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

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Basic information

Entry
Database: PDB / ID: 4qir
TitleCrystal structure of Aminopeptidase N in complex with the phosphinic dipeptide analogue LL-(R,S)-2-(pyridin-3-yl)ethylGlyP[CH2]Phe
ComponentsAminopeptidase N
KeywordsHYDROLASE / alanine aminopeptidase / Aminopeptidase N / M1 family peptidases / 3-{[(R)-1-amino-3-(pyridin-3-yl)propyl](hydroxy)phosphoryl}-(S)-2-benzylpropanoic acid
Function / homology
Function and homology information


membrane alanyl aminopeptidase / aminopeptidase activity / metallopeptidase activity / proteolysis / zinc ion binding
Similarity search - Function
Peptidase M1, alanyl aminopeptidase, C-terminal domain / Aminopeptidase N, middle-beta 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 ...Peptidase M1, alanyl aminopeptidase, C-terminal domain / Aminopeptidase N, middle-beta 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-379 / IMIDAZOLE / Aminopeptidase N
Similarity search - Component
Biological speciesNeisseria meningitidis MC58 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.701 Å
AuthorsNocek, B. / Joachimiak, A. / Berlicki, L. / Vassiliou, S. / Mucha, 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 1, 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 / 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.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 1.5Dec 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)100,10811
Polymers98,9631
Non-polymers1,14510
Water16,430912
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)223.813, 223.813, 57.958
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 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, 922 molecules

#2: Chemical ChemComp-379 / 3-{[(R)-1-amino-3-(pyridin-3-yl)propyl](hydroxy)phosphoryl}-(S)-2-benzylpropanoic acid


Mass: 362.360 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H23N2O4P
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#5: Chemical ChemComp-ZN / ZINC ION


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


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 912 / 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: 56.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2 M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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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: 1.7→40 Å / Num. all: 108021 / Num. obs: 108021 / % possible obs: 90.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 1.8 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 17
Reflection shellResolution: 1.7→1.73 Å / % possible all: 92.4

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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: 1.701→27.764 Å / SU ML: 0.15 / σ(F): 1.97 / σ(I): 2 / Phase error: 18.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.185 5148 5.03 %RANDOM
Rwork0.1496 ---
all0.153 107572 --
obs0.1514 102424 90.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.701→27.764 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6816 0 72 912 7800
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0147091
X-RAY DIFFRACTIONf_angle_d1.2839618
X-RAY DIFFRACTIONf_dihedral_angle_d13.8492593
X-RAY DIFFRACTIONf_chiral_restr0.0521055
X-RAY DIFFRACTIONf_plane_restr0.0071262
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.701-1.72040.25031100.20452008X-RAY DIFFRACTION54
1.7204-1.74060.2857990.21222282X-RAY DIFFRACTION61
1.7406-1.76180.24751380.20212586X-RAY DIFFRACTION68
1.7618-1.78410.2581610.19632686X-RAY DIFFRACTION73
1.7841-1.80760.22551400.19272942X-RAY DIFFRACTION77
1.8076-1.83240.20911790.18943155X-RAY DIFFRACTION84
1.8324-1.85850.24381850.19043337X-RAY DIFFRACTION89
1.8585-1.88630.19711610.18343401X-RAY DIFFRACTION91
1.8863-1.91570.21921960.1773469X-RAY DIFFRACTION92
1.9157-1.94710.20571970.17323487X-RAY DIFFRACTION92
1.9471-1.98070.22121990.16853461X-RAY DIFFRACTION93
1.9807-2.01670.22131690.16523484X-RAY DIFFRACTION92
2.0167-2.05550.19361890.16643493X-RAY DIFFRACTION93
2.0555-2.09740.20071790.1593511X-RAY DIFFRACTION93
2.0974-2.1430.2161760.15323510X-RAY DIFFRACTION92
2.143-2.19280.19781860.15023457X-RAY DIFFRACTION93
2.1928-2.24770.1771770.14773511X-RAY DIFFRACTION93
2.2477-2.30840.1811790.14123472X-RAY DIFFRACTION93
2.3084-2.37630.1961600.14453500X-RAY DIFFRACTION93
2.3763-2.4530.20541910.14563480X-RAY DIFFRACTION93
2.453-2.54060.18331940.13833488X-RAY DIFFRACTION93
2.5406-2.64220.16991880.13963480X-RAY DIFFRACTION92
2.6422-2.76240.17431750.14423442X-RAY DIFFRACTION92
2.7624-2.90780.19031790.14713428X-RAY DIFFRACTION91
2.9078-3.08980.20141730.14013414X-RAY DIFFRACTION91
3.0898-3.3280.17211800.14353340X-RAY DIFFRACTION89
3.328-3.66230.14731750.1333326X-RAY DIFFRACTION88
3.6623-4.19060.12891650.12373236X-RAY DIFFRACTION86
4.1906-5.27380.15211800.12143140X-RAY DIFFRACTION84
5.2738-27.7680.19071680.16222750X-RAY DIFFRACTION74
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)
10.71670.04920.37170.51920.10021.3497-0.06890.01630.0146-0.0441-0.0035-0.0801-0.25070.13790.02390.1656-0.025-0.03430.04690.0010.118828.488750.33758.2392
20.28640.06950.05990.58160.15611.5251-0.0512-0.05370.02870.0377-0.06720.1423-0.2698-0.48350.05520.15380.1049-0.03280.2005-0.0510.1357-2.822748.662520.9233
30.57840.2980.34340.84480.40021.0567-0.0025-0.1583-0.05370.1273-0.12390.14460.2204-0.67670.08020.175-0.12760.06140.2849-0.06950.2396-10.880121.562223.7131
41.04070.1660.04640.9016-0.23350.9090.00440.1325-0.25160.1471-0.04860.00210.0131-0.04690.0240.2099-0.04740.00620.017-0.01870.191211.069619.683918.655
51.46760.7063-0.6581.0184-0.19261.6447-0.0375-0.0416-0.02030.0835-0.00710.00640.21040.00770.03080.16340.0028-0.00990.05210.00640.116117.169228.697534.8065
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 190 )
2X-RAY DIFFRACTION2chain 'A' and (resid 191 through 555 )
3X-RAY DIFFRACTION3chain 'A' and (resid 556 through 736 )
4X-RAY DIFFRACTION4chain 'A' and (resid 737 through 789 )
5X-RAY DIFFRACTION5chain 'A' and (resid 790 through 867 )

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