7VX3

OXA-58 crystal structure of acylated meropenem complex 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.169 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

OXA-58 crystal structure of acylated meropenem complex 2

Saino, H.Sugiyabu, T.Miyano, M.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-lactamase280Acinetobacter baumanniiMutation(s): 0 
Gene Names: blaOXA-58bla-oxa-58bla-oxa58
EC: 3.5.2.6
UniProt
Find proteins for Q2TR58 (Acinetobacter baumannii)
Explore Q2TR58 
Go to UniProtKB:  Q2TR58
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2TR58
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DWZ (Subject of Investigation/LOI)
Query on DWZ

Download Ideal Coordinates CCD File 
D [auth A](2S,3R,4S)-4-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-2-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-3-methyl-3,4-dihydro-2H-pyrrole-5-carboxylic acid
C17 H27 N3 O5 S
UUIYVKJXUXGPKB-VGWSNGFZSA-N
MER (Subject of Investigation/LOI)
Query on MER

Download Ideal Coordinates CCD File 
C [auth A](4R,5S)-3-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-5-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-4-methyl-4,5-d ihydro-1H-pyrrole-2-carboxylic acid
C17 H27 N3 O5 S
DYQHXZPAIVAJRU-HTXLXMOSSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
KCX
Query on KCX
A
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.169 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.29α = 90
b = 75.29β = 90
c = 119.47γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
MOLREPphasing
CrystalCleardata collection
iMOSFLMdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)JapanS1311005
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan18K07118

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-23
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description