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- PDB-4iku: Crystal structure of truncated (delta 1-89) human methionine amin... -

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Basic information

Entry
Database: PDB / ID: 4iku
TitleCrystal structure of truncated (delta 1-89) human methionine aminopeptidase Type 1 in complex with 2-((5-chloro-6-methyl-2-(pyridin-2-yl)pyrimidin-4-yl)amino)-3-phenylpropanamide
ComponentsMethionine aminopeptidase 1
KeywordsHYDROLASE / pita-bread fold / aminopeptidase / ribosome
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 / protein maturation / aminopeptidase activity / cytosolic ribosome / platelet aggregation ...N-terminal protein amino acid modification / peptidyl-methionine modification / methionyl aminopeptidase / initiator methionyl aminopeptidase activity / metalloexopeptidase activity / metalloaminopeptidase activity / protein maturation / aminopeptidase activity / cytosolic ribosome / platelet aggregation / Inactivation, recovery and regulation of the phototransduction cascade / regulation of translation / proteolysis / metal ion binding / cytosol / cytoplasm
Similarity search - Function
MYND-like zinc finger / zf-MYND-like zinc finger, mRNA-binding / Zinc finger C6H2-type profile. / Methionine aminopeptidase subfamily 1 signature. / Peptidase M24A, methionine aminopeptidase, subfamily 1 / Peptidase M24, methionine aminopeptidase / Creatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily / Peptidase M24 / Metallopeptidase family M24 ...MYND-like zinc finger / zf-MYND-like zinc finger, mRNA-binding / Zinc finger C6H2-type profile. / Methionine aminopeptidase subfamily 1 signature. / Peptidase M24A, methionine aminopeptidase, subfamily 1 / Peptidase M24, methionine aminopeptidase / Creatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
: / : / Chem-SHX / Methionine aminopeptidase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsAddlagatta, A. / Kishor, C. / Arya, T.
CitationJournal: J.Med.Chem. / Year: 2013
Title: Identification, Biochemical and Structural Evaluation of Species-Specific Inhibitors against Type I Methionine Aminopeptidases
Authors: Kishor, C. / Arya, T. / Reddi, R. / Chen, X. / Saddanapu, V. / Marapaka, A.K. / Gumpena, R. / Ma, D. / Liu, J.O. / Addlagatta, A.
History
DepositionDec 28, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Database references / Derived calculations
Category: pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif
Item: _struct_ref_seq_dif.details
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methionine aminopeptidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5206
Polymers36,9361
Non-polymers5845
Water3,765209
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.493, 77.377, 48.088
Angle α, β, γ (deg.)90.00, 90.76, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Methionine aminopeptidase 1 / MAP 1 / MetAP 1 / Peptidase M 1


Mass: 36935.926 Da / Num. of mol.: 1 / Fragment: UNP residues 81-384
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: METAP1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P53582, methionyl aminopeptidase
#2: Chemical ChemComp-SHX / Nalpha-[5-chloro-6-methyl-2-(pyridin-2-yl)pyrimidin-4-yl]-D-phenylalaninamide


Mass: 367.832 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H18ClN5O
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Co
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 2.39 Å3/Da / Density % sol: 48.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 6% PEG 10000, 100mM HEPES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 5, 2007
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. all: 75896 / Num. obs: 75896 / % possible obs: 89 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.033 / Rsym value: 0.04 / Net I/σ(I): 37.293
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.268 / Mean I/σ(I) obs: 2.46 / Num. unique all: 4103 / Rsym value: 0.317 / % possible all: 48.4

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Processing

Software
NameVersionClassification
HKL-3000data collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→34.02 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.656 / SU ML: 0.032 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.061 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20382 3833 5.1 %RANDOM
Rwork0.18896 ---
all0.18972 75896 --
obs0.18972 72035 88.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.717 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å2-0.07 Å2
2---0.02 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.3→34.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2396 0 30 209 2635
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0212493
X-RAY DIFFRACTIONr_angle_refined_deg1.1071.9643386
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9365305
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.00223.13115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.20215407
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9181520
X-RAY DIFFRACTIONr_chiral_restr0.0770.2363
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021934
X-RAY DIFFRACTIONr_nbd_refined0.1970.21271
X-RAY DIFFRACTIONr_nbtor_refined0.3030.21718
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.090.2174
X-RAY DIFFRACTIONr_metal_ion_refined0.1530.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1650.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2550.212
X-RAY DIFFRACTIONr_mcbond_it0.7641.51522
X-RAY DIFFRACTIONr_mcangle_it1.32322469
X-RAY DIFFRACTIONr_scbond_it3.9883986
X-RAY DIFFRACTIONr_scangle_it3.2284.5917
X-RAY DIFFRACTIONr_rigid_bond_restr4.37732508
X-RAY DIFFRACTIONr_sphericity_free3.9053213
X-RAY DIFFRACTIONr_sphericity_bonded3.51132430
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 134 -
Rwork0.272 2680 -
obs--45.09 %

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