1EQ2

THE CRYSTAL STRUCTURE OF ADP-L-GLYCERO-D-MANNOHEPTOSE 6-EPIMERASE

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.217 

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This is version 1.4 of the entry. See complete history. 


Literature

The crystal structure of ADP-L-glycero-D-mannoheptose 6-epimerase: catalysis with a twist.

Deacon, A.M., Ni, Y.S., Coleman Jr., W.G., Ealick, S.E.

(2000) Structure 8: 453-462

  • DOI: https://doi.org/10.1016/s0969-2126(00)00128-3
  • Primary Citation of Related Structures:  
    1EQ2

  • PubMed Abstract: 

    ADP-L-glycero--mannoheptose 6-epimerase (AGME) is required for lipopolysaccharide (LPS) biosynthesis in most genera of pathogenic and non-pathogenic Gram-negative bacteria. It catalyzes the interconversion of ADP-D-glycero-D-mannoheptose and ADP-L-glycero-D-mannoheptose, a precursor of the seven-carbon sugar L-glycero-mannoheptose (heptose). Heptose is an obligatory component of the LPS core domain; its absence results in a truncated LPS structure resulting in susceptibility to hydrophobic antibiotics. Heptose is not found in mammalian cells, thus its biosynthetic pathway in bacteria presents a unique target for the design of novel antimicrobial agents.

    • Organizational Affiliation: 

    Department ofChemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ADP-L-GLYCERO-D-MANNOHEPTOSE 6-EPIMERASE
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
310Escherichia coliMutation(s): 1 
EC: 5.1.3.20
UniProt
Find proteins for P67910 (Escherichia coli (strain K12))
Explore P67910 
Go to UniProtKB:  P67910
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP67910
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP
Download Ideal Coordinates CCD File 
AA [auth I]
CA [auth J]
K [auth A]
M [auth B]
O [auth C]
AA [auth I],
CA [auth J],
K [auth A],
M [auth B],
O [auth C],
Q [auth D],
S [auth E],
U [auth F],
W [auth G],
Y [auth H]
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
ADQ
Query on ADQ
Download Ideal Coordinates CCD File 
BA [auth I]
DA [auth J]
L [auth A]
N [auth B]
P [auth C]
BA [auth I],
DA [auth J],
L [auth A],
N [auth B],
P [auth C],
R [auth D],
T [auth E],
V [auth F],
X [auth G],
Z [auth H]
ADENOSINE-5'-DIPHOSPHATE-GLUCOSE
C16 H25 N5 O15 P2
WFPZSXYXPSUOPY-ROYWQJLOSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSO
Query on CSO
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.217 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.46α = 90
b = 109.76β = 91.04
c = 181.54γ = 90
Software Package:
Software NamePurpose
SnBphasing
X-PLORrefinement
MOSFLMdata reduction
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-11-08
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description
  • Version 1.4: 2024-03-13
    Changes: Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary