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 Diffraction	resolution	1.00 Å
ligand	3FG, AAC, BGC, CL, GHP, MLU, OMY, OMZ, RER, VAN	enzyme
Primary reference	Vancomycin 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. 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. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

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_A] [1qd8_B] SWISS-PROT database: Domain organization of by SWISSPFAM Alignments of the sequence of 1QD8 with the sequences similar proteins can be viewed for 1QD8's classification at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list. A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification at ProtoMap. Click on the Cluster number.

Other resources with information on 1QD8

Community annotation for 1QD8 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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