MolNFT v1 · #104877 · protein
Crystal structure of rhomboid intramembrane protease glpg F146I in complex with peptide derived inhibitor ac-fata-cmk
4QNZ · Rhomboid protease glpg: “Crystal structure of rhomboid intramembrane protease glpg F146I in complex with peptide derived inhibitor…”. X-ray diffraction, 4 ligands (ACE, BNG, 0QE), 3 pockets (best druggability 0.61). MolNFT v1…
- PDB
- 4QNZ
- Type
- protein
- Length
- 186 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rhomboid protease glpg; ACE-phe-ala-thr-ala-0QE
- EC
- 3.4.21.105
- UniProt
- U6NA71
- Ligands
- ACE, BNG, 0QE, CL
- Pockets
- 3 · best druggability 0.61
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 | 182 | 75% helix, 2% strand | U6NA71 |
| B | ACE-phe-ala-thr-ala-0QE | protein | 4 | 0% helix, 50% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains A, B
- BNG · nonyl beta-D-glucopyranoside · ligand · chains A
- 0QE · Chloromethane · ion · chains A, B
- CL · Chloride ion · ion · 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 | 58 | 0.61 | 0.91 | 21 | empty |
| 2 | 64 | 0.35 | 0.77 | 12 | empty |
| 3 | 65 | 0.34 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 423 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 4QNZ · Crystal structure of rhomboid intramembrane protease GlpG F146I in complex with peptide… · 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 U6NA71
- Elsewhere: RCSB PDB 4QNZ · PDBe 4QNZ · UniProt U6NA71
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