4PW4 | pdb_00004pw4

Crystal structure of Aminopeptidase N in complex with phosphonic acid analogue of homophenylalanine L-(R)-hPheP

• PDB DOI: https://doi.org/10.2210/pdb4PW4/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Neisseria meningitidis MC58
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-03-18 Released: 2014-06-25 
• Deposition Author(s): Nocek, B., Mulligan, R., Vassiliou, S., Berlicki, L., Mucha, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.193 (Depositor), 0.201 (DCC) 
• R-Value Work: 
  0.156 (Depositor) 
• R-Value Observed: 
  0.158 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Aminopeptidase N in complex with phosphonic analogs of homophenylalanine

Nocek, B., Vassiliou, S., Mulligan, R., Weglarz-Tomczak, E., Berlicki, L., Pawelczak, M., Joachimiak, A., Mucha, A., Midwest Center for Structural Genomics (MCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 100 kDa 
• Atom Count: 7,742 
• Modeled Residue Count: 865 
• Deposited Residue Count: 867 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminopeptidase N	A	867	Neisseria meningitidis MC58	Mutation(s): 0  Gene Names: pepN, NMB1416 EC: 3.4.11.2
UniProt
Find proteins for Q9JYV4 (Neisseria meningitidis serogroup B (strain ATCC BAA-335 / MC58)) Explore Q9JYV4  Go to UniProtKB:  Q9JYV4

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2X0	B [auth A]	[(1R)-1-amino-3-phenylpropyl]phosphonic acid C9 H14 N O3 P NAPHUBPIUWHFCT-SECBINFHSA-N
SO4	F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
IMD	D [auth A]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.193 (Depositor), 0.201 (DCC) 
• R-Value Work:  0.156 (Depositor) 
• R-Value Observed: 0.158 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 224.047	α = 90
b = 224.047	β = 90
c = 57.807	γ = 120

Software Package:

Software Name	Purpose
SBC-Collect	data collection
CCP4	model building
MOLREP	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-06-25 
Deposition Author(s): Nocek, B., Mulligan, R., Vassiliou, S., Berlicki, L., Mucha, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2014-06-25
  Type: Initial release
  
• Version 1.1: 2020-05-13
  Changes: Derived calculations, Structure summary
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-12-06
  Changes: Data collection
• Version 1.4: 2024-11-06
  Changes: Structure summary