6M5E Peptide Binding Protein date Mar 10, 2020
title Human Serum Albumin With Cyclic Peptide Dalbavancin
authors S.Ito, A.Senoo, S.Nagatoishi, M.Ohue, M.Yamamoto, K.Tsumoto, N.Wak
compound source
Molecule: Serum Albumin
Chain: A, B, C
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Alb, Gig20, Gig42, Pro0903, Pro1708, Pro2044, Pro2619 Pro2675, Unq696pro1341;
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606

Molecule: Dalbavancin
Chain: F, G, H
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dalbavancin
Chain: I, J
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: C 1 2 1
R_factor 0.180 R_Free 0.228
crystal
cell
length a length b length c angle alpha angle beta angle gamma
197.050 125.680 125.740 90.00 90.32 90.00
method X-Ray Diffractionresolution 2.80 Å
ligand 5PG, D3P, D4P, DIB, F8F, F8X, F93, HCL, JEF, M12, MAN, OMZ, WOO enzyme
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (602 Kb) [Save to disk]
  • Biological Unit Coordinates (6m5e.pdb1.gz) 198 Kb
  • Biological Unit Coordinates (6m5e.pdb2.gz) 201 Kb
  • Biological Unit Coordinates (6m5e.pdb3.gz) 200 Kb
  • LPC: Ligand-Protein Contacts for 6M5E
  • CSU: Contacts of Structural Units for 6M5E
  • Structure Factors (1429 Kb)
  • Retrieve 6M5E in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6M5E from S2C, [Save to disk]
    • View 6M5E in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
    • Visual 3D analysis of 6M5E
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6m5e_B] [6m5e_C] [6m5e_F] [6m5e_G] [6m5e_A] [6m5e_H] [6m5e_J] [6m5e_I]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 6M5E
  • Community annotation for 6M5E at PDBWiki (http://pdbwiki.org)

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