MolNFT v1 · #106161 · protein
Re-refinement of 1SOZ, crystal structure of degs protease in complex with an activating peptide
4RQZ · Protease degs: “Re-refinement of 1SOZ, crystal structure of degs protease in complex with an activating peptide”. X-ray diffraction, 11 pockets (best druggability 0.71). MolNFT v1 #106161 on GenesisL1: 3D structure, binding sites…
- PDB
- 4RQZ
- Type
- protein
- Length
- 827 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protease degs; Activating peptide
- UniProt
- H9UXC8
- Pockets
- 11 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 16% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protease degs | protein | 272 | 17% helix, 35% strand | H9UXC8 |
| B | Protease degs | protein | 274 | 17% helix, 38% strand | H9UXC8 |
| C | Protease degs | protein | 271 | 14% helix, 36% strand | H9UXC8 |
| D, F | Activating peptide | protein | 3 | 0% helix, 0% strand | — |
| E | Activating peptide | protein | 4 | 0% helix, 0% strand | — |
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 64 | 0.71 | 0.98 | 19 | empty |
| 2 | 258 | 0.61 | 0.80 | 49 | empty |
| 3 | 321 | 0.60 | 0.78 | 32 | empty |
| 4 | 226 | 0.59 | 0.79 | 27 | empty |
| 5 | 269 | 0.58 | 0.78 | 37 | empty |
Interfaces
6 interfaces between chains.
- B–C · 1123 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1093 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 1084 Ų buried · 22 hydrogen bonds · protein-protein
- B–E · 374 Ų buried · 5 hydrogen bonds · protein-protein
- C–F · 266 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4RQZ · re-refinement of 1soz, Crystal Structure of DegS protease in complex with an activating… · 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 H9UXC8
- Elsewhere: RCSB PDB 4RQZ · PDBe 4RQZ · UniProt H9UXC8
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