MolNFT v1 · #152742 · protein
Crystal structure of peptidase E from deinococcus radiodurans in P6422 space group
6IRU · Peptidase DR_1070: “Crystal structure of peptidase E from deinococcus radiodurans in P6422 space group”. X-ray diffraction, 5 pockets (best druggability 0.77). MolNFT v1 #152742 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6IRU
- Type
- protein
- Length
- 606 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidase DR_1070
- EC
- 3.4.21.-
- UniProt
- Q9RVF9
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptidase DR_1070 (EC 3.4.21.-) | protein | 203 | 35% helix, 21% strand | Q9RVF9 |
| B | Peptidase DR_1070 (EC 3.4.21.-) | protein | 201 | 36% helix, 21% strand | Q9RVF9 |
| C | Peptidase DR_1070 (EC 3.4.21.-) | protein | 202 | 38% helix, 20% strand | Q9RVF9 |
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 905 | 0.77 | 0.80 | 104 | empty |
| 2 | 189 | 0.56 | 0.80 | 24 | empty |
| 3 | 144 | 0.49 | 0.78 | 19 | empty |
| 4 | 163 | 0.49 | 0.78 | 18 | empty |
| 5 | 183 | 0.48 | 0.76 | 30 | empty |
Interfaces
3 interfaces between chains.
- B–C · 987 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 526 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 279 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6IRU · Crystal structure of Peptidase E from Deinococcus radiodurans in P6422 space group · the same entry in another collection · chain A against A, TM-score 1.00
- Q9RVF9 · AlphaFold monomer V2.0 prediction for uncharacterized peptidase DR_1070 (Q9RVF9) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 Q9RVF9
- Elsewhere: RCSB PDB 6IRU · PDBe 6IRU · UniProt Q9RVF9
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