5XEW

Crystal structure of the [Ni2+-(chromomycin A3)2]-CCG repeats complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.238
  • R-Value Work: 0.207

Literature

Macromolecules
Sequence Display for 5XEW

Classification: DNA / ANTIBIOTIC

Total Structure Weight: 10451.83

Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*TP*TP*CP*CP*GP*CP*CP*GP*CP*CP*GP*AP*A)-3') A, B 13 Synthetic construct

Small Molecules
Ligands 6 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
CPH
Query on CPH

A, B (1S)-5-deoxy-1-O-methyl-1-C-[(2R,3S)-3,5,7,10- tetrahydroxy-6-methyl-4-oxo-1,2,3,4-tetrahydroanthracen- 2-yl]-D-xylulose
None (Synonym)
C21 H24 O9
AOCJXLJIUYHXRS-PKRZCTMMSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ERI
Query on ERI

A, B 4-O-ACETYL-2,6-DIDEOXY-3-C-METHYL-BETA-L- ARABINO-HEXOPYRANOSE
C9 H16 O5
YJOQPCPEUGDGFS-VHKYIWFCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ARI
Query on ARI

A, B [O4]-ACETOXY-2,3-DIDEOXYFUCOSE
C8 H14 O4
NNWBJOVUTCFRGH-LPBLVHEISA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
1GL
Query on 1GL

A, B 4-O-METHYL-2,6-DIDEOXY-ALPHA-D-GALACTO-HEXOPYRANOSE
C7 H14 O4
CDRBUGSWTNDUSM-JWXFUTCRSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CDR
Query on CDR

A, B 2,3-DIDEOXYFUCOSE
C6 H12 O3
ZCYMCBOUZXAAJG-NGJCXOISSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NI
Query on NI

A, B NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.238
  • R-Value Work: 0.207
  • Space Group: P 32 1 2

Unit Cell:

Length (Å) Angle (°)
a = 48.29 α = 90.00
b = 48.29 β = 90.00
c = 83.36 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2017-04-06
  • Released Date: 2017-06-21
  • Deposition author(s): Tseng, W.H., Wu, P.C., Hou, M.H.
  • This entry supercedes: 5ERZ

Revision History

  • Version 1_0: 2017-06-21

    Type: Initial release

  • Version 1_1: 2017-06-28

    Type: Database references

  • Version 1_2: 2017-07-19

    Type: Database references