MolNFT v1 · #152414 · protein
Crystal structure of S9 peptidase (S514A mutant in inactive state) from deinococcus radiodurans R1
6IGR · Acyl-peptide hydrolase, putative: “Crystal structure of S9 peptidase (S514A mutant in inactive state) from deinococcus radiodurans R1”. X-ray diffraction, 20 pockets (best druggability 0.76). MolNFT v1 #152414 on GenesisL1: 3D…
- 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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