MolNFT v1 · #7062 · protein

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

1FVM: “Complex of vancomycin with di-acetyl-lys-D-ala-D-ala”. X-ray diffraction, 2 ligands (RER, BGC). MolNFT v1 #7062 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

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).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Vancomycin	protein	7	0% helix, 14% strand	—
G, H, I, J, K, L	Di-acetyl-lys-D-ala-D-ala	protein	3	0% 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 Å² buried · 8 hydrogen bonds · protein-protein
B–F · 286 Å² buried · 8 hydrogen bonds · protein-protein
A–D · 279 Å² buried · 8 hydrogen bonds · protein-protein
A–G · 273 Å² buried · 5 hydrogen bonds · protein-protein
F–L · 272 Å² 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

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 1FVM · PDBe 1FVM

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