MolNFT v1 · #84236 · protein
A complex of glpg with isocoumarin inhibitor covalently bonded to serine 201 and histidine 150
3ZEB · Rhomboid protease glpg: “A complex of glpg with isocoumarin inhibitor covalently bonded to serine 201 and histidine 150”. X-ray diffraction, 3 ligands (BNG, SV1, CL), 4 pockets (best druggability 0.58). MolNFT v1 #84236 on…
- PDB
- 3ZEB
- Type
- protein
- Length
- 179 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rhomboid protease glpg
- EC
- 3.4.21.105
- UniProt
- P09391
- Ligands
- BNG, SV1, CL
- Pockets
- 4 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rhomboid protease glpg (EC 3.4.21.105) | protein | 179 | 77% helix, 0% strand | P09391 |
Ligands and binding sites
- BNG · nonyl beta-D-glucopyranoside · ligand · 5 copies · chains A
- SV1 · 2-phenylethyl 2-(4-azanyl-2-methanoyl-phenyl)ethanoate · ligand · chains A
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 141 | 0.58 | 0.83 | 23 | CL |
| 2 | 88 | 0.42 | 0.78 | 17 | SV1 |
| 3 | 86 | 0.37 | 0.76 | 17 | BNG |
| 4 | 55 | 0.37 | 0.79 | 12 | empty |
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 3ZEB · A complex of GlpG with isocoumarin inhibitor covalently bonded to serine 201 and… · 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 0.98
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 3ZEB · PDBe 3ZEB · UniProt P09391
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