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- PDB-3ked: Crystal structure of Aminopeptidase N in complex with 2,4-diamino... -

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Basic information

Entry
Database: PDB / ID: 3ked
TitleCrystal structure of Aminopeptidase N in complex with 2,4-diaminobutyric acid
ComponentsAminopeptidase N
KeywordsHYDROLASE / aminopeptidase / thermolysin like active site / amino switch / inhibitor / ligand design / Cell inner membrane / Cell membrane / Membrane / Metal-binding / Metalloprotease / Protease
Function / homology
Function and homology information


membrane alanyl aminopeptidase / aminopeptidase activity / metallopeptidase activity / proteolysis / zinc ion binding / identical protein binding / plasma membrane
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 / Aminopeptidase N-like , N-terminal domain / Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1, membrane alanine aminopeptidase / 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 / Neutral zinc metallopeptidases, zinc-binding region signature. / Alpha Horseshoe / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2,4-DIAMINOBUTYRIC ACID / MALONIC ACID / Aminopeptidase N
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsAddlagatta, A. / Gumpena, R.
CitationJournal: Chemmedchem / Year: 2011
Title: Discovery of alpha, beta- and alpha, gamma-Diamino Acid Scaffolds for the Inhibition of M1 Family Aminopeptidases
Authors: Gumpena, R. / Kishor, C. / Ganji, R.J. / Addlagatta, A.
History
DepositionOct 25, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 16, 2011Group: Database references
Revision 1.3Apr 29, 2015Group: Non-polymer description
Revision 1.4Nov 1, 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)102,81217
Polymers101,4411
Non-polymers1,37116
Water8,629479
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)120.601, 120.601, 170.479
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Aminopeptidase N / Alpha-aminoacylpeptide hydrolase


Mass: 101441.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: APN / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P04825, membrane alanyl aminopeptidase

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Non-polymers , 6 types, 495 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-DAB / 2,4-DIAMINOBUTYRIC ACID


Type: L-peptide linking / Mass: 118.134 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10N2O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H4O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 479 / Source method: isolated from a natural source / Formula: H2O

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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: 3.53 Å3/Da / Density % sol: 65.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.0M malonic acid, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 25, 2007 / Details: KOHZU: Double Crystal Si(111)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 63115 / Num. obs: 63115 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Rmerge(I) obs: 0.11 / Rsym value: 0.087 / Net I/σ(I): 79.1
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 12.1 / Num. unique all: 5880 / Rsym value: 0.591 / % possible all: 92.2

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Processing

Software
NameVersionClassification
APEXdata collection
MOLREPphasing
REFMAC5.5.0066refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2hpo

2hpo


Resolution: 2.3→49.94 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.585 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.18 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.19838 1908 3 %RANDOM
Rwork0.15449 ---
obs0.15585 61036 97.58 %-
all-63115 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.331 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å20.31 Å20 Å2
2--0.63 Å20 Å2
3----0.94 Å2
Refinement stepCycle: LAST / Resolution: 2.3→49.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6940 0 86 479 7505
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0227246
X-RAY DIFFRACTIONr_angle_refined_deg1.9971.9579826
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.445879
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.75424.124371
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.168151208
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4061556
X-RAY DIFFRACTIONr_chiral_restr0.1260.21071
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0215598
X-RAY DIFFRACTIONr_mcbond_it1.0571.54388
X-RAY DIFFRACTIONr_mcangle_it2.05427080
X-RAY DIFFRACTIONr_scbond_it3.85732858
X-RAY DIFFRACTIONr_scangle_it6.0784.52746
LS refinement shellResolution: 2.297→2.357 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 129 -
Rwork0.235 4036 -
obs--88.64 %

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