MolNFT v1 · #127319 · protein
Structure of E.COLI glpg in complex with peptide derived inhibitor ac- rvrha-phenylethyl-ketoamide
5MT6 · Rhomboid protease glpg: “Structure of E.COLI glpg in complex with peptide derived inhibitor ac- rvrha-phenylethyl-ketoamide”. X-ray diffraction, 3 ligands (BNG, ACE, V9C), 3 pockets (best druggability 0.64). MolNFT v1 #127319 on…
- PDB
- 5MT6
- Type
- protein
- Length
- 185 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rhomboid protease glpg; ACE-arg-val-arg-his-ala-V9C
- EC
- 3.4.21.105
- UniProt
- P09391
- Ligands
- BNG, ACE, V9C
- Pockets
- 3 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 74% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rhomboid protease glpg (EC 3.4.21.105) | protein | 180 | 76% helix, 2% strand | P09391 |
| B | ACE-arg-val-arg-his-ala-V9C | protein | 5 | 0% helix, 40% strand | — |
Ligands and binding sites
- BNG · nonyl beta-D-glucopyranoside · ligand · 2 copies · chains A
- ACE · Acetyl group · ligand · chains B
- V9C · 2-phenylethylcarbamic acid · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 61 | 0.64 | 0.93 | 16 | V9C |
| 2 | 76 | 0.35 | 0.75 | 17 | empty |
| 3 | 50 | 0.25 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 505 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5MT6 · Structure of E.coli GlpG in complex with peptide derived inhibitor… · 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 0.97
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 5MT6 · PDBe 5MT6 · UniProt P09391
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