6MWK

Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (IspF) Burkholderia pseudomallei in complex with ligand HGN-0883


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.143 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (IspF) Burkholderia pseudomallei in complex with ligand HGN-0456.

Abendroth, J.Dranow, D.M.Pierce, P.G.Horn, J.R.Hagen, T.J.Lorimer, D.D.Horanyi, P.S.Edwards, T.E.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
A, B, C
166Burkholderia pseudomallei 1710bMutation(s): 0 
Gene Names: ispFBURPS1710b_2511
EC: 4.6.1.12
UniProt
Find proteins for Q3JRA0 (Burkholderia pseudomallei (strain 1710b))
Explore Q3JRA0 
Go to UniProtKB:  Q3JRA0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3JRA0
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
K4Y (Subject of Investigation/LOI)
Query on K4Y

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E [auth A],
J [auth B],
N [auth C]
4-amino-N-(6-methoxypyrimidin-4-yl)benzene-1-sulfonamide
C11 H12 N4 O3 S
WMPXPUYPYQKQCX-UHFFFAOYSA-N
MLA
Query on MLA

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L [auth B]MALONIC ACID
C3 H4 O4
OFOBLEOULBTSOW-UHFFFAOYSA-N
DMS
Query on DMS

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F [auth A],
G [auth A],
K [auth B],
O [auth C]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN
Query on ZN

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D [auth A],
I [auth B],
M [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

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H [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.33α = 90
b = 68.04β = 96.46
c = 60.67γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-06
    Type: Initial release
  • Version 1.1: 2019-11-20
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description