Research workbench
Crystal structure of apo prolyl oligopeptidase from microbulbifer arenaceous
Analyse Crystal structure of apo prolyl oligopeptidase from microbulbifer arenaceous in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VGB
- Type
- protein
- Length
- 1,362 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prolyl oligopeptidase
- EC
- 3.4.21.26
- Ligands
- TMO, NI
- Pockets
- 14 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 22% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Prolyl oligopeptidase (EC 3.4.21.26) | protein | 681 | 22% helix, 33% strand | — |
Ligands and binding sites
- TMO · trimethylamine oxide · ligand · 2 copies · chains A, B
- NI · Nickel (II) ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 7 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 4 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A
- IMD · Imidazole · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 765 | 0.78 | 0.82 | 70 | empty |
| 2 | 686 | 0.76 | 0.81 | 60 | empty |
| 3 | 645 | 0.75 | 0.81 | 88 | TRS |
| 4 | 459 | 0.72 | 0.82 | 56 | GOL |
| 5 | 381 | 0.68 | 0.81 | 52 | GOL |
Interfaces
1 interface between chains.
- A–B · 880 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7VGB · Crystal structure of apo prolyl oligopeptidase from Microbulbifer arenaceous · 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
- Elsewhere: RCSB PDB 7VGB · PDBe 7VGB
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