3NDV | pdb_00003ndv

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

• PDB DOI: https://doi.org/10.2210/pdb3NDV/pdb

• Classification: HYDROLASE/ANTIBIOTIC
• Organism(s): Sphingosinicella xenopeptidilytica
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-06-08 Released: 2011-09-28 
• Deposition Author(s): Merz, T., Heck, T., Geueke, B., Kohler, H.-P.E., Gruetter, M.G.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.192 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Starting Model: experimental

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.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 157.01 kDa 
• Atom Count: 11,974 
• Modeled Residue Count: 1,465 
• Deposited Residue Count: 1,492 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-peptidyl aminopeptidase	A, B, C, D	373	Sphingosinicella xenopeptidilytica	Mutation(s): 0  Gene Names: bapA EC: 3.4.11.25
UniProt
Find proteins for Q52VH2 (Sphingosinicella xenopeptidilytica) Explore Q52VH2  Go to UniProtKB:  Q52VH2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDV	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	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	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 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.9	α = 90
b = 96.4	β = 108.4
c = 101.5	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
PHASER	phasing
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-09-28 
Deposition Author(s): Merz, T., Heck, T., Geueke, B., Kohler, H.-P.E., Gruetter, M.G.

Revision History  

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