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Complex of vancomycin with di-acetyl-lys-D-ala-D-ala

Analyse Complex of vancomycin with di-acetyl-lys-D-ala-D-ala in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
1FVM
Type
protein
Length
60 residues
Chains
12
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Vancomycin; Di-acetyl-lys-D-ala-D-ala
Ligands
RER, BGC

Structure

x-ray diffraction · 2 distinct chains · 0% helix, 20% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
A, B, C, D, E, FVancomycinprotein70% helix, 14% strand—
G, H, I, J, K, LDi-acetyl-lys-D-ala-D-alaprotein30% helix, 33% strand—

Ligands and binding sites

  • RER · vancosamine · ligand · 6 copies · chains A, G, B, C, I, D, L, E, K, F, J
  • BGC · beta-D-glucopyranose · sugar · 6 copies · chains A, B, H, C, D, J, L, E, F

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Interfaces

25 interfaces between chains.

  • C–I · 301 Ų buried · 8 hydrogen bonds · protein-protein
  • B–F · 286 Ų buried · 8 hydrogen bonds · protein-protein
  • A–D · 279 Ų buried · 8 hydrogen bonds · protein-protein
  • A–G · 273 Ų buried · 5 hydrogen bonds · protein-protein
  • F–L · 272 Ų buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 42 modified, 12 d-amino, 6 glycan (nonstandard, D-amino acid, glycosylation).

Compared structures

  • 1FVM · Complex of vancomycin with DI-acetyl-LYS-D-ALA-D-ALA · the same entry in another collection · chain A against A, TM-score 1.00

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