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- PDB-5lyw: CRYSTAL STRUCTURE OF HUMAN METHIONINE AMINOPEPTIDASE-2 IN COMPLEX... -

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Basic information

Entry
Database: PDB / ID: 5lyw
TitleCRYSTAL STRUCTURE OF HUMAN METHIONINE AMINOPEPTIDASE-2 IN COMPLEX; WITH AN INHIBITOR 6-((R)-2-o-Tolyloxymethyl-pyrrolidin-1-yl)-9H-purine
ComponentsMethionine aminopeptidase 2
KeywordsHYDROLASE / PEPTIDASE / METAL ION BINDING / PROTEOLYSIS / HYDROLASE- HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


N-terminal protein amino acid modification / peptidyl-methionine modification / methionyl aminopeptidase / initiator methionyl aminopeptidase activity / metalloexopeptidase activity / metalloaminopeptidase activity / aminopeptidase activity / protein processing / Inactivation, recovery and regulation of the phototransduction cascade / RNA binding ...N-terminal protein amino acid modification / peptidyl-methionine modification / methionyl aminopeptidase / initiator methionyl aminopeptidase activity / metalloexopeptidase activity / metalloaminopeptidase activity / aminopeptidase activity / protein processing / Inactivation, recovery and regulation of the phototransduction cascade / RNA binding / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Peptidase M24A, methionine aminopeptidase, subfamily 2 / : / Peptidase M24A, methionine aminopeptidase, subfamily 2, binding site / Methionine aminopeptidase subfamily 2 signature. / Peptidase M24, methionine aminopeptidase / Creatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like ...Peptidase M24A, methionine aminopeptidase, subfamily 2 / : / Peptidase M24A, methionine aminopeptidase, subfamily 2, binding site / Methionine aminopeptidase subfamily 2 signature. / Peptidase M24, methionine aminopeptidase / Creatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-7BH / : / Methionine aminopeptidase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.69 Å
AuthorsMusil, D. / Heinrich, T. / Knoechel, T. / Lehmann, M.
CitationJournal: Bioorg. Med. Chem. Lett. / Year: 2017
Title: Novel reversible methionine aminopeptidase-2 (MetAP-2) inhibitors based on purine and related bicyclic templates.
Authors: Heinrich, T. / Buchstaller, H.P. / Cezanne, B. / Rohdich, F. / Bomke, J. / Friese-Hamim, M. / Krier, M. / Knochel, T. / Musil, D. / Leuthner, B. / Zenke, F.
History
DepositionSep 28, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methionine aminopeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8894
Polymers42,4701
Non-polymers4193
Water4,612256
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-7 kcal/mol
Surface area15870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.780, 100.230, 100.380
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Methionine aminopeptidase 2 / MetAP 2 / Initiation factor 2-associated 67 kDa glycoprotein / p67eIF2 / Peptidase M


Mass: 42470.207 Da / Num. of mol.: 1 / Fragment: 108-478 / Mutation: none
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: METAP2, MNPEP, P67EIF2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P50579, methionyl aminopeptidase
#2: Chemical ChemComp-7BH / 6-[(2~{R})-2-[(2-methylphenoxy)methyl]pyrrolidin-1-yl]-7~{H}-purine


Mass: 309.366 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H19N5O
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 2.66 Å3/Da / Density % sol: 53.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 24% methanol, 100 mM citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 1, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→56 Å / Num. obs: 59218 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Biso Wilson estimate: 27.43 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Net I/σ(I): 15.7
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
1.6-1.641.0252.220.768199.9
1.64-1.690.8382.630.851100
1.69-1.740.6263.390.9141100
1.74-1.790.4664.370.9491100
1.79-1.850.3745.290.9651100
1.85-1.910.296.620.976199.9
1.91-1.980.1979.070.988199.9
1.98-2.070.13412.480.9941100
2.07-2.160.10215.670.996199.9
2.16-2.260.0818.230.997199.8
2.26-2.390.06421.650.998199.9
2.39-2.530.05424.340.998199.8
2.53-2.70.04727.670.999199.8
2.7-2.920.04331.10.999199.7
2.92-3.20.0433.660.999199.7
3.2-3.580.03837.610.999199.7
3.58-4.130.03737.690.998196.5
4.13-5.060.03238.360.999195.4
5.06-7.160.03436.950.998193.9
7.160.03632.880.997150.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
BUSTER-TNT2.11.6refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.69→16.13 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.948 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.089 / SU Rfree Blow DPI: 0.085 / SU Rfree Cruickshank DPI: 0.083
RfactorNum. reflection% reflectionSelection details
Rfree0.193 2445 5.02 %RANDOM
Rwork0.171 ---
obs0.172 48712 95.3 %-
Displacement parametersBiso max: 174.48 Å2 / Biso mean: 40.44 Å2 / Biso min: 17.26 Å2
Baniso -1Baniso -2Baniso -3
1--7.3183 Å20 Å20 Å2
2--7.0364 Å20 Å2
3---0.2819 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: final / Resolution: 1.69→16.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2814 0 25 256 3095
Biso mean--34.87 45.83 -
Num. residues----359
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetRestraint functionWeight
X-RAY DIFFRACTIONc_mcbond_it1.3671.5SINUSOIDAL2
X-RAY DIFFRACTIONc_scbond_it2.0142HARMONIC2
X-RAY DIFFRACTIONc_mcangle_it2.1122HARMONIC5
X-RAY DIFFRACTIONc_scangle_it2.9582.5HARMONIC20
LS refinement shellResolution: 1.69→1.74 Å / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.226 121 5.2 %
Rwork0.199 2206 -
all-2327 -
obs--56.39 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2adp.par
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4ion.param
X-RAY DIFFRACTION5emd.par

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