Research workbench
Crystal structure of a xaa-pro dipeptidase with bound methionine in the active site
Analyse Crystal structure of a xaa-pro dipeptidase with bound methionine in the active… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QS8
- Type
- protein
- Length
- 811 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xaa-pro dipeptidase
- Ligands
- MET, MG
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Xaa-pro dipeptidase | protein | 406 | 34% helix, 23% strand | — |
| B | Xaa-pro dipeptidase | protein | 405 | 34% helix, 23% strand | — |
Ligands and binding sites
- MET · Methionine · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 903 | 0.76 | 0.79 | 78 | MG, MET |
| 2 | 822 | 0.76 | 0.80 | 71 | MG, MET |
| 3 | 65 | 0.32 | 0.75 | 10 | empty |
| 4 | 60 | 0.32 | 0.76 | 14 | empty |
| 5 | 65 | 0.29 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 893 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 2QS8 · Crystal structure of a Xaa-Pro dipeptidase with bound methionine in the active site · the same entry in another collection · chain B against B, 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
- Elsewhere: RCSB PDB 2QS8 · PDBe 2QS8
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