MolNFT v1 · #127321 · protein
Structure of E.COLI glpg in complex with peptide derived inhibitor ac- rvrha-cmk
5MT8 · Rhomboid protease glpg: “Structure of E.COLI glpg in complex with peptide derived inhibitor ac- rvrha-cmk”. X-ray diffraction, 4 ligands (BNG, ACE, 0QE), 3 pockets (best druggability 0.38). MolNFT v1 #127321 on GenesisL1: 3D…
- PDB
- 5MT8
- Type
- protein
- Length
- 184 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-0QE
- EC
- 3.4.21.105
- UniProt
- P09391
- Ligands
- BNG, ACE, 0QE, CL
- Pockets
- 3 · best druggability 0.38
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 | 179 | 76% helix, 2% strand | P09391 |
| B | ACE-arg-val-arg-his-ala-0QE | protein | 5 | 0% helix, 40% strand | — |
Ligands and binding sites
- BNG · nonyl beta-D-glucopyranoside · ligand · 5 copies · chains A
- ACE · Acetyl group · ligand · chains B
- 0QE · Chloromethane · ion · chains A, B
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 53 | 0.38 | 0.79 | 10 | empty |
| 2 | 83 | 0.37 | 0.75 | 16 | BNG |
| 3 | 60 | 0.29 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 465 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5MT8 · Structure of E.coli GlpG in complex with peptide derived inhibitor Ac-RVRHA-cmk · 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 0.99
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 5MT8 · PDBe 5MT8 · UniProt P09391
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