5XJW

Crystal Structure of the [Co2+-(Chromomycin A3)2]-CCG repeats Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.097 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.225 

wwPDB Validation 3D Report Full Report


This is version 2.2 of the entry. See complete history

Literature

Crystal Structure of the [Co2+-(Chromomycin A3)2]-CCG repeats Complex

Tseng, W.H.Wu, P.C.Satange, R.B.Hou, M.H.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*TP*CP*GP*CP*CP*GP*CP*CP*GP*AP*A)-3')A,B13synthetic construct
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DDA
Query on DDA

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A, B
2,6-DIDEOXY-BETA-D-GLUCOSE
2,6-DIDEOXY-BETA-D-MANNOSE
C6 H12 O4
FDWRIIDFYSUTDP-KVTDHHQDSA-N
 Ligand Interaction
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
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
CO
Query on CO

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A, B
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
2GL
Query on 2GL

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A, B
4-O-ACETYL-2,6-DIDEOXY-ALPHA-D-GALACTO-HEXOPYRANOSE
C8 H14 O5
VJCDYXNEQSTOMG-JBBNEOJLSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_001136
Query on PRD_001136
A,BChromomycin A3, MonomerOligosaccharide / Antibiotic

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.097 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.225 
  • Space Group: P 32 1 2
Unit Cell:
Length (Å)Angle (°)
a = 48.309α = 90.00
b = 48.309β = 90.00
c = 83.636γ = 120.00
Software Package:
Software NamePurpose
Blu-Icedata collection
SCALEPACKdata scaling
PHENIXmodel building
PHENIXrefinement
HKL-2000data processing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-05-16
    Type: Initial release
  • Version 2.0: 2018-06-06
    Type: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2018-09-12
    Type: Data collection, Structure summary
  • Version 2.2: 2018-10-03
    Type: Data collection, Structure summary