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

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Basic information

Entry
Database: PDB / ID: 4qhp
TitleCrystal structure of Aminopeptidase N in complex with the phosphinic dipeptide analogue LL-(R,S)-hPheP[CH2]Phe(4-CH2NH2)
ComponentsAminopeptidase N
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Zn-dependent / APN / (S)-2-[4-(aminomethyl)benzyl]-3-[(R)-1-amino-3-phenylpropyl(hydroxy)phosphoryl]propanoic acid / HYDROLASE-HYDROLASE INHIBITOR complex
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-32Q / Chem-32R / IMIDAZOLE / Aminopeptidase N
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsNocek, B. / 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
DepositionMay 28, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 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_ref_seq_dif / 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_ref_seq_dif.details / _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 27, 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)101,20719
Polymers98,9631
Non-polymers2,24418
Water17,637979
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)223.760, 223.760, 57.876
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: 98962.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Gene: pepN, NMB1416 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9JYV4, membrane alanyl aminopeptidase

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Non-polymers , 7 types, 997 molecules

#2: Chemical ChemComp-32Q / (2S)-2-[4-(aminomethyl)benzyl]-3-[(R)-[(1R)-1-amino-3-phenylpropyl](hydroxy)phosphoryl]propanoic acid


Mass: 390.413 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H27N2O4P
#3: Chemical ChemComp-32R / (2R)-2-[4-(aminomethyl)benzyl]-3-[(R)-[(1R)-1-amino-3-phenylpropyl](hydroxy)phosphoryl]propanoic acid


Mass: 390.413 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H27N2O4P
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-ZN / ZINC ION


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


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 979 / 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: 2.82 Å3/Da / Density % sol: 56.46 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 2 M ammonium sulfate, 0.1 M Bis-Tris, pH 6.5, 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 14, 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→32.297 Å / Num. all: 142458 / Num. obs: 142174 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 16.32
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: 1.6→32.297 Å / SU ML: 0.14 / σ(F): 1.68 / Phase error: 18.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1782 5472 5.03 %RANDOM
Rwork0.1538 ---
obs0.155 133975 86.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→32.297 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6850 0 134 979 7963
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0127237
X-RAY DIFFRACTIONf_angle_d1.3339841
X-RAY DIFFRACTIONf_dihedral_angle_d14.0662656
X-RAY DIFFRACTIONf_chiral_restr0.0551074
X-RAY DIFFRACTIONf_plane_restr0.0081282
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.61840.22291650.20812840X-RAY DIFFRACTION32
1.6184-1.63740.25841590.22083487X-RAY DIFFRACTION38
1.6374-1.65740.24991970.23234164X-RAY DIFFRACTION46
1.6574-1.67830.23952380.22024919X-RAY DIFFRACTION55
1.6783-1.70040.26392930.21825643X-RAY DIFFRACTION62
1.7004-1.72370.24043280.21716194X-RAY DIFFRACTION69
1.7237-1.74830.22883520.2166746X-RAY DIFFRACTION74
1.7483-1.77440.23563190.20847130X-RAY DIFFRACTION79
1.7744-1.80220.23583580.20467477X-RAY DIFFRACTION83
1.8022-1.83170.23824320.19787824X-RAY DIFFRACTION87
1.8317-1.86330.20174030.19148151X-RAY DIFFRACTION89
1.8633-1.89720.20775030.18278241X-RAY DIFFRACTION92
1.8972-1.93360.22134710.17698407X-RAY DIFFRACTION93
1.9336-1.97310.20745020.1698402X-RAY DIFFRACTION95
1.9731-2.0160.19774940.16558529X-RAY DIFFRACTION95
2.016-2.06290.1864790.15288548X-RAY DIFFRACTION95
2.0629-2.11450.18444270.14928600X-RAY DIFFRACTION96
2.1145-2.17160.16974750.14318588X-RAY DIFFRACTION95
2.1716-2.23550.1654200.14258707X-RAY DIFFRACTION96
2.2355-2.30770.17444520.13598721X-RAY DIFFRACTION97
2.3077-2.39010.17814550.13678665X-RAY DIFFRACTION97
2.3901-2.48580.16884590.13468798X-RAY DIFFRACTION97
2.4858-2.59890.15775250.14128807X-RAY DIFFRACTION98
2.5989-2.73580.17724720.1428879X-RAY DIFFRACTION99
2.7358-2.90710.16024600.15348944X-RAY DIFFRACTION99
2.9071-3.13140.19834880.1568986X-RAY DIFFRACTION100
3.1314-3.44620.17634620.14659018X-RAY DIFFRACTION100
3.4462-3.94410.13994760.12688937X-RAY DIFFRACTION99
3.9441-4.96630.13025260.11848922X-RAY DIFFRACTION100
4.9663-32.30350.18834050.179076X-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)
10.06590.02760.06410.02330.010.0515-0.0592-0.0488-0.0226-0.0369-0.022-0.0188-0.13490.1148-0.01430.1468-0.0345-0.04860.0874-0.00280.113432.777754.4966-5.0126
20.11090.01740.01530.121-0.0750.4654-0.0229-0.00450.00810.0173-0.0056-0.0088-0.1242-0.0621-0.07610.1030.013-0.02840.0319-0.00570.06389.651747.7141-7.3234
30.02610.01320.00060.1637-0.07990.1287-0.04140.022-0.01260.1539-0.04760.0871-0.2448-0.1217-0.06470.12750.15240.02940.2019-0.06520.1359-15.296552.836517.0893
40.01090.04030.02820.185-0.0210.08350.0027-0.03380.03120.0767-0.00120.0730.0182-0.21230.00010.1335-0.01330.02140.2151-0.02920.1556-14.927730.233410.4685
50.0395-0.0372-0.03790.03530.02250.0816-0.03070.013-0.1124-0.01090.0020.00020.0253-0.0515-0.00810.1212-0.0284-0.00770.05190.00080.13264.367316.1257-2.6153
60.02570.01770.00880.0210.03740.05120.0094-0.0020.01850.0606-0.0131-0.00490.04850.0348-0.00090.1432-0.0029-0.01110.07850.00790.107317.233628.738715.3554
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 78 )
2X-RAY DIFFRACTION2chain 'A' and (resid 79 through 451 )
3X-RAY DIFFRACTION3chain 'A' and (resid 452 through 507 )
4X-RAY DIFFRACTION4chain 'A' and (resid 508 through 689 )
5X-RAY DIFFRACTION5chain 'A' and (resid 690 through 789 )
6X-RAY DIFFRACTION6chain 'A' and (resid 790 through 867 )

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