› 6m5e

X-ray diffraction
2.8Å resolution

Human serum albumin with cyclic peptide dalbavancin

Released:
DOI: 10.2210/pdb6m5e/pdb
PDB entry 6m5e coloured by chain, front view.
PDB entry 6m5e coloured by chain, side view.
PDB entry 6m5e coloured by chain, top view.
Source organisms:
Primary publication:
Structural Basis for the Binding Mechanism of Human Serum Albumin Complexed with Cyclic Peptide Dalbavancin.
Ito S, Senoo A, Nagatoishi S, Ohue M, Yamamoto M, Tsumoto K, Wakui N
J Med Chem 63 14045-14053 (2020)
PMID: 33183011

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assemblies composition:
hetero dimer
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-136181 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Albumin Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 585 amino acids
Theoretical weight: 66.57 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P02768 (Residues: 25-609; Coverage: 99%)
Gene names: ALB, GIG20, GIG42, PRO0903, PRO1708, PRO2044, PRO2619, PRO2675, UNQ696/PRO1341
Sequence domains: Serum albumin family
dalbavancin Chains: F, G, H
Molecule details ›
Chains: F, G, H
Length: 8 amino acids
Theoretical weight: 1.31 KDa
Source organism: synthetic construct
Expression system: Not provided
dalbavancin Chains: I, J
Molecule details ›
Chains: I, J
Length: 8 amino acids
Theoretical weight: 1.31 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

6 bound ligands:
Ligand JEF 6 x JEF
Ligand F8F 3 x F8F
Ligand M12 5 x M12
Ligand MAN 3 x MAN
Ligand F8X 2 x F8X
Ligand WOO 2 x WOO
3 modified residues:
Ligand 5PG 5 x 5PG
Ligand D4P 10 x D4P
Ligand D3P 5 x D3P

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL32XU
Spacegroup: C2
Unit cell:
a: 197.05Å b: 125.68Å c: 125.74Å
α: 90° β: 90.32° γ: 90°
R-values:
R R work R free
0.182 0.18 0.228
Expression systems:
  • Homo sapiens
  • Not provided

Quick links

Citations

5 citation in other articles

Enantioselective Human Serum Albumin Binding of Apremilast: Liquid Chromatographic, Fluorescence and Molecular Docking Study.
Dombi et al. (2023)
4 more

1 mention without citation

Antibiotics and Carbohydrate-Containing Drugs Targeting Bacterial Cell Envelopes: An Overview.
Riu et al. (2022)