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- PDB-4qme: Crystal structure of Aminopeptidase N in complex with the phosphi... -

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Basic information

Entry
Database: PDB / ID: 4qme
TitleCrystal structure of Aminopeptidase N in complex with the phosphinic dipeptide analogue LL-(R,S)-hPheP[CH2]Phe
ComponentsAminopeptidase N
KeywordsHYDROLASE / APN / alanine aminopeptidase / M1 peptidase / 3-{[(R)-1-amino-3-phenylpropyl](hydroxy)phosphoryl}-(S)-2-benzylpropanoic 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-37B / IMIDAZOLE / Aminopeptidase N
Similarity search - Component
Biological speciesNeisseria meningitidis MC58 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.601 Å
AuthorsNocek, B. / Vassilious, S. / Mulligan, R. / Berlicki, L. / 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 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2014Group: Database references
Revision 1.2Sep 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aminopeptidase N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,93414
Polymers98,5121
Non-polymers1,42213
Water20,9511163
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)224.000, 224.000, 57.872
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Aminopeptidase N


Mass: 98512.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis MC58 (bacteria) / Gene: pepN, NMB1416 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9JYV4, membrane alanyl aminopeptidase

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Non-polymers , 6 types, 1176 molecules

#2: Chemical ChemComp-37B / (2S)-3-[(S)-[(1R)-1-amino-3-phenylpropyl](hydroxy)phosphoryl]-2-benzylpropanoic acid


Mass: 361.372 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H24NO4P
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#6: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 1163 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 56.63 %
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: Oct 20, 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: 1.6→40 Å / Num. all: 141851 / Num. obs: 141851 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 16.8
Reflection shellResolution: 1.6→1.63 Å / % possible all: 99.6

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Processing

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

2gtq


Resolution: 1.601→32.332 Å / SU ML: 0.13 / σ(F): 1.97 / σ(I): 2 / Phase error: 16.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1721 6999 5.02 %RANDOM
Rwork0.1436 ---
all0.15 146300 --
obs0.1451 139291 97.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.601→32.332 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6856 0 83 1163 8102
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017174
X-RAY DIFFRACTIONf_angle_d1.2969750
X-RAY DIFFRACTIONf_dihedral_angle_d13.6942640
X-RAY DIFFRACTIONf_chiral_restr0.0511067
X-RAY DIFFRACTIONf_plane_restr0.0071275
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.601-1.61920.21491470.19692970X-RAY DIFFRACTION66
1.6192-1.63820.23261940.19273901X-RAY DIFFRACTION87
1.6382-1.65820.21622310.19294281X-RAY DIFFRACTION95
1.6582-1.67920.2352320.18394381X-RAY DIFFRACTION97
1.6792-1.70130.21282360.18154528X-RAY DIFFRACTION99
1.7013-1.72460.21922270.17654453X-RAY DIFFRACTION99
1.7246-1.74920.22372350.17474542X-RAY DIFFRACTION100
1.7492-1.77530.20352380.17314462X-RAY DIFFRACTION100
1.7753-1.80310.19652690.16744486X-RAY DIFFRACTION100
1.8031-1.83260.20432310.16534487X-RAY DIFFRACTION100
1.8326-1.86420.19242210.15974549X-RAY DIFFRACTION100
1.8642-1.89810.16322290.15534504X-RAY DIFFRACTION100
1.8981-1.93460.2022320.15614500X-RAY DIFFRACTION100
1.9346-1.97410.21662560.15464461X-RAY DIFFRACTION100
1.9741-2.0170.19162650.15154478X-RAY DIFFRACTION99
2.017-2.06390.18522450.14954491X-RAY DIFFRACTION100
2.0639-2.11560.17792280.14494481X-RAY DIFFRACTION99
2.1156-2.17270.16372420.13974486X-RAY DIFFRACTION100
2.1727-2.23670.15622270.13554526X-RAY DIFFRACTION99
2.2367-2.30880.162500.13264488X-RAY DIFFRACTION100
2.3088-2.39130.15782340.13514514X-RAY DIFFRACTION100
2.3913-2.4870.16142330.13064496X-RAY DIFFRACTION100
2.487-2.60020.16432620.13654497X-RAY DIFFRACTION100
2.6002-2.73720.16332320.13744515X-RAY DIFFRACTION100
2.7372-2.90860.15452250.14254521X-RAY DIFFRACTION100
2.9086-3.1330.18272230.14084518X-RAY DIFFRACTION100
3.133-3.4480.15532480.13734484X-RAY DIFFRACTION99
3.448-3.94610.13712500.12114385X-RAY DIFFRACTION98
3.9461-4.96880.14322250.11444385X-RAY DIFFRACTION97
4.9688-32.33820.18862320.15424522X-RAY DIFFRACTION100
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)
10.62070.1020.310.48120.08561.1628-0.04450.00630.0133-0.0136-0.017-0.0806-0.19250.1040.03010.1457-0.0086-0.03430.05730.00240.108928.642350.3302-30.0853
20.26830.0330.02090.58830.0911.186-0.0419-0.04090.03010.0555-0.02970.1382-0.2103-0.34980.03470.13850.0832-0.02210.1643-0.03130.127-2.738748.4173-17.7194
31.9113-0.07380.43791.3818-0.30231.01830.0126-0.2701-0.05020.2685-0.05680.23940.1461-0.6776-0.02390.2383-0.10090.09190.4145-0.08720.2106-16.414526.5711-2.2748
40.60860.2590.11470.72210.12671.1932-0.0145-0.0339-0.03470.0605-0.03430.07890.1596-0.3710.03370.1375-0.05830.01260.1731-0.02720.1693-9.040619.6785-18.326
51.51060.14240.23821.9329-0.71262.4608-0.00110.0097-0.09550.0334-0.0187-0.01170.0486-0.01740.01930.1252-0.0149-0.00690.0344-0.01510.120411.134919.8675-19.8855
61.85070.9527-0.89331.451-0.28442.2203-0.0065-0.04660.01890.0751-0.03860.00670.10540.03660.05060.12360.0229-0.01980.05520.00480.099117.273528.7199-3.9476
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 190 )
2X-RAY DIFFRACTION2chain 'A' and (resid 191 through 555 )
3X-RAY DIFFRACTION3chain 'A' and (resid 556 through 599 )
4X-RAY DIFFRACTION4chain 'A' and (resid 600 through 736 )
5X-RAY DIFFRACTION5chain 'A' and (resid 737 through 789 )
6X-RAY DIFFRACTION6chain 'A' and (resid 790 through 867 )

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