Research workbench
Crystal structure of glpg, a rhomboid intramembrane serine protease
Analyse Crystal structure of glpg, a rhomboid intramembrane serine protease in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IRV
- Type
- protein
- Length
- 355 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein glpg
- UniProt
- P09391
- Ligands
- PGV, PO4
- Pockets
- 5 · best druggability 0.51
Structure
x-ray diffraction · 2 distinct chains · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein glpg | protein | 176 | 74% helix, 0% strand | P09391 |
| B | Protein glpg | protein | 179 | 75% helix, 0% strand | P09391 |
Ligands and binding sites
- PGV · (1R)-2-{[{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy) phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11E)-octadec-11-enoate · ligand · 4 copies · chains B
- PO4 · Phosphate ion · ion · chains B
- LDA · Lauryl dimethylamine-N-oxide · additive · 16 copies · chains A, B
- LMT · Dodecyl-beta-D-maltoside · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 209 | 0.51 | 0.76 | 30 | PGV |
| 2 | 166 | 0.49 | 0.77 | 29 | empty |
| 3 | 97 | 0.39 | 0.75 | 17 | empty |
| 4 | 68 | 0.33 | 0.75 | 17 | empty |
| 5 | 58 | 0.27 | 0.72 | 14 | LDA |
Interfaces
1 interface between chains.
- A–B · 76 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2IRV · Crystal structure of GlpG, a rhomboid intramembrane serine protease · the same entry in another collection · chain A against A, TM-score 1.00
- P09391 · AlphaFold monomer V2.0 prediction for rhomboid protease glpg (P09391) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P09391
- Elsewhere: RCSB PDB 2IRV · PDBe 2IRV · UniProt P09391
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