Research workbench
New strategy to analyze structures of glycopeptide-target complexes
Analyse New strategy to analyze structures of glycopeptide-target complexes in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RUL
- Type
- protein
- Length
- 344 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin; Dalbavancin
- UniProt
- P0CG48
- Ligands
- N1L, M12, MAN, CL
- Pockets
- 3 · best druggability 0.42
Structure
x-ray diffraction · 2 distinct chains · 17% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Ubiquitin | protein | 79 | 19% helix, 33% strand | P0CG48 |
| E, F, G, H | Dalbavancin | protein | 7 | 0% helix, 14% strand | — |
Ligands and binding sites
- N1L · 2-amino-2-deoxy-beta-D-glucopyranuronic acid · ligand · 4 copies · chains A, E, B, F, C, G, D, H
- M12 · 10-methylundecanoic acid · ligand · 4 copies · chains E, F, G, H
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A, E, B, F, C, G, D, H
- CL · Chloride ion · ion · chains B
- TLA · L(+)-tartaric acid · additive · 4 copies · 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 145 | 0.42 | 0.74 | 28 | empty |
| 2 | 148 | 0.42 | 0.74 | 30 | empty |
| 3 | 95 | 0.40 | 0.77 | 18 | empty |
Interfaces
7 interfaces between chains.
- C–G · 300 Ų buried · 5 hydrogen bonds · protein-protein
- B–F · 297 Ų buried · 5 hydrogen bonds · protein-protein
- A–E · 291 Ų buried · 4 hydrogen bonds · protein-protein
- D–H · 289 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 254 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 modified, 12 d-amino, 4 covalent, 4 glycan (nonstandard, D-amino acid, covalent ligand, glycosylation).
Compared structures
- 3RUL · New strategy to analyze structures of glycopeptide-target complexes · 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 P0CG48
- Elsewhere: RCSB PDB 3RUL · PDBe 3RUL · UniProt P0CG48
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