Research workbench
Crystal structure of S9 peptidase (S514A mutant in inactive state) from deinococcus radiodurans R1
Analyse Crystal structure of S9 peptidase (S514A mutant in inactive state) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IGR
- Type
- protein
- Length
- 2,384 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 0.76
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 | 19% helix, 37% strand | Q9RXY9 |
| B | Acyl-peptide hydrolase, putative | protein | 597 | 19% helix, 36% strand | Q9RXY9 |
| C | Acyl-peptide hydrolase, putative | protein | 595 | 20% helix, 36% strand | Q9RXY9 |
| D | Acyl-peptide hydrolase, putative | protein | 593 | 20% helix, 37% strand | Q9RXY9 |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains A
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 | 688 | 0.76 | 0.81 | 54 | GOL |
| 2 | 605 | 0.76 | 0.82 | 51 | empty |
| 3 | 855 | 0.75 | 0.79 | 75 | empty |
| 4 | 526 | 0.75 | 0.83 | 42 | empty |
| 5 | 532 | 0.74 | 0.82 | 37 | empty |
Interfaces
4 interfaces between chains.
- A–D · 1240 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 1193 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 698 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 698 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6IGR · Crystal structure of S9 peptidase (S514A mutant in inactive state) from Deinococcus… · 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 6IGR · PDBe 6IGR · UniProt Q9RXY9
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