Research workbench
Structure of E.COLI rhomboid protease glpg in complex with monobactam L29 (data set 2)
Analyse Structure of E.COLI rhomboid protease glpg in complex with monobactam L29 (data… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZOT
- Type
- protein
- Length
- 178 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, L6C, CL
- Pockets
- 2 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 76% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rhomboid protease glpg (EC 3.4.21.105) | protein | 178 | 76% helix, 0% strand | P09391 |
Ligands and binding sites
- BNG · nonyl beta-D-glucopyranoside · ligand · 9 copies · chains A
- L6C · phenyl N-[(1R)-3-oxidanylidene-1-phenyl-propyl]carbamate · ligand · chains A
- CL · Chloride ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 281 | 0.74 | 0.87 | 38 | L6C |
| 2 | 66 | 0.34 | 0.76 | 15 | BNG |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 3ZOT · Structure of E.coli rhomboid protease GlpG in complex with monobactam L29 (data set 2) · 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 3ZOT · PDBe 3ZOT · UniProt P09391
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