Research workbench
E.COLI glpg Y205F mutant complexed with aldehyde inhibitor in DMPC/CHAPSO bicelle
Analyse E.COLI glpg Y205F mutant complexed with aldehyde inhibitor in DMPC/CHAPSO… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5F5J
- Type
- protein
- Length
- 185 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rhomboid protease glpg; Peptidic derivative of gurken: ACE-val-arg-met-ala- aldehyde
- EC
- 3.4.21.105
- UniProt
- A0A0J2E248
- Ligands
- ACE
- Pockets
- 2 · best druggability 0.45
Structure
x-ray diffraction · 2 distinct chains · 76% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rhomboid protease glpg (EC 3.4.21.105) | protein | 181 | 78% helix, 2% strand | A0A0J2E248 |
| B | Peptidic derivative of gurken: ACE-val-arg-met-ala- aldehyde | protein | 4 | 0% helix, 50% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 82 | 0.45 | 0.80 | 16 | empty |
| 2 | 61 | 0.32 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 474 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent, 1 modified (covalent ligand, nonstandard).
Compared structures
- 5F5J · E.coli GlpG Y205F mutant complexed with aldehyde inhibitor in DMPC/CHAPSO bicelle · 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
- Every structure of UniProt A0A0J2E248
- Elsewhere: RCSB PDB 5F5J · PDBe 5F5J · UniProt A0A0J2E248
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