1QD8 Antibiotic date Jul 15, 1999
title Complex Of Vancomycin With N-Acetyl Glycine
authors P.J.Loll, J.Kaplan, B.Selinsky, P.H.Axelsen
compound source
Molecule: Vancomycin
Chain: A, B
Engineered: Yes
Organism_scientific: Amycolatopsis Orientalis
Organism_taxid: 31958
symmetry Space Group: P 43 21 2
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
28.710 28.710 66.770 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.00 Å
ligand 3FG, AAC, BGC, CL, GHP, MLU, OMY, OMZ, RER, VAN enzyme
Primary referenceVancomycin binding to low-affinity ligands: delineating a minimum set of interactions necessary for high-affinity binding., Loll PJ, Kaplan J, Selinsky BS, Axelsen PH, J Med Chem 1999 Nov 4;42(22):4714-9. PMID:10579833
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (12 Kb) [Save to disk]
  • Biological Unit Coordinates (1qd8.pdb1.gz) 6 Kb
  • Biological Unit Coordinates (1qd8.pdb2.gz) 5 Kb
  • LPC: Ligand-Protein Contacts for 1QD8
  • CSU: Contacts of Structural Units for 1QD8
  • Likely Quarternary Molecular Structure file(s) for 1QD8
  • Retrieve 1QD8 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1QD8 from S2C, [Save to disk]
  • View 1QD8 in 3D
  • Proteopedia, because life has more than 2D.
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  • Visual 3D analysis of 1QD8
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1QD8, from MSDmotif at EBI
  • Fold representative 1qd8 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1qd8] [1qd8_B] [1qd8_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 1QD8
  • Community annotation for 1QD8 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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