Research workbench
Crystal structure of S9 peptidase (inactive STATE)FROM deinococcus radiodurans R1 in P212121
Analyse Crystal structure of S9 peptidase (inactive STATE)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
- 6IGP
- Type
- protein
- Length
- 2,342 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 0.78
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 | 594 | 20% helix, 37% strand | Q9RXY9 |
| B | Acyl-peptide hydrolase, putative | protein | 587 | 19% helix, 38% strand | Q9RXY9 |
| C | Acyl-peptide hydrolase, putative | protein | 582 | 20% helix, 36% strand | Q9RXY9 |
| D | Acyl-peptide hydrolase, putative | protein | 579 | 20% helix, 37% strand | Q9RXY9 |
Ligands and binding sites
- GOL · Glycerol · additive · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 603 | 0.78 | 0.83 | 59 | empty |
| 2 | 776 | 0.76 | 0.81 | 74 | empty |
| 3 | 538 | 0.75 | 0.83 | 44 | empty |
| 4 | 538 | 0.75 | 0.83 | 39 | empty |
| 5 | 599 | 0.75 | 0.82 | 51 | empty |
Interfaces
4 interfaces between chains.
- A–D · 1278 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 1255 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 517 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 437 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6IGP · Crystal structure of S9 peptidase (inactive state)from Deinococcus radiodurans R1 in… · 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 6IGP · PDBe 6IGP · UniProt Q9RXY9
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