Research workbench
Crystal structure of glpg in complex with peptide ketoamide inhibitor, ac-rvwha-ketoamide-phenylbutyl
Analyse Crystal structure of glpg in complex with peptide ketoamide inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XRP
- Type
- protein
- Length
- 186 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rhomboid protease glpg; Peptide ketoamide inhibitor
- EC
- 3.4.21.105
- UniProt
- A0A0J2E248
- Ligands
- V87
- Pockets
- 2 · best druggability 0.57
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 | 77% helix, 2% strand | A0A0J2E248 |
| B | Peptide ketoamide inhibitor | protein | 6 | 0% helix, 33% strand | — |
Ligands and binding sites
- V87 · N-(4-phenylbutyl)formamide · ligand · chains A, 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 79 | 0.57 | 0.87 | 16 | V87 |
| 2 | 78 | 0.34 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 485 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6XRP · Crystal structure of GlpG in complex with peptide ketoamide inhibitor… · 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 6XRP · PDBe 6XRP · UniProt A0A0J2E248
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