1HHZ

Deglucobalhimycin in complex with cell wall pentapeptide

Structural Biology Knowledgebase: 1HHZ SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.99 Å
  • R-Value Observed: 0.108

Literature

Macromolecules
Sequence Display for 1HHZ

Classification: ANTIBIOTIC / PEPTIDE

Total Structure Weight: 5754.60

Macromolecule Entities
Molecule Chains Length Organism Details
DEGLUCOBALHIMYCIN A, B, C 7 Amycolatopsis sp.
CELL WALL PEPTIDE D, E, F 5 synthetic

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

A, B, C (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)
PGR
Query on PGR

A, B, C R-1,2-PROPANEDIOL
C3 H8 O2
DNIAPMSPPWPWGF-GSVOUGTGSA-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, C Deglucobalhimycin Glycopeptide /
Antibiotic, Antimicrobial
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
DAL
Query on DAL
D, E, F D-PEPTIDE LINKING C3 H7 N O2 --
FGA
Query on FGA
D, E, F D-gamma-peptide, C-delta linking C5 H9 N O4 --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.99 Å
  • R-Value Observed: 0.108
  • Space Group: P 32 2 1

Unit Cell:

Length (Å) Angle (°)
a = 48.29 α = 90.00
b = 48.29 β = 90.00
c = 39.30 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: Atom nomenclature | Details: HETATM
  • 2012-07-25
    Type: Non-polymer description | Details: HETNAM, HET
  • 2012-07-25
    Type: Binding sites and description | Details: SITE, REMARK 800
  • 2012-07-25
    Type: Other | Details: ANISOU
  • 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