MolNFT v1 · #152413 · protein
Crystal structure of inactive state of S9 peptidase from deinococcus radiodurans R1 (pmsf treated)
6IGQ · Acyl-peptide hydrolase, putative: “Crystal structure of inactive state of S9 peptidase from deinococcus radiodurans R1 (pmsf treated)”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.78). MolNFT v1 #152413 on…
- 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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