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The structure of monodechloro-teicoplanin in complex with its ligand, using mbp as a ligand carrier
Analyse The structure of monodechloro-teicoplanin in complex with its ligand, using mbp… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VFJ
- Type
- protein
- Length
- 384 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Maltose-binding periplasmic protein, C-terminal fused by cys-lys-D-ala-D-ala…
- UniProt
- P0AEX9
- Ligands
- T55, GCS, NAG, MAN, ZN
- Pockets
- 4 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Maltose-binding periplasmic protein, C-terminal fused by cys-lys-D-ala-D-ala | protein | 377 | 44% helix, 21% strand | P0AEX9 |
| 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
- ZN · Zinc ion · metal · 8 copies · chains A
- ACT · Acetate ion · additive · 2 copies · chains A
- CAC · Cacodylate ion · additive · 2 copies · chains A, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 261 | 0.56 | 0.77 | 36 | ZN, ACT |
| 2 | 78 | 0.41 | 0.79 | 19 | empty |
| 3 | 90 | 0.36 | 0.75 | 17 | empty |
| 4 | 68 | 0.29 | 0.73 | 21 | empty |
Interfaces
1 interface between chains.
- A–G · 326 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified, 3 glycan, 2 d-amino (nonstandard, glycosylation, D-amino acid).
Compared structures
- 3VFJ · The structure of monodechloro-teicoplanin in complex with its ligand, using MBP as a… · 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 P0AEX9
- Elsewhere: RCSB PDB 3VFJ · PDBe 3VFJ · UniProt P0AEX9
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