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- PDB-6qej: CRYSTAL STRUCTURE OF HUMAN METHIONINE AMINOPEPTIDASE-2 IN COMPLEX... -

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Basic information

Entry
Database: PDB / ID: 6qej
TitleCRYSTAL STRUCTURE OF HUMAN METHIONINE AMINOPEPTIDASE-2 IN COMPLEX WITH AN INHIBITOR Thiophene-2-sulfonic acid (4-fluoro-benzyl)-(4H-[1,2,4]triazol-3-ylmethyl)-amide
ComponentsMethionine aminopeptidase 2Methionyl aminopeptidase
KeywordsHYDROLASE / PEPTIDASE / METAL ION BINDING / PROTEOLYSIS / 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 / aminopeptidase activity / protein processing / Inactivation, recovery and regulation of the phototransduction cascade / RNA binding ...N-terminal protein amino acid modification / peptidyl-methionine modification / initiator methionyl aminopeptidase activity / methionyl aminopeptidase / 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 / Creatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain ...Peptidase M24A, methionine aminopeptidase, subfamily 2 / Peptidase M24A, methionine aminopeptidase, subfamily 2, binding site / Methionine aminopeptidase subfamily 2 signature. / Peptidase M24, methionine aminopeptidase / Creatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-HZT / : / TERTIARY-BUTYL ALCOHOL / Methionine aminopeptidase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.62 Å
AuthorsMusil, D. / Heinrich, T. / Lehmann, M.
CitationJournal: J.Med.Chem. / Year: 2019
Title: Discovery and Structure-Based Optimization of Next-Generation Reversible Methionine Aminopeptidase-2 (MetAP-2) Inhibitors.
Authors: Heinrich, T. / Seenisamy, J. / Blume, B. / Bomke, J. / Calderini, M. / Eckert, U. / Friese-Hamim, M. / Kohl, R. / Lehmann, M. / Leuthner, B. / Musil, D. / Rohdich, F. / Zenke, F.T.
History
DepositionJan 7, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 1, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID

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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)43,0696
Polymers42,4701
Non-polymers5985
Water8,053447
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area400 Å2
ΔGint1 kcal/mol
Surface area15890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.565, 99.929, 100.941
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-503-

TBU

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 42470.207 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: Spodoptera frugiperda (fall armyworm) / References: UniProt: P50579, methionyl aminopeptidase

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Non-polymers , 5 types, 452 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-HZT / ~{N}-[(4-fluorophenyl)methyl]-~{N}-(1~{H}-1,2,4-triazol-5-ylmethyl)thiophene-2-sulfonamide


Mass: 352.407 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H13FN4O2S2
#4: Chemical ChemComp-TBU / TERTIARY-BUTYL ALCOHOL / 2-METHYL-2-PROPANOL / Tert-Butyl alcohol


Mass: 74.122 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O
#5: Chemical ChemComp-MN / MANGANESE (II) ION


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


Mass: 18.015 Da / Num. of mol.: 447 / 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: 2.69 Å3/Da / Density % sol: 54.25 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 20% METHANOL, 0.1 M CITRATE, PH 6.0,

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Feb 9, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.62→24.26 Å / Num. obs: 56275 / % possible obs: 95.5 % / Redundancy: 3.3 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 16.7
Reflection shellResolution: 1.62→1.69 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.224 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 5301 / % possible all: 72.9

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementResolution: 1.62→24.25 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.954 / SU R Cruickshank DPI: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.084 / SU Rfree Blow DPI: 0.078 / SU Rfree Cruickshank DPI: 0.074
RfactorNum. reflection% reflectionSelection details
Rfree0.184 2767 4.94 %RANDOM
Rwork0.167 ---
obs0.167 55968 96 %-
Displacement parametersBiso mean: 25.32 Å2
Baniso -1Baniso -2Baniso -3
1--1.2676 Å20 Å20 Å2
2---1.2939 Å20 Å2
3---2.5615 Å2
Refine analyzeLuzzati coordinate error obs: 0.18 Å
Refinement stepCycle: 1 / Resolution: 1.62→24.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2827 0 34 447 3308
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013016HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.054091HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1066SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes517HARMONIC5
X-RAY DIFFRACTIONt_it3016HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4.21
X-RAY DIFFRACTIONt_other_torsion13.9
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion391SEMIHARMONIC5
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_contact4102SEMIHARMONIC4
LS refinement shellResolution: 1.62→1.64 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2576 -4.29 %
Rwork0.1943 1072 -
all0.1969 1120 -
obs--64.16 %
Refinement TLS params.Method: refined / Origin x: 22.9829 Å / Origin y: 24.183 Å / Origin z: 14.7208 Å
111213212223313233
T-0.0343 Å2-0.0197 Å20.0287 Å2--0.0411 Å2-0.0018 Å2---0.0576 Å2
L0.378 °2-0.0609 °2-0.0513 °2-0.8108 °20.4681 °2--0.9184 °2
S0.038 Å °0.0201 Å °0.0416 Å °-0.1107 Å °0.0519 Å °-0.1319 Å °-0.1033 Å °0.1058 Å °-0.0899 Å °
Refinement TLS groupSelection details: { A|* }

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