3RUN

New strategy to analyze structures of glycopeptide antibiotic-target complexes

Structural Biology Knowledgebase: 3RUN SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.180
  • R-Value Work: 0.147

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3RUN

Classification: HYDROLASE / ANTIBIOTIC

Total Structure Weight: 21219.57

Macromolecule Entities
Molecule Chains Length Organism Details
LYSOZYME A 168 Enterobacteria phage t4 sensu lato EC#: 3.2.1.17 IUBMB
Mutation: C54T, C97A, L164A
Gene Name(s): E
VANCOMYCIN B 7 Amycolatopsis orientalis

Small Molecules
Ligands 8 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
BGC
Query on BGC

B BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
RER
Query on RER

B (1R,3S,4S,5S)-3-amino-2,3,6-trideoxy-3-methyl- alpha-L-arabino-hexopyranose
VANCOSAMINE (Synonym)
C7 H15 N O3
OIJZDPGKNVKVBL-WNJXEPBRSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
TRS
Query on TRS

A 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER (Synonym)
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MPD
Query on MPD

A (4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MRD
Query on MRD

A, B (4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

A PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
IPA
Query on IPA

A ISOPROPYL ALCOHOL
2-PROPANOL (Synonym)
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_000204 (GHP,MLU,OMZ,ASN,3FG,OMY) B VANCOMYCIN Glycopeptide /
Antibiotic
Ligand Explorer Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol)
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
CCS
Query on CCS
A L-PEPTIDE LINKING C5 H9 N O4 S CYS
DAL
Query on DAL
A D-PEPTIDE LINKING C3 H7 N O2 --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.180
  • R-Value Work: 0.147
  • Space Group: P 32 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 60.44 α = 90.00
b = 60.44 β = 90.00
c = 96.83 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-05-05
  • Released Date: 2012-06-06
  • Deposition author(s): Economou, N.J., Townsend, T.M., Loll, P.J.

Revision History

  • 2013-02-27
    Type: Other | Details: Add PRD info