3VFJ

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

Structural Biology Knowledgebase: 3VFJ SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.231
  • R-Value Work: 0.188

Literature

Macromolecules
Sequence Display for 3VFJ

Classification: SUGAR BINDING PROTEIN / ANTIBIOTIC

Total Structure Weight: 44183.64

Macromolecule Entities
Molecule Chains Length Organism Details
Maltose-binding periplasmic protein, C-terminal fused by Cys-Lys-D-Ala-D-Ala A 378 Escherichia coli Gene Name(s): malE b4034 JW3994
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
MonodeChloro- Teicoplanin A2-2 G 7 Actinoplanes teichomyceticus

Membrane Protein

Source: inferred by homology | Group: ALPHA-HELICAL

Subgroup Name: ATP Binding Cassette (ABC) Transporters

Protein Name: MalFGK2-MBP Maltose uptake transporter complex


Small Molecules
Ligands 7 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 NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MAN
Query on MAN

G ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
Ligand Explorer NGL
 
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 NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
T55
Query on T55

G 8-METHYLNONANOIC ACID
C10 H20 O2
OAOABCKPVCUNKO-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CAC
Query on CAC

A, G CACODYLATE ION
dimethylarsinate (Synonym)
C2 H6 As O2
OGGXGZAMXPVRFZ-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ACT
Query on ACT

A ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_000882
Query on PRD_000882
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: 2.05 Å
  • R-Value Free: 0.231
  • R-Value Work: 0.188
  • Space Group: C 2 2 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 40.32 α = 90.00
b = 123.61 β = 90.00
c = 156.74 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

  • 2014-12-10
    Type: Polymer description | Details: --
  • 2013-06-19
    Type: Citation | Details: Citation update
  • 2013-04-03
    Type: Binding sites and description | Details: --
  • 2013-03-27
    Type: Linkage | Details: --
  • 2013-03-13
    Type: Polymer description | Details: --
  • 2013-03-06
    Type: Polymer description | Details: --