Research workbench
Crystal structure of S9 peptidase mutant (S514A) from deinococcus radiodurans R1
Analyse Crystal structure of S9 peptidase mutant (S514A) from deinococcus radiodurans R1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YZO
- Type
- protein
- Length
- 2,579 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acyl-peptide hydrolase, putative
- UniProt
- Q9RXY9
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acyl-peptide hydrolase, putative | protein | 649 | 18% helix, 36% strand | Q9RXY9 |
| B | Acyl-peptide hydrolase, putative | protein | 644 | 19% helix, 37% strand | Q9RXY9 |
| C, D | Acyl-peptide hydrolase, putative | protein | 643 | 19% helix, 37% strand | Q9RXY9 |
Ligands and binding sites
- DMS · Dimethyl sulfoxide · additive · 9 copies · chains A, B, C, D
- GOL · Glycerol · additive · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1023 | 0.78 | 0.80 | 115 | DMS, GOL |
| 2 | 703 | 0.76 | 0.81 | 71 | DMS |
| 3 | 556 | 0.75 | 0.83 | 41 | empty |
| 4 | 593 | 0.75 | 0.82 | 46 | empty |
| 5 | 715 | 0.75 | 0.81 | 79 | DMS, GOL |
Interfaces
4 interfaces between chains.
- A–D · 2644 Ų buried · 47 hydrogen bonds · protein-protein
- B–C · 2639 Ų buried · 46 hydrogen bonds · protein-protein
- A–C · 735 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 725 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5YZO · Crystal structure of S9 peptidase mutant (S514A) from Deinococcus radiodurans R1 · 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 Q9RXY9
- Elsewhere: RCSB PDB 5YZO · PDBe 5YZO · UniProt Q9RXY9
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