3VFK

The structure of monodechloro-teicoplanin in complex with its ligand, using ubiquitin as a ligand carrier

Structural Biology Knowledgebase: 3VFK SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.306
  • R-Value Work: 0.278

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3VFK

Classification: SUGAR BINDING PROTEIN / ANTIBIOTIC

Total Structure Weight: 10877.74

Macromolecule Entities
Molecule Chains Length Organism Details
MonodeChloro- Teicoplanin A2-2 G 7 Actinoplanes teichomyceticus

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NAG
Query on NAG

G N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MAN
Query on MAN

G ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GCS
Query on GCS

G D-GLUCOSAMINE
2-AMINO-2-DEOXY-D-GLUCOSE (Synonym)
C6 H13 N O5
MSWZFWKMSRAUBD-QZABAPFNSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
T55
Query on T55

G 8-METHYLNONANOIC ACID
C10 H20 O2
OAOABCKPVCUNKO-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_000882 (3MY,GHP,3FG,OMX) G MonodeChloro- Teicoplanin A2-2 Glycopeptide /
Antibiotic
Ligand Explorer 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: 2.8 Å
  • R-Value Free: 0.306
  • R-Value Work: 0.278
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 88.01 α = 90.00
b = 25.18 β = 109.18
c = 38.71 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-01-09
  • Released Date: 2013-01-09
  • Deposition author(s): Economou, N.J., Weeks, S.D., Grasty, K.C., Loll, P.J.

Revision History

  • 2013-06-19
    Type: Citation | Details: Citation update
  • 2013-04-03
    Type: Binding sites and description | Details: --
  • 2013-03-27
    Type: Polymer description | Details: --