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- PDB-2adu: Human Methionine Aminopeptidase Complex with 4-Aryl-1,2,3-triazol... -

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Basic information

Entry
Database: PDB / ID: 2adu
TitleHuman Methionine Aminopeptidase Complex with 4-Aryl-1,2,3-triazole Inhibitor
ComponentsMethionine aminopeptidase 2
KeywordsHYDROLASE / aminopeptidase / metal binding / protease
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
: / 4-(3-METHYLPHENYL)-1H-1,2,3-TRIAZOLE / Methionine aminopeptidase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKallander, L.S. / Lu, Q. / Chen, W. / Tomaszek, T. / Yang, G. / Tew, D. / Meek, T.D. / Hofmann, G.A. / Schulz-Pritchard, C.K. / Smith, W.W. ...Kallander, L.S. / Lu, Q. / Chen, W. / Tomaszek, T. / Yang, G. / Tew, D. / Meek, T.D. / Hofmann, G.A. / Schulz-Pritchard, C.K. / Smith, W.W. / Janson, C.A. / Ryan, M.D. / Zhang, G.F. / Johanson, K.O. / Kirkpatrick, R.B. / Ho, T.F. / Fisher, P.W. / Mattern, M.R. / Johnson, R.K. / Hansbury, M.J. / Winkler, J.D. / Ward, K.W. / Veber, D.F. / Thompson, S.K.
CitationJournal: J.Med.Chem. / Year: 2005
Title: 4-Aryl-1,2,3-triazole: A Novel Template for a Reversible Methionine Aminopeptidase 2 Inhibitor, Optimized To Inhibit Angiogenesis in Vivo
Authors: Kallander, L.S. / Lu, Q. / Chen, W. / Tomaszek, T. / Yang, G. / Tew, D. / Meek, T.D. / Hofmann, G.A. / Schulz-Pritchard, C.K. / Smith, W.W. / Janson, C.A. / Ryan, M.D. / Zhang, G.F. / ...Authors: Kallander, L.S. / Lu, Q. / Chen, W. / Tomaszek, T. / Yang, G. / Tew, D. / Meek, T.D. / Hofmann, G.A. / Schulz-Pritchard, C.K. / Smith, W.W. / Janson, C.A. / Ryan, M.D. / Zhang, G.F. / Johanson, K.O. / Kirkpatrick, R.B. / Ho, T.F. / Fisher, P.W. / Mattern, M.R. / Johnson, R.K. / Hansbury, M.J. / Winkler, J.D. / Ward, K.W. / Veber, D.F. / Thompson, S.K.
History
DepositionJul 20, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Aug 23, 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_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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_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.ptnr1_label_seq_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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE According to authors,V347I is a mutation, probably inadvertent when the protein was syntesized

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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)41,6474
Polymers41,3701
Non-polymers2773
Water5,513306
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.819, 99.264, 101.282
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-621-

HOH

21A-631-

HOH

31A-640-

HOH

41A-689-

HOH

51A-721-

HOH

61A-730-

HOH

71A-749-

HOH

81A-769-

HOH

91A-788-

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 / Mutation: V347I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: METAP2, MNPEP, P67EIF2 / Plasmid: pFastbac-1 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / 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-R20 / 4-(3-METHYLPHENYL)-1H-1,2,3-TRIAZOLE


Mass: 159.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H9N3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / 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: 3.1 Å3/Da / Density % sol: 60.6 %
Crystal growTemperature: 274 K / pH: 5.4
Details: 100 MM CITRATE BUFFER, 30% BUTANOL, pH 5.4, VAPOR DIFFUSION, temperature 274 K, pH 5.40

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 1, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→99 Å / Num. obs: 62773 / % possible obs: 90.6 % / Rmerge(I) obs: 0.069
Reflection shellResolution: 1.9→1.93 Å / Rmerge(I) obs: 0.767

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT1.7data extraction
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BN5

1bn5


Resolution: 1.9→99 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.355 2831 -RANDOM
Rwork0.335 ---
obs0.335 56841 5 %-
Displacement parametersBiso mean: 41.47 Å2
Refinement stepCycle: LAST / Resolution: 1.9→99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2787 0 14 306 3107
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006925
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3298
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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