Research workbench
The structure of monodechloro-teicoplanin in complex with its ligand, using ubiquitin as a ligand carrier
Analyse The structure of monodechloro-teicoplanin in complex with its ligand, using… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VFK
- Type
- protein
- Length
- 86 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.8
- Source
- Actinoplanes teichomyceticus; Homo sapiens
- Molecule
- ubiquitin, C-terminal fused by Cys-Lys-D-Ala-D-Ala; MonodeChloro- Teicoplanin A2-2
- UniProt
- P0CG48
- Ligands
- T55, GCS, NAG, MAN
Structure
x-ray diffraction · resolution 2.8 · 2 distinct chains · 20% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ubiquitin, C-terminal fused by Cys-Lys-D-Ala-D-Ala | protein | 79 | 22% helix, 34% strand | P0CG48 |
| G | MonodeChloro- Teicoplanin A2-2 | protein | 7 | 0% helix, 14% strand | — |
Ligands and binding sites
- T55 · 8-methylnonanoic acid · ligand · chains G
- GCS · 2-amino-2-deoxy-beta-D-glucopyranose · sugar · chains A, G
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A, G
- MAN · alpha-D-mannopyranose · sugar · chains A, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
1 interface between chains.
- A–G · 296 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified, 3 glycan, 2 d-amino (nonstandard, glycosylation, D-amino acid).
Compared structures
- 3VFK · The structure of monodechloro-teicoplanin in complex with its ligand, using ubiquitin as… · the same entry in another collection · chain A against A, TM-score 1.00
- P0CG48 · AlphaFold monomer V2.0 prediction for polyubiquitin-C (P0CG48) · a predicted model of the same protein · chain A against A, TM-score 0.88
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 3VFK · PDBe 3VFK · UniProt P0CG48
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.