5YZE

Crystal structure of the [Co2+-(chromomycin A3)2]-d(CCG)3 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

CoII(Chromomycin)2 Complex Induces a Conformational Change of CCG Repeats from i-Motif to Base-Extruded DNA Duplex

Chen, Y.W.Satange, R.Wu, P.C.Jhan, C.R.Chang, C.K.Chung, K.R.Waring, M.J.Lin, S.W.Hsieh, L.C.Hou, M.H.

(2018) Int J Mol Sci 19: --


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*CP*CP*GP*CP*CP*GP*CP*CP*GP*A)-3')A,B11synthetic construct
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1GL
Query on 1GL

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A, B
4-O-METHYL-2,6-DIDEOXY-ALPHA-D-GALACTO-HEXOPYRANOSE
C7 H14 O4
CDRBUGSWTNDUSM-JWXFUTCRSA-N
 Ligand Interaction
ERI
Query on ERI

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A, B
4-O-ACETYL-2,6-DIDEOXY-3-C-METHYL-BETA-L-ARABINO-HEXOPYRANOSE
C9 H16 O5
YJOQPCPEUGDGFS-VHKYIWFCSA-N
 Ligand Interaction
ARI
Query on ARI

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A, B
[O4]-ACETOXY-2,3-DIDEOXYFUCOSE
C8 H14 O4
NNWBJOVUTCFRGH-LPBLVHEISA-N
 Ligand Interaction
CPH
Query on CPH

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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
C21 H24 O9
AOCJXLJIUYHXRS-PKRZCTMMSA-N
 Ligand Interaction
CDR
Query on CDR

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A, B
2,3-DIDEOXYFUCOSE
C6 H12 O3
ZCYMCBOUZXAAJG-NGJCXOISSA-N
 Ligand Interaction
CO
Query on CO

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A, B
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.194 
  • Space Group: P 32 1 2
Unit Cell:
Length (Å)Angle (°)
a = 46.401α = 90.00
b = 46.401β = 90.00
c = 73.822γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data reduction
Cootmodel building
SHELXDEphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-10-17
    Type: Initial release