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- PDB-4u1b: HsMetAP in complex with (1-amino-2-propylpentyl)phosphonic acid -

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Basic information

Entry
Database: PDB / ID: 4u1b
TitleHsMetAP in complex with (1-amino-2-propylpentyl)phosphonic acid
ComponentsMethionine aminopeptidase 1
KeywordsHYDROLASE
Function / homology
Function and homology information


methionyl aminopeptidase / initiator methionyl aminopeptidase activity / metalloexopeptidase activity / metalloaminopeptidase activity / aminopeptidase activity / cytosolic ribosome / protein maturation / platelet aggregation / Inactivation, recovery and regulation of the phototransduction cascade / regulation of translation ...methionyl aminopeptidase / initiator methionyl aminopeptidase activity / metalloexopeptidase activity / metalloaminopeptidase activity / aminopeptidase activity / cytosolic ribosome / protein maturation / platelet aggregation / Inactivation, recovery and regulation of the phototransduction cascade / regulation of translation / proteolysis / zinc ion binding / cytoplasm / cytosol
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
: / [(1R)-1-amino-2-propylpentyl]phosphonic acid / Methionine aminopeptidase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.89 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 15, 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_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _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

Downloads & links

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Assembly

Deposited unit
A: Methionine aminopeptidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8735
Polymers34,4541
Non-polymers4194
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area340 Å2
ΔGint-6 kcal/mol
Surface area12910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.026, 76.929, 47.170
Angle α, β, γ (deg.)90.00, 92.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Methionine aminopeptidase 1 / 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-Q08 / [(1R)-1-amino-2-propylpentyl]phosphonic acid


Mass: 209.223 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H20NO3P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.47 Å3/Da / Density % sol: 50.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 2000, potassium chloride, hepes, sodium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, 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: 1.89→22.53 Å / Num. obs: 26171 / % possible obs: 98 % / Redundancy: 3.6 % / Net I/σ(I): 3.16

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Processing

Software
NameVersionClassification
REFMACrefinement
HKL-30005.7.0029data processing
MOLREPphasing
RefinementResolution: 1.89→20 Å / SU B: 3.054 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.139 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.221 1310 5 %RANDOM
Rwork0.169 ---
obs0.171 24819 97.6 %-
Displacement parametersBiso mean: 33.14 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20.01 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.89→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2395 0 21 171 2587

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