MolNFT v1 · #169942 · protein
Crystal structure of glpg in complex with peptide boronate inhibitor, ac-krfrsmqysa-B(OH)2
6XRO · Rhomboid protease glpg: “Crystal structure of glpg in complex with peptide boronate inhibitor, ac-krfrsmqysa-B(OH)2”. X-ray diffraction, 3 ligands (B2A, NA, CL), 1 pocket (best druggability 0.38). MolNFT v1 #169942 on GenesisL1: 3D…
- PDB
- 6XRO
- Type
- protein
- Length
- 185 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rhomboid protease glpg; Peptide boronate inhibitor
- EC
- 3.4.21.105
- UniProt
- A0A0J2E248
- Ligands
- B2A, NA, CL
- Pockets
- 1 · best druggability 0.38
Structure
x-ray diffraction · 2 distinct chains · 75% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rhomboid protease glpg (EC 3.4.21.105) | protein | 182 | 76% helix, 1% strand | A0A0J2E248 |
| B | Peptide boronate inhibitor | protein | 3 | 0% helix, 33% strand | — |
Ligands and binding sites
- B2A · Alanine boronic acid · ligand · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 101 | 0.38 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 390 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6XRO · Crystal structure of GlpG in complex with peptide boronate inhibitor, Ac-KRFRSMQYSA-B(OH)2 · 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 6XRO · PDBe 6XRO · UniProt A0A0J2E248
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