Research workbench
Crystal structure of S9 peptidase (inactive form) from deinococcus radiodurans R1
Analyse Crystal structure of S9 peptidase (inactive form) from deinococcus radiodurans… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YZM
- Type
- protein
- Length
- 2,382 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 0.79
Structure
x-ray diffraction · 4 distinct chains · 20% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acyl-peptide hydrolase, putative | protein | 598 | 20% helix, 38% strand | Q9RXY9 |
| B | Acyl-peptide hydrolase, putative | protein | 601 | 20% helix, 36% strand | Q9RXY9 |
| C | Acyl-peptide hydrolase, putative | protein | 593 | 20% helix, 37% strand | Q9RXY9 |
| D | Acyl-peptide hydrolase, putative | protein | 590 | 20% helix, 37% strand | Q9RXY9 |
Ligands and binding sites
- ACT · Acetate ion · additive · 4 copies · chains A, B, C, D
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 | 802 | 0.79 | 0.82 | 73 | ACT |
| 2 | 854 | 0.79 | 0.82 | 75 | ACT |
| 3 | 790 | 0.78 | 0.82 | 70 | empty |
| 4 | 542 | 0.76 | 0.83 | 47 | ACT |
| 5 | 577 | 0.76 | 0.83 | 46 | empty |
Interfaces
4 interfaces between chains.
- A–D · 1320 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1293 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 475 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 452 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5YZM · Crystal structure of S9 peptidase (inactive form) 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 5YZM · PDBe 5YZM · UniProt Q9RXY9
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