3.4.21.62) | protein | 303 | 32% helix, 22% strand | D0AB41 |
| B, F | Intracellular subtilisin protease (EC 3.4.21.62) | protein | 307 | 29% helix, 22% strand | D0AB41 |
| C | Intracellular subtilisin protease (EC 3.4.21.62) | protein | 304 | 32% helix, 22% strand | D0AB41 |
| D | Intracellular subtilisin protease (EC 3.4.21.62) | protein | 308 | 31% helix, 22% strand | D0AB41 |
| E | Intracellular subtilisin protease (EC 3.4.21.62) | protein | 307 | 32% helix, 22% strand | D0AB41 |
Ligands and binding sites
- NA · Sodium ion · metal · 6 copies · chains A, B, C, D, E, F
- 1PE · Pentaethylene glycol · additive · 6 copies · chains A, B, C, D, E, F
- GOL · Glycerol · additive · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 240 | 0.57 | 0.79 | 28 | 1PE |
| 2 | 229 | 0.57 | 0.79 | 28 | 1PE |
| 3 | 220 | 0.56 | 0.79 | 27 | 1PE |
| 4 | 162 | 0.53 | 0.80 | 26 | empty |
| 5 | 162 | 0.53 | 0.80 | 27 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1620 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1604 Ų buried · 20 hydrogen bonds · protein-protein
- E–F · 1602 Ų buried · 20 hydrogen bonds · protein-protein
- B–E · 156 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 modified (oxidation).
Compared structures
- 2X8J · Intracellular subtilisin precursor from B. clausii · 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 D0AB41
- Elsewhere: RCSB PDB 2X8J · PDBe 2X8J · UniProt D0AB41
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