1HHY

Deglucobalhimycin in complex with D-Ala-D-Ala

Structural Biology Knowledgebase: 1HHY SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.89 Å
  • R-Value Observed: 0.121

Literature

Macromolecules
Sequence Display for 1HHY

Classification: ANTIBIOTIC

Total Structure Weight: 3132.83

Macromolecule Entities
Molecule Chains Length Organism Details
DEGLUCOBALHIMYCIN A, B 7 Amycolatopsis sp.

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

A, B (2R,4S,6S)-4-azanyl-4,6-dimethyl-oxane-2,5,5- triol
C7 H15 N O4
ATGUYZRYRGIDLC-JKUQZMGJSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
DAL
Query on DAL

A, B D-ALANINE
C3 H7 N O2
QNAYBMKLOCPYGJ-UWTATZPHSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PGO
Query on PGO

B S-1,2-PROPANEDIOL
C3 H8 O2
DNIAPMSPPWPWGF-VKHMYHEASA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A, B SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_000485
Query on PRD_000485
A, B Deglucobalhimycin Glycopeptide /
Antibiotic, Antimicrobial
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: 0.89 Å
  • R-Value Observed: 0.121
  • Space Group: P 63 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 48.44 α = 90.00
b = 48.44 β = 90.00
c = 43.09 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2000-12-29
  • Released Date: 2003-09-05
  • Deposition author(s): Lehmann, C., Bunkoczi, G., Sheldrick, G.M., Vertesy, L.

Revision History

  • 2012-12-12
    Type: Other | Details: Add PRD info
  • 2012-07-25
    Type: Linkage | Details: CONECT, LINK
  • 2012-07-25
    Type: Atom nomenclature | Details: HETATM
  • 2012-07-25
    Type: Other | Details: REMARK 375, ANISOU
  • 2012-07-25
    Type: Non-polymer description | Details: HET, REMARK 620, HETNAM
  • 2012-07-25
    Type: Binding sites and description | Details: REMARK 800, SITE
  • 2011-07-13
    Type: Version format compliance | Details: Compliance with PDBx exchange dictionary V4
  • 2011-07-13
    Type: Polymer description | Details: Changed inhibitor presentation or chemistry
  • 2011-07-13
    Type: Binding sites and description | Details: Binding sites and description
  • 2011-07-13
    Type: Atom nomenclature | Details: Atom nomenclature
  • 2011-07-13
    Type: Function and keywords | Details: Function and keywords
  • 2011-07-13
    Type: Sequence database correspondence | Details: Sequence database correspondence
  • 2011-07-13
    Type: Linkage | Details: Linkage