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

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Basic information

Entry
Database: PDB / ID: 4quo
TitleCrystal structure of Aminopeptidase N in complex with the phosphinic dipeptide analogue LL-(R,S)-hPheP[CH2]Phe(3-CH2NH2)
ComponentsAminopeptidase N
KeywordsHYDROLASE/HYDROLASE INHIBITOR / M1 family aminopeptidase / metalloprotease / APN / HYDROLASE-HYDROLASE INHIBITOR complex
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-3DZ / IMIDAZOLE / Aminopeptidase N / Aminopeptidase N
Similarity search - Component
Biological speciesNeisseria meningitidis MC58 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å
AuthorsNocek, B. / Mulligan, R. / Joachimiak, A. / Vassiliou, S. / Berlicki, L. / 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
DepositionJul 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2014Group: Database references / Derived calculations
Revision 1.2Oct 22, 2014Group: Database references
Revision 1.3May 13, 2020Group: Database references / Derived calculations / Structure summary
Category: audit_author / struct_conn / struct_ref_seq_dif
Item: _audit_author.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
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_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_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)100,94219
Polymers98,6971
Non-polymers2,24418
Water18,7541041
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)223.707, 223.707, 57.769
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 / Membrane alanyl aminopeptidase


Mass: 98697.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis MC58 (bacteria) / Gene: pepN, NMBH4476_0804, NMH_0477 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: E6MUM9, UniProt: Q9JYV4*PLUS, membrane alanyl aminopeptidase

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Non-polymers , 6 types, 1059 molecules

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


Mass: 390.413 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H27N2O4P
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / 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.: 10 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1041 / 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: 56.36 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.0 M ammonium sulfate, pH 7.0, VAPOR DIFFUSION, SITTING 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: Rosenbaum-Rock high-resolution 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: 1.65→40 Å / Num. all: 129700 / Num. obs: 129700 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 18
Reflection shellResolution: 1.65→1.68 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
MOLREPphasing
CCP4model building
REFMAC5.7.0029refinement
HKL-3000data reduction
HKL-3000data scaling
CCP4phasing
RefinementMethod to determine structure: SAD
Starting model: PDB ENTRY 2GTQ

2gtq


Resolution: 1.65→27.98 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.942 / SU ML: 0.052 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.082 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18188 5953 5.1 %RANDOM
Rwork0.14813 ---
all0.15 117723 --
obs0.14983 111770 90.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.803 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20.16 Å20 Å2
2--0.16 Å20 Å2
3----0.52 Å2
Refinement stepCycle: LAST / Resolution: 1.65→27.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6847 0 134 1041 8022
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0197264
X-RAY DIFFRACTIONr_bond_other_d0.0020.026827
X-RAY DIFFRACTIONr_angle_refined_deg2.0351.9829874
X-RAY DIFFRACTIONr_angle_other_deg0.938315691
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0035897
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.63924.141355
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.145151142
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1781550
X-RAY DIFFRACTIONr_chiral_restr0.1250.21084
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0218250
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021724
LS refinement shellResolution: 1.65→1.692 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 151 -
Rwork0.196 3042 -
obs--33.28 %
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)
10.4082-0.0511-0.33870.4227-0.15640.5252-0.0280.0130.01990.02440.00050.0357-0.0252-0.08910.02750.02360.0092-0.00050.0674-0.0360.0551-64.92890.747-24.2494
20.3663-0.0699-0.02570.30880.1710.4123-0.02250.02070.0477-0.02930.00520.0029-0.0262-0.02540.01730.0175-0.00720.00310.0422-0.01170.0497-52.0082-1.4353-34.8512
30.1064-0.00980.02040.10640.0140.3539-0.0016-0.0025-0.00110.0105-0.0102-0.00370.0717-0.00740.01180.0321-0.01110.00810.0313-0.01350.0386-43.0889-21.1329-23.7448
41.3217-0.8683-0.26371.54490.54230.35460.0911-0.101-0.1590.1656-0.1890.00470.1964-0.11350.09790.2028-0.1010.03230.08550.01910.0957-37.9128-41.0859-0.7795
50.92420.21210.17560.2895-0.22260.39410.0457-0.0456-0.1537-0.0272-0.1162-0.10120.14440.06790.07050.1828-0.0220.02890.06740.02710.0756-26.6577-37.3057-4.8331
60.95960.11480.19450.6213-0.0851.30710.0259-0.115-0.12170.0487-0.0614-0.05350.28950.04950.03550.07980.02560.00980.06670.03890.0434-14.3109-27.8368-5.1552
71.5552-1.1347-1.55591.32471.33331.76880.0174-0.0994-0.03770.0627-0.09660.0490.07660.05020.07920.0439-0.01210.01770.08280.00680.0322-20.9582-15.364-0.6599
81.0742-0.24880.55930.0598-0.14290.63190.02630.0622-0.098-0.0106-0.0240.01590.15480.1364-0.00240.05960.04090.01460.0659-0.00150.0562-9.0201-21.7485-21.818
90.4193-0.0218-0.05120.50060.37010.57340.00330.04380.02620.00220.0103-0.0740.00030.0649-0.01360.0064-0.01380.0030.0496-0.00390.0562-16.795-3.4857-22.476
100.5998-0.09910.0950.2706-0.17030.830.0001-0.03210.00330.0121-0.01060.021-0.04430.01990.01050.026-0.0154-0.00190.0378-0.01390.0462-32.61250.3512-4.9772
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 85
2X-RAY DIFFRACTION2A86 - 194
3X-RAY DIFFRACTION3A195 - 444
4X-RAY DIFFRACTION4A445 - 519
5X-RAY DIFFRACTION5A520 - 560
6X-RAY DIFFRACTION6A561 - 611
7X-RAY DIFFRACTION7A612 - 639
8X-RAY DIFFRACTION8A640 - 699
9X-RAY DIFFRACTION9A700 - 780
10X-RAY DIFFRACTION10A781 - 867

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