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- PDB-4u6e: HsMetAP in complex with (amino(phenyl)methyl)phosphonic acid -

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Basic information

Entry
Database: PDB / ID: 4u6e
TitleHsMetAP in complex with (amino(phenyl)methyl)phosphonic acid
ComponentsMethionine aminopeptidase 1Methionyl aminopeptidase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE / inhibitor / HYDROLASE-HYDROLASE INHIBITOR complex
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 / protein maturation / aminopeptidase activity / platelet aggregation / Inactivation, recovery and regulation of the phototransduction cascade ...N-terminal protein amino acid modification / peptidyl-methionine modification / initiator methionyl aminopeptidase activity / methionyl aminopeptidase / metalloexopeptidase activity / metalloaminopeptidase activity / protein maturation / aminopeptidase activity / platelet aggregation / Inactivation, recovery and regulation of the phototransduction cascade / regulation of translation / proteolysis / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Zinc finger C6H2-type profile. / MYND-like zinc finger / zf-MYND-like zinc finger, mRNA-binding / 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 ...Zinc finger C6H2-type profile. / MYND-like zinc finger / zf-MYND-like zinc finger, mRNA-binding / 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
: / [(R)-amino(phenyl)methyl]phosphonic acid / Methionine aminopeptidase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsArya, T. / Addlagatta, A.
CitationJournal: J.Med.Chem. / Year: 2015
Title: Identification of the Molecular Basis of Inhibitor Selectivity between the Human and Streptococcal Type I Methionine Aminopeptidases
Authors: Arya, T. / Reddi, R. / Kishor, C. / Ganji, R.J. / Bhukya, S. / Gumpena, R. / McGowan, S. / Drag, M. / Addlagatta, A.
History
DepositionJul 28, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Database references / Derived calculations / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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)34,7594
Polymers34,4541
Non-polymers3053
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.433, 77.209, 48.379
Angle α, β, γ (deg.)90.00, 91.12, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 34454.207 Da / Num. of mol.: 1 / Fragment: UNP residues 81-386
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: METAP1, KIAA0094 / Production host: Escherichia coli (E. coli) / References: UniProt: P53582, 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-Q02 / [(R)-amino(phenyl)methyl]phosphonic acid


Mass: 187.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H10NO3P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 15% PEG-MME 2000, 100 mM HEPES, pH=6.0, VAPOR DIFFUSION, temperature 298K
PH range: 5.6 - 6.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.85→20 Å / Num. obs: 29959 / % possible obs: 99.6 % / Redundancy: 3.4 % / Net I/σ(I): 2.09

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Processing

SoftwareName: PHENIX / Version: (PHENIX.REFINE: 1.8.1_1168) / Classification: refinement
RefinementResolution: 1.9→20 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.264 1521 5.08 %
Rwork0.212 --
obs0.215 29955 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2396 0 14 193 2603
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072468
X-RAY DIFFRACTIONf_angle_d1.0653352
X-RAY DIFFRACTIONf_dihedral_angle_d13.02916
X-RAY DIFFRACTIONf_chiral_restr0.077362
X-RAY DIFFRACTIONf_plane_restr0.006439
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8441-1.90360.35251250.3022476X-RAY DIFFRACTION96
1.9036-1.97160.31591630.25772569X-RAY DIFFRACTION100
1.9716-2.05050.27421420.23772564X-RAY DIFFRACTION100
2.0505-2.14370.27921300.22422599X-RAY DIFFRACTION100
2.1437-2.25670.27371230.21872600X-RAY DIFFRACTION100
2.2567-2.39790.27071400.22612597X-RAY DIFFRACTION100
2.3979-2.58280.27131220.2352597X-RAY DIFFRACTION100
2.5828-2.84230.31661380.23222623X-RAY DIFFRACTION100
2.8423-3.25260.28651340.222587X-RAY DIFFRACTION100
3.2526-4.09430.25091500.19162592X-RAY DIFFRACTION100
4.0943-23.08090.21841540.18162630X-RAY DIFFRACTION100

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