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

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Basic information

Entry
Database: PDB / ID: 6qeg
TitleCRYSTAL STRUCTURE OF HUMAN METHIONINE AMINOPEPTIDASE-2 IN COMPLEX WITH AN INHIBITOR 2-Oxo-1-phenyl-pyrrolidine-3-carboxylic acid (2-thiophen-2-yl-ethyl)-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-K4K / : / Methionine aminopeptidase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.08 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 1.1May 8, 2019Group: Data collection / Refinement description / Category: pdbx_refine_tls / Item: _pdbx_refine_tls.pdbx_refine_id
Revision 1.2May 15, 2019Group: Data collection / Refinement description / Category: pdbx_refine_tls_group / Item: _pdbx_refine_tls_group.pdbx_refine_id
Revision 1.3Jun 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
Revision 1.4May 15, 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 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0035
Polymers42,4701
Non-polymers5324
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-1 kcal/mol
Surface area16200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.265, 99.853, 100.417
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#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
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-K4K / (3~{S})-3-oxidanyl-2-oxidanylidene-1-phenyl-~{N}-(2-thiophen-2-ylethyl)pyrrolidine-3-carboxamide


Mass: 330.401 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H18N2O3S
#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 / Water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.63 Å3/Da / Density % sol: 53.31 %
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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Feb 17, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.08→40.08 Å / Num. obs: 23388 / % possible obs: 85.5 % / Redundancy: 1.9 % / Biso Wilson estimate: 34.82 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 11.4
Reflection shellResolution: 2.08→2.15 Å / Rmerge(I) obs: 0.364 / % possible all: 79.1

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementResolution: 2.08→40.08 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.917 / SU R Cruickshank DPI: 0.203 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.211 / SU Rfree Blow DPI: 0.181 / SU Rfree Cruickshank DPI: 0.18
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1202 5.14 %RANDOM
Rwork0.178 ---
obs0.18 23383 86.1 %-
Displacement parametersBiso mean: 43.29 Å2
Baniso -1Baniso -2Baniso -3
1--9.1264 Å20 Å20 Å2
2--7.9494 Å20 Å2
3---1.177 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: 1 / Resolution: 2.08→40.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2852 0 31 179 3062
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012943HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.083987HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1026SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes500HARMONIC5
X-RAY DIFFRACTIONt_it2943HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.4
X-RAY DIFFRACTIONt_other_torsion16.23
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion388SEMIHARMONIC5
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_contact3586SEMIHARMONIC4
LS refinement shellResolution: 2.08→2.1 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3674 -5.77 %
Rwork0.2182 441 -
all0.2261 468 -
obs--79.83 %
Refinement TLS params.Method: refined / Origin x: 23.1063 Å / Origin y: 24.6867 Å / Origin z: 13.9479 Å
111213212223313233
T-0.0727 Å2-0.0228 Å20.0478 Å2--0.1286 Å20.0018 Å2---0.0511 Å2
L0.5066 °2-0.3892 °2-0.1116 °2-2.9044 °20.8179 °2--1.0057 °2
S0.1358 Å °0.0098 Å °0.1001 Å °-0.1844 Å °0.0458 Å °-0.6564 Å °-0.1557 Å °0.0652 Å °-0.1816 Å °
Refinement TLS groupSelection details: { A|* }

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