3NDV

Crystal structure of the N-terminal beta-aminopeptidase BapA in complex with ampicillin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.168 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Crystal structures and inhibition of the beta-aminopeptidase BapA, a new ampicillin-recognizing member of the N-terminal nucleophile hydrolase family

Heck, T.Merz, T.Geueke, B.Gruetter, M.G.Kohler, H.-P.E.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-peptidyl aminopeptidase
A, B, C, D
373Sphingosinicella xenopeptidilyticaMutation(s): 0 
Gene Names: bapA
EC: 3.4.11.25
UniProt
Find proteins for Q52VH2 (Sphingosinicella xenopeptidilytica)
Explore Q52VH2 
Go to UniProtKB:  Q52VH2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ52VH2
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NDV
Query on NDV

Download Ideal Coordinates CCD File 
G [auth A],
N [auth D]
(2S,4S)-2-[(1R)-1-{[(2R)-2-amino-2-phenylacetyl]amino}-2-oxoethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid
C16 H21 N3 O4 S
WHAIWIUXAXKSOT-NMKXLXIOSA-N
AIC
Query on AIC

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B],
L [auth C],
M [auth D]
(2S,5R,6R)-6-{[(2R)-2-AMINO-2-PHENYLETHANOYL]AMINO}-3,3-DIMETHYL-7-OXO-4-THIA-1-AZABICYCLO[3.2.0]HEPTANE-2-CARBOXYLIC ACID
C16 H19 N3 O4 S
AVKUERGKIZMTKX-NJBDSQKTSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
I [auth B],
K [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.168 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.9α = 90
b = 96.4β = 108.4
c = 101.5γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
PHASERphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-09-28
    Type: Initial release
  • Version 1.1: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description