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- PDB-4qpe: Crystal structure of Aminopeptidase N in complex with N-cyclohexy... -

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Basic information

Entry
Database: PDB / ID: 4qpe
TitleCrystal structure of Aminopeptidase N in complex with N-cyclohexyl-1,2-diaminoethylphosphonic acid
ComponentsAminopeptidase N
KeywordsHYDROLASE / alanine aminopeptidase / Aminopeptidase N / M1 family peptidases / N-cyclohexyl-1 / 2-diaminoethylphosphonic acid
Function / homology
Function and homology information


alanyl aminopeptidase activity / membrane alanyl aminopeptidase / metallopeptidase activity / proteolysis / zinc ion binding
Similarity search - Function
Aminopeptidase N, middle-beta domain / Peptidase M1, alanyl aminopeptidase, C-terminal domain / Peptidase M1, alanyl aminopeptidase / Peptidase M1, alanyl aminopeptidase, C-terminal / Peptidase M1, alanyl aminopeptidase, Ig-like fold / Peptidase M1, alanyl aminopeptidase, C-terminal domain superfamily / Alanyl aminopeptidase, Ig-like domain superfamily / Domain of unknown function (DUF3458) Ig-like fold / Domain of unknown function (DUF3458_C) ARM repeats / Zincin-like fold ...Aminopeptidase N, middle-beta domain / Peptidase M1, alanyl aminopeptidase, C-terminal domain / Peptidase M1, alanyl aminopeptidase / Peptidase M1, alanyl aminopeptidase, C-terminal / Peptidase M1, alanyl aminopeptidase, Ig-like fold / Peptidase M1, alanyl aminopeptidase, C-terminal domain superfamily / Alanyl aminopeptidase, Ig-like domain superfamily / Domain of unknown function (DUF3458) Ig-like fold / Domain of unknown function (DUF3458_C) ARM repeats / Zincin-like fold / Zincin-like - #30 / Zincin-like / tricorn interacting facor f3 domain / Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1, membrane alanine aminopeptidase / Aminopeptidase N-like , N-terminal domain / Peptidase family M1 domain / Peptidase M1 N-terminal domain / Aminopeptidase N-like , N-terminal domain superfamliy / Neutral Protease Domain 2 / Neutral Protease; domain 2 / Peptidase M4/M1, CTD superfamily / Alpha Horseshoe / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-37E / Aminopeptidase N
Similarity search - Component
Biological speciesNeisseria meningitidis MC58 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.004 Å
AuthorsNocek, B. / Mulligan, R. / Berlicki, L. / Vassilious, S. / Mucha, A. / Joachimiak, A.
CitationJournal: J.Med.Chem. / Year: 2014
Title: Structure-guided, single-point modifications in the phosphinic dipeptide structure yield highly potent and selective inhibitors of neutral aminopeptidases.
Authors: Vassiliou, S. / Weglarz-Tomczak, E. / Berlicki, L. / Paweczak, M. / Nocek, B. / Mulligan, R. / Joachimiak, A. / Mucha, A.
History
DepositionJun 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aminopeptidase N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,92310
Polymers98,9631
Non-polymers9609
Water12,647702
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)224.495, 224.495, 57.951
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Aminopeptidase N


Mass: 98962.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis MC58 (bacteria) / Gene: pepN, NMB1416 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9JYV4, membrane alanyl aminopeptidase
#2: Chemical ChemComp-37E / [(1R)-1-amino-2-(cyclohexylamino)ethyl]phosphonic acid


Mass: 222.222 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19N2O3P
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 702 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 56.69 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.0 M ammonium sulfate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 10, 2013 / Details: mirrors
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2→28.062 Å / Num. all: 71931 / Num. obs: 71931 / % possible obs: 98.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.3
Reflection shellResolution: 2→2.03 Å / % possible all: 94

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1639)refinement
CCP4model building
MOLREPphasing
REFMAC(phenix.refine: dev_1639)refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GTQ

2gtq


Resolution: 2.004→28.062 Å / SU ML: 0.23 / σ(F): 1.99 / σ(I): 3 / Phase error: 21.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2017 3205 5.03 %RANDOM
Rwork0.1708 ---
all0.173 66871 --
obs0.1724 63666 88.53 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.004→28.062 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6829 0 50 702 7581
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037052
X-RAY DIFFRACTIONf_angle_d0.6989585
X-RAY DIFFRACTIONf_dihedral_angle_d12.9122568
X-RAY DIFFRACTIONf_chiral_restr0.0271055
X-RAY DIFFRACTIONf_plane_restr0.0031254
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.004-2.03380.2909660.22871163X-RAY DIFFRACTION19
2.0338-2.06560.2529770.22961365X-RAY DIFFRACTION23
2.0656-2.09950.2577990.22051527X-RAY DIFFRACTION26
2.0995-2.13570.242930.23361761X-RAY DIFFRACTION29
2.1357-2.17450.26751060.23512033X-RAY DIFFRACTION34
2.1745-2.21630.28831220.23152392X-RAY DIFFRACTION39
2.2163-2.26150.23711580.22592583X-RAY DIFFRACTION43
2.2615-2.31070.2711470.21752750X-RAY DIFFRACTION46
2.3107-2.36440.22761300.2192873X-RAY DIFFRACTION47
2.3644-2.42350.23651650.21352890X-RAY DIFFRACTION48
2.4235-2.4890.24721410.20662965X-RAY DIFFRACTION49
2.489-2.56220.23381410.20393012X-RAY DIFFRACTION50
2.5622-2.64480.21091610.1983002X-RAY DIFFRACTION50
2.6448-2.73920.22261490.22998X-RAY DIFFRACTION50
2.7392-2.84880.24221570.19352992X-RAY DIFFRACTION50
2.8488-2.97830.23231470.18523032X-RAY DIFFRACTION50
2.9783-3.13520.21461580.17853007X-RAY DIFFRACTION50
3.1352-3.33130.22281570.16663022X-RAY DIFFRACTION50
3.3313-3.5880.16121660.14623025X-RAY DIFFRACTION50
3.588-3.94820.16261740.13153018X-RAY DIFFRACTION50
3.9482-4.51750.14451720.11813000X-RAY DIFFRACTION50
4.5175-5.68380.16851540.12923027X-RAY DIFFRACTION50
5.6838-28.06460.18621650.1583024X-RAY DIFFRACTION50
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1617-0.1643-0.25770.7030.64522.1017-0.11980.0085-0.07730.05320.0641-0.01620.42510.30.0210.33060.00450.07420.16570.01360.214731.8301-51.81796.2894
20.2979-0.1131-0.05280.46980.06881.371-0.05960.0314-0.0555-0.0554-0.05020.11790.283-0.48570.05570.3074-0.14660.05230.2753-0.05560.24120.5666-46.55080.1324
30.8825-0.1815-0.26840.48740.30361.483-0.01470.0030.0744-0.071-0.05050.0529-0.1707-0.29180.05580.26290.0321-0.01350.153-0.01640.25132.6399-22.3325-4.9031
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 115 )
2X-RAY DIFFRACTION2chain 'A' and (resid 116 through 599 )
3X-RAY DIFFRACTION3chain 'A' and (resid 600 through 867 )

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