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- PDB-5cls: Structure of human methionine aminopeptidase-2 complexed with spi... -

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Basic information

Entry
Database: PDB / ID: 5cls
TitleStructure of human methionine aminopeptidase-2 complexed with spiroepoxytriazole inhibitor (+)-31a
ComponentsMethionine aminopeptidase 2
KeywordsHYDROLASE / MetAP2 / methionine aminopeptidase-2 / inhibitor / spiroepoxytriazole
Function / homology
Function and homology information


methionyl aminopeptidase / initiator methionyl aminopeptidase activity / metalloexopeptidase activity / regulation of translational initiation / metalloaminopeptidase activity / aminopeptidase activity / protein processing / Inactivation, recovery and regulation of the phototransduction cascade / RNA binding / metal ion binding ...methionyl aminopeptidase / initiator methionyl aminopeptidase activity / metalloexopeptidase activity / regulation of translational initiation / metalloaminopeptidase activity / aminopeptidase activity / protein processing / Inactivation, recovery and regulation of the phototransduction cascade / RNA binding / metal ion binding / plasma membrane / cytoplasm / cytosol
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-52T / CITRIC ACID / : / Methionine aminopeptidase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsJanowski, R. / Miller, A.K. / Niessing, D.
CitationJournal: Acs Chem.Biol. / Year: 2016
Title: Spiroepoxytriazoles Are Fumagillin-like Irreversible Inhibitors of MetAP2 with Potent Cellular Activity.
Authors: Morgen, M. / Jost, C. / Malz, M. / Janowski, R. / Niessing, D. / Klein, C.D. / Gunkel, N. / Miller, A.K.
History
DepositionJul 16, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 1.2Apr 27, 2016Group: Database references
Revision 1.3Nov 20, 2019Group: Derived calculations
Category: pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn
Revision 1.4Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)42,5129
Polymers41,5101
Non-polymers1,0018
Water5,873326
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1060 Å2
ΔGint-18 kcal/mol
Surface area16540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.620, 101.180, 100.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-502-

DMS

21A-832-

HOH

31A-895-

HOH

41A-919-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 41510.141 Da / Num. of mol.: 1 / Fragment: UNP residues 108-478
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: METAP2, MNPEP, P67EIF2 / Plasmid: pFastBac1-HM / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: P50579, methionyl aminopeptidase

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Non-polymers , 7 types, 334 molecules

#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-52T / (4R,7R)-7-hydroxy-1-(4-methoxybenzyl)-7-methyl-4,5,6,7-tetrahydro-1H-benzotriazol-4-yl propan-2-ylcarbamate


Mass: 374.434 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H26N4O4
#6: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / 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

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Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.08 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.4 / Details: Na Citrate, Tert-butanol / PH range: 5.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.75→56 Å / Num. obs: 45986 / % possible obs: 99.5 % / Redundancy: 3.58 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 16.2
Reflection shellResolution: 1.75→1.795 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.758 / Mean I/σ(I) obs: 2 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→55.82 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.966 / SU B: 4.763 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18885 1425 3.1 %RANDOM
Rwork0.16001 ---
obs0.16095 44561 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.373 Å2
Baniso -1Baniso -2Baniso -3
1-1.8 Å20 Å2-0 Å2
2---2.04 Å2-0 Å2
3---0.23 Å2
Refinement stepCycle: 1 / Resolution: 1.75→55.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2894 0 62 326 3282
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0193088
X-RAY DIFFRACTIONr_bond_other_d0.0010.022931
X-RAY DIFFRACTIONr_angle_refined_deg2.0181.9834191
X-RAY DIFFRACTIONr_angle_other_deg0.9183.0016774
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9245388
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.55724.286140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.72615532
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8531520
X-RAY DIFFRACTIONr_chiral_restr0.1310.2463
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213475
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02678
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9971.9251495
X-RAY DIFFRACTIONr_mcbond_other1.9971.9251494
X-RAY DIFFRACTIONr_mcangle_it2.9782.881872
X-RAY DIFFRACTIONr_mcangle_other2.9772.881873
X-RAY DIFFRACTIONr_scbond_it2.6082.2521593
X-RAY DIFFRACTIONr_scbond_other2.5722.2461591
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7583.2582309
X-RAY DIFFRACTIONr_long_range_B_refined7.86317.6313751
X-RAY DIFFRACTIONr_long_range_B_other7.70316.453577
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 96 -
Rwork0.273 3263 -
obs--99.64 %

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