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- PDB-7a14: CRYSTAL STRUCTURE OF HUMAN METHIONINE AMINOPEPTIDASE-2 IN COMPLEX... -

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Basic information

Entry
Database: PDB / ID: 7a14
TitleCRYSTAL STRUCTURE OF HUMAN METHIONINE AMINOPEPTIDASE-2 IN COMPLEX WITH AN INHIBITOR GSK2218325A (COMPOUND 32)
ComponentsMethionine aminopeptidase 2
KeywordsHYDROLASE / METHIONINE AMINOPEPTIDASE-2
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 / aminopeptidase activity / protein processing / Inactivation, recovery and regulation of the phototransduction cascade / RNA binding ...N-terminal protein amino acid modification / peptidyl-methionine modification / methionyl aminopeptidase / initiator methionyl aminopeptidase activity / metalloexopeptidase activity / metalloaminopeptidase activity / aminopeptidase activity / protein processing / Inactivation, recovery and regulation of the phototransduction cascade / RNA binding / metal ion binding / plasma membrane / cytosol / cytoplasm
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 / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
: / PHOSPHATE ION / Chem-QVB / Methionine aminopeptidase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsThorpe, J.H.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2020
Title: Structure-based optimisation of orally active & reversible MetAP-2 inhibitors maintaining a tight 'molecular budget'.
Authors: Hirst, D.J. / Brandt, M. / Bruton, G. / Christodoulou, E. / Cutler, L. / Deeks, N. / Goodacre, J.D. / Jack, T. / Lindon, M. / Miah, A. / Page, K. / Parr, N. / Shukla, L. / Sims, M. / Thomas, ...Authors: Hirst, D.J. / Brandt, M. / Bruton, G. / Christodoulou, E. / Cutler, L. / Deeks, N. / Goodacre, J.D. / Jack, T. / Lindon, M. / Miah, A. / Page, K. / Parr, N. / Shukla, L. / Sims, M. / Thomas, P. / Thorpe, J. / Holmes, D.S.
History
DepositionAug 11, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2020Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)42,63211
Polymers41,5101
Non-polymers1,12110
Water5,296294
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
ΔGint-54 kcal/mol
Surface area15990 Å2
Unit cell
Length a, b, c (Å)87.343, 100.812, 99.047
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-507-

PO4

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Components

#1: Protein Methionine aminopeptidase 2 / MetAP 2 / Initiation factor 2-associated 67 kDa glycoprotein / p67eIF2 / Peptidase M


Mass: 41510.141 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: METAP2, MNPEP, P67EIF2 / Production host: unidentified baculovirus / References: UniProt: P50579, methionyl aminopeptidase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-QVB / 5-chloranyl-6-fluoranyl-3-(2-propan-2-yloxyphenyl)-1~{H}-indole-2-carboxamide


Mass: 346.783 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H16ClFN2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / Source method: isolated from a natural source / Formula: H2O
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: 2.65 Å3/Da / Density % sol: 53.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 200mM potassium phosphate pH 7.4, 100mM MnCl2, 5mM dithiothreitol (DTT) and 25-50% 2-methyl-2,4-pentanediol (MPD)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 5, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.14→29.9 Å / Num. all: 163869 / Num. obs: 23219 / % possible obs: 94.81 % / Redundancy: 7.1 % / Biso Wilson estimate: 31.2 Å2 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.033 / Rrim(I) all: 0.089 / Net I/σ(I): 19.7
Reflection shellResolution: 2.14→2.227 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.434 / Mean I/σ(I) obs: 3.9 / Num. unique obs: 21398 / Rpim(I) all: 0.179 / Rrim(I) all: 0.47 / % possible all: 92.52

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Processing

Software
NameVersionClassification
BUSTER2.11.7 (6-FEB-2020)refinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OAZ

2oaz


Resolution: 2.14→29.9 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.891 / SU R Cruickshank DPI: 0.219 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.245 / SU Rfree Blow DPI: 0.18 / SU Rfree Cruickshank DPI: 0.174
RfactorNum. reflection% reflectionSelection details
Rfree0.2147 1190 5.12 %RANDOM
Rwork0.1791 ---
obs0.1809 23219 95 %-
Displacement parametersBiso max: 132.23 Å2 / Biso mean: 40.58 Å2 / Biso min: 14.05 Å2
Baniso -1Baniso -2Baniso -3
1--20.8384 Å20 Å20 Å2
2--11.8966 Å20 Å2
3---8.9418 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: final / Resolution: 2.14→29.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2877 0 61 294 3232
Biso mean--64.28 50.73 -
Num. residues----366
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1055SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes516HARMONIC5
X-RAY DIFFRACTIONt_it3026HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion397SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2580SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3026HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg4115HARMONIC20.92
X-RAY DIFFRACTIONt_omega_torsion3.33
X-RAY DIFFRACTIONt_other_torsion14.99
LS refinement shellResolution: 2.14→2.15 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.2652 20 4.3 %
Rwork0.199 445 -
all0.202 2228 -
obs--90.8 %

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