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- PDB-2oaz: Human Methionine Aminopeptidase-2 Complexed with SB-587094 -

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Basic information

Entry
Database: PDB / ID: 2oaz
TitleHuman Methionine Aminopeptidase-2 Complexed with SB-587094
Componentshuman Methionine Amino Peptidase 2
KeywordsHYDROLASE / MetAP2 / Methionine / Amino Peptidase
Function / homology
Function and homology information


N-terminal protein amino acid modification / peptidyl-methionine modification / initiator methionyl aminopeptidase activity / methionyl aminopeptidase / 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 / initiator methionyl aminopeptidase activity / methionyl aminopeptidase / metalloexopeptidase activity / 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 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain ...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-I96 / Methionine aminopeptidase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMarino Jr., J.P. / Fisher, P.W. / Hofmann, G.A. / Kirkpatrick, R. / Janson, C.A. / Johnson, R.K. / Ma, C. / Mattern, M. / Meek, T.D. / Ryan, D. ...Marino Jr., J.P. / Fisher, P.W. / Hofmann, G.A. / Kirkpatrick, R. / Janson, C.A. / Johnson, R.K. / Ma, C. / Mattern, M. / Meek, T.D. / Ryan, D. / Schulz, C. / Smith, W.W. / Tew, D.G. / Tomazek Jr., T.A. / Veber, D.F. / Xiong, W.C. / Yamamoto, Y. / Yamashita, K. / Yang, G. / Thompson, S.K.
CitationJournal: J.Med.Chem. / Year: 2007
Title: Highly potent inhibitors of methionine aminopeptidase-2 based on a 1,2,4-triazole pharmacophore.
Authors: Marino, J.P. / Fisher, P.W. / Hofmann, G.A. / Kirkpatrick, R.B. / Janson, C.A. / Johnson, R.K. / Ma, C. / Mattern, M. / Meek, T.D. / Ryan, M.D. / Schulz, C. / Smith, W.W. / Tew, D.G. / ...Authors: Marino, J.P. / Fisher, P.W. / Hofmann, G.A. / Kirkpatrick, R.B. / Janson, C.A. / Johnson, R.K. / Ma, C. / Mattern, M. / Meek, T.D. / Ryan, M.D. / Schulz, C. / Smith, W.W. / Tew, D.G. / Tomazek, T.A. / Veber, D.F. / Xiong, W.C. / Yamamoto, Y. / Yamashita, K. / Yang, G. / Thompson, S.K.
History
DepositionDec 18, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: human Methionine Amino Peptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8184
Polymers41,3701
Non-polymers4483
Water5,477304
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.698, 99.217, 101.304
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-512-

HOH

21A-524-

HOH

31A-526-

HOH

41A-606-

HOH

51A-612-

HOH

61A-647-

HOH

71A-650-

HOH

81A-704-

HOH

91A-717-

HOH

101A-775-

HOH

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Components

#1: Protein human Methionine Amino Peptidase 2


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


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-I96 / N-(2-ISOPROPYLPHENYL)-3-[(2-THIENYLMETHYL)THIO]-1H-1,2,4-TRIAZOL-5-AMINE


Mass: 330.471 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H18N4S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / 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: 2.72 Å3/Da / Density % sol: 54.83 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 50553 / % possible obs: 73.4 % / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→50 Å / σ(F): 0 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.287 2494 -
Rwork0.255 --
all-68850 -
obs-50553 73.4 %
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2787 0 24 304 3115
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.45591
X-RAY DIFFRACTIONx_bond_d0.00698

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