Research workbench
Solid-state NMR structure of the D-ARG4,L10-teixobactin - lipid II complex in lipid bilayers
Analyse Solid-state NMR structure of the D-ARG4,L10-teixobactin - lipid II complex in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YFY
- Type
- protein
- Length
- 64 residues
- Chains
- 8
- Method
- solid-state nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-ARG4,LEU10-teixobactin; Lipid II
- Ligands
- P1W, 2PO, MUB, NAG
Structure
solid-state nmr · 2 distinct chains · 0% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E, F | D-ARG4,LEU10-teixobactin | protein | 11 | 0% helix, 45% strand | — |
| C, D, G, H | Lipid II | protein | 5 | 0% helix, 0% strand | — |
Ligands and binding sites
- P1W · 3-methylbut-2-en-1-ol · ligand · 12 copies · chains A, G, B, D, E, F
- 2PO · Phosphonate · ligand · 8 copies · chains A, B, E, F
- MUB · N-acetyl-alpha-muramic acid · ligand · 4 copies · chains A, C, B, E, D, G, F, H
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains C, D, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
10 interfaces between chains.
- B–E · 459 Ų buried · 7 hydrogen bonds · protein-protein
- E–F · 415 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 396 Ų buried · 11 hydrogen bonds · protein-protein
- F–H · 74 Ų buried · 0 hydrogen bonds · protein-protein
- E–G · 70 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 20 d-amino, 8 modified, 4 covalent (D-amino acid, nonstandard, covalent ligand).
Compared structures
- 6YFY · Solid-state NMR structure of the D-Arg4,L10-teixobactin - Lipid II complex in lipid… · 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
- Elsewhere: RCSB PDB 6YFY · PDBe 6YFY
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