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- PDB-1r58: Crystal Structure of MetAP2 complexed with A357300 -

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Basic information

Entry
Database: PDB / ID: 1r58
TitleCrystal Structure of MetAP2 complexed with A357300
ComponentsMethionine aminopeptidase 2
KeywordsHYDROLASE
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-AO5 / : / Methionine aminopeptidase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSheppard, G.S. / Wang, J. / Kawai, M. / BaMaung, N.Y. / Craig, R.A. / Ericken, S.A. / Lynch, L. / Patel, J. / Yang, F. / Searle, X.B. ...Sheppard, G.S. / Wang, J. / Kawai, M. / BaMaung, N.Y. / Craig, R.A. / Ericken, S.A. / Lynch, L. / Patel, J. / Yang, F. / Searle, X.B. / Lou, P. / Park, C. / Kim, K.H. / Henkin, J. / Lesniewski, R.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2004
Title: 3-Amino-2-hydroxyamides and related compounds as inhibitors of methionine aminopeptidase-2.
Authors: Sheppard, G.S. / Wang, J. / Kawai, M. / BaMaung, N.Y. / Craig, R.A. / Erickson, S.A. / Lynch, L. / Patel, J. / Yang, F. / Searle, X.B. / Lou, P. / Park, C. / Kim, K.H. / Henkin, J. / Lesniewski, R.
History
DepositionOct 9, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methionine aminopeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8404
Polymers41,3701
Non-polymers4703
Water7,494416
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.179, 99.138, 101.065
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-

HOH

21A-525-

HOH

31A-731-

HOH

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Components

#1: Protein Methionine aminopeptidase 2 / MetAP 2 / Peptidase M 2 / Initiation factor 2 associated 67 kDa glycoprotein / p67 / p67eIF2


Mass: 41370.004 Da / Num. of mol.: 1 / Fragment: residues 110-478 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P50579, methionyl aminopeptidase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-AO5 / N'-((2S,3R)-3-AMINO-2-HYDROXY-5-(ISOPROPYLSULFANYL)PENTANOYL)-N-3-CHLOROBENZOYL HYDRAZIDE


Mass: 359.871 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22ClN3O3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 416 / 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: 2.73 Å3/Da / Density % sol: 54.95 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: isopropyl alcohol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 5, 2000
RadiationMonochromator: Osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Observed criterion σ(F): 2 / Biso Wilson estimate: 18.2 Å2

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Processing

Software
NameVersionClassification
CNX2000refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→19.96 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 307765.99 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.247 2816 9.9 %RANDOM
Rwork0.204 ---
obs-28348 78.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.9197 Å2 / ksol: 0.34167 e/Å3
Displacement parametersBiso mean: 24.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20 Å20 Å2
2---0.29 Å20 Å2
3---0.02 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.21 Å
Luzzati d res low-6 Å
Luzzati sigma a0.14 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.9→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2895 0 25 416 3336
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_mcbond_it0.661.5
X-RAY DIFFRACTIONc_mcangle_it1.092
X-RAY DIFFRACTIONc_scbond_it0.982
X-RAY DIFFRACTIONc_scangle_it1.462.5
LS refinement shellResolution: 1.9→1.97 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.289 167 9.7 %
Rwork0.244 1554 -
obs--48.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMA35.TOP
X-RAY DIFFRACTION3ION.PARAM
X-RAY DIFFRACTION4A35.PAR

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