Research workbench
Crystal structure of inactive state of S9 peptidase from deinococcus radiodurans R1 (pmsf treated)
Analyse Crystal structure of inactive state of S9 peptidase from deinococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IGQ
- Type
- protein
- Length
- 2,363 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acyl-peptide hydrolase, putative
- UniProt
- Q9RXY9
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 20% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acyl-peptide hydrolase, putative | protein | 599 | 20% helix, 37% strand | Q9RXY9 |
| B | Acyl-peptide hydrolase, putative | protein | 595 | 20% helix, 36% strand | Q9RXY9 |
| C | Acyl-peptide hydrolase, putative | protein | 583 | 20% helix, 37% strand | Q9RXY9 |
| D | Acyl-peptide hydrolase, putative | protein | 586 | 20% helix, 37% strand | Q9RXY9 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 11 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 851 | 0.78 | 0.81 | 79 | empty |
| 2 | 529 | 0.78 | 0.85 | 46 | SO4 |
| 3 | 753 | 0.77 | 0.82 | 76 | GOL, SO4 |
| 4 | 549 | 0.77 | 0.84 | 44 | GOL, SO4 |
| 5 | 779 | 0.77 | 0.81 | 75 | empty |
Interfaces
4 interfaces between chains.
- B–C · 1388 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 1328 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 563 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 528 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6IGQ · Crystal structure of inactive state of S9 peptidase from Deinococcus radiodurans R1 (PMSF… · 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 6IGQ · PDBe 6IGQ · UniProt Q9RXY9
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