1HHF

Decaplanin second P6122-Form

Structural Biology Knowledgebase: 1HHF SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Observed: 0.180

Literature

Macromolecules
Sequence Display for 1HHF

Classification: ANTIBIOTIC

Total Structure Weight: 6743.94

Macromolecule Entities
Molecule Chains Length Organism Details
DECAPLANIN A, B, C, D 7 Uncultured actinomycete

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
BGC
Query on BGC

A, B, C, D BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
RAM
Query on RAM

A, B, C, D ALPHA-L-RHAMNOSE
C6 H12 O5
SHZGCJCMOBCMKK-HGVZOGFYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ERE
Query on ERE

A, B, C, D (1R,3S,4R,5S)-3-amino-2,3,6-trideoxy-3-methyl- alpha-L-arabino-hexopyranose
4-EPI-VANCOSAMINE (Synonym)
C7 H15 N O3
OIJZDPGKNVKVBL-VZFHVOOUSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

C PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A, C CHLORIDE ION
Cl
VEXZGXHMUGYJMC-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_000207
Query on PRD_000207
A, B, C, D Decaplanin Glycopeptide /
Antibiotic
Ligand Explorer Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Observed: 0.180
  • Space Group: P 61 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 60.10 α = 90.00
b = 60.10 β = 90.00
c = 131.39 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2000-12-22
  • Released Date: 2005-07-11
  • Deposition author(s): Lehmann, C., Vertessy, L., Sheldrick, G.M., Dauter, Z., Dauter, M.

Revision History

  • 2013-05-01
    Type: Non-polymer description | Details: HETSYN
  • 2012-11-30
    Type: Other | Details: Add PRD info
  • 2012-07-11
    Type: Other | Details: Binding sites and description, Linkage, Non-polymer description, Other, Atom nomenclature
  • 2011-07-13
    Type: Atom nomenclature | Details: Atom nomenclature
  • 2011-07-13
    Type: Binding sites and description | Details: Binding sites and description
  • 2011-07-13
    Type: Polymer description | Details: Changed inhibitor presentation or chemistry
  • 2011-07-13
    Type: Version format compliance | Details: Compliance with PDBx exchange dictionary V4
  • 2011-07-13
    Type: Linkage | Details: Linkage
  • 2011-07-13
    Type: Sequence database correspondence | Details: Sequence database correspondence
  • 2011-07-13
    Type: Function and keywords | Details: Function and keywords