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- PDB-6lzc: crystal structure of Human Methionine aminopeptidase (HsMetAP1b) ... -

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Basic information

Entry
Database: PDB / ID: 6lzc
Titlecrystal structure of Human Methionine aminopeptidase (HsMetAP1b) in complex with KV-P2-4H-05
ComponentsMethionine aminopeptidase 1
KeywordsHYDROLASE / Methionine aminopeptidase
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 / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like
Similarity search - Domain/homology
: / Chem-EYL / Methionine aminopeptidase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.35 Å
AuthorsSandeep, C.B. / Addlagatta, A.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Science & Technology (DST, India)EMR/2015/000461 India
CitationJournal: Bioorg.Chem. / Year: 2021
Title: Selective inhibition of Helicobacter pylori methionine aminopeptidase by azaindole hydroxamic acid derivatives: Design, synthesis, in vitro biochemical and structural studies.
Authors: Bala, S. / Yellamanda, K.V. / Kadari, A. / Ravinuthala, V.S.U. / Kattula, B. / Singh, O.V. / Gundla, R. / Addlagatta, A.
History
DepositionFeb 18, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 24, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 18, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)37,6459
Polymers36,9361
Non-polymers7098
Water3,261181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-12 kcal/mol
Surface area12840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.552, 77.219, 48.651
Angle α, β, γ (deg.)90.000, 91.550, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 36935.926 Da / Num. of mol.: 1
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

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Non-polymers , 6 types, 189 molecules

#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EYL / ~{N}-oxidanyl-1-(phenylmethyl)pyrrolo[2,3-b]pyridine-4-carboxamide


Mass: 267.283 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H13N3O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.42 Å3/Da / Density % sol: 49.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2 / Details: 0.1M Bistris pH-6.2, 19% PEG 3350, 5% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.95 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.35→47.58 Å / Num. obs: 76213 / % possible obs: 99.7 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.017 / Rrim(I) all: 0.046 / Net I/σ(I): 20.1
Reflection shell

Diffraction-ID: 1 / Redundancy: 6.5 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.35-1.380.7222409337180.9070.3020.7852.598.5
7.41-47.530.02831944950.9990.0120.03157.999.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.46
Highest resolutionLowest resolution
Rotation47.54 Å1.68 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
Aimless0.7.4data scaling
MOLREP11.7.01phasing
PDB_EXTRACT3.25data extraction
Coot0.8.9.2model building
PDB_EXTRACTdata extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2G3H

2g3h


Resolution: 1.35→47.53 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.899 / SU ML: 0.051 / SU R Cruickshank DPI: 0.055 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.055 / ESU R Free: 0.053
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1972 3636 4.8 %RANDOM
Rwork0.1674 ---
obs0.1689 72016 98.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 111.38 Å2 / Biso mean: 26.657 Å2 / Biso min: 10.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å2-0 Å2-0.35 Å2
2---0.38 Å20 Å2
3---0.12 Å2
Refinement stepCycle: final / Resolution: 1.35→47.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2396 0 42 183 2621
Biso mean--39.13 34.18 -
Num. residues----304
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0132586
X-RAY DIFFRACTIONr_bond_other_d0.0050.0172351
X-RAY DIFFRACTIONr_angle_refined_deg2.2931.6643520
X-RAY DIFFRACTIONr_angle_other_deg1.6051.5825459
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1675323
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.3420.748147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.49215426
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8561524
X-RAY DIFFRACTIONr_chiral_restr0.0990.2326
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.022943
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02577
X-RAY DIFFRACTIONr_rigid_bond_restr6.69934937
LS refinement shellResolution: 1.353→1.388 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 294 -
Rwork0.268 5263 -
all-5557 -
obs--98.9 %

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