4PW4

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.193
R-Value Work: 0.156
R-Value Observed: 0.158

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

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 MC58)) Explore Q9JYV4 Go to UniProtKB: Q9JYV4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9JYV4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
2X0 Query on 2X0 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	[(1R)-1-amino-3-phenylpropyl]phosphonic acid C₉ H₁₄ N O₃ P NAPHUBPIUWHFCT-SECBINFHSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A]	F [auth A] G [auth A] H [auth A] I [auth A] J [auth A] 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		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A]	E [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
IMD Query on IMD Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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
R-Value Work: 0.156
R-Value Observed: 0.158
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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-06-25

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

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

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4PW4

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

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)