6PTV

Crystal structure of a DnaN sliding clamp (DNA polymerase III subunit beta) from Rickettsia rickettsii bound to griselimycin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.169 

wwPDB Validation 3D Report Full Report



Literature

Crystal structure of a DnaN sliding clamp (DNA polymerase III subunit beta) from Rickettsia rickettsii bound to griselimycin

Edwards, T.E.Abendroth, J.Horanyi, P.S.Lorimer, D.D.Seattle Structural Genomics Center for Infectious Disease (SSGCID)

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta sliding clamp
A, B, C, D
387Rickettsia rickettsii str. 'Sheila SmithMutation(s): 0 
Gene Names: A1G_03290
Find proteins for A0A0H3AWV3 (Rickettsia rickettsii (strain Sheila Smith))
Go to UniProtKB:  A0A0H3AWV3
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ACE-MVA-MP8-NZC-LEU-MP8-LEU-MVA-PRO-MLU-GLY
X, Y
11Streptomyces griseusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MPD
Query on MPD

Download CCD File 
A, D
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_002311
Query on PRD_002311
X, YACE-MVA-MP8-NZC-LEU-MP8-LEU-MVA-PRO-MLU-GLYPeptide-like /  Inhibitor

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Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
MP8
Query on MP8
X,Y
L-PEPTIDE LINKINGC6 H11 N O2PRO
MVA
Query on MVA
X,Y
L-PEPTIDE LINKINGC6 H13 N O2VAL
NZC
Query on NZC
X,Y
L-PEPTIDE LINKINGC5 H11 N O3THR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.169 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.21α = 109.38
b = 82.79β = 89.94
c = 82.86γ = 106.53
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-08-07
    Type: Initial release