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- PDB-4flk: Human MetAP1 with bengamide analog Y10, in Mn form -

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Basic information

Entry
Database: PDB / ID: 4flk
TitleHuman MetAP1 with bengamide analog Y10, in Mn form
ComponentsMethionine aminopeptidase 1
Keywordshydrolase/hydrolase inhibitor / hydrolase / enzyme-inhibitor complex / hydrolase-hydrolase inhibitor complex
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 / 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
: / Chem-Y10 / Methionine aminopeptidase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.47 Å
AuthorsYe, Q.Z. / Xu, W.
CitationJournal: J.Med.Chem. / Year: 2012
Title: Structural analysis of bengamide derivatives as inhibitors of methionine aminopeptidases.
Authors: Xu, W. / Lu, J.P. / Ye, Q.Z.
History
DepositionJun 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2012Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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)37,3555
Polymers36,8451
Non-polymers5104
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.777, 77.506, 48.620
Angle α, β, γ (deg.)90.000, 90.430, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 36844.887 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIAA0094, map1, METAP1 / Plasmid: pGS21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P53582, methionyl aminopeptidase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-Y10 / (E,2R,3R,4S,5R)-N-(2,3-dihydro-1H-inden-2-yl)-2-methoxy-8,8-dimethyl-3,4,5-tris(oxidanyl)non-6-enamide


Mass: 377.475 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H31NO5
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.44 Å3/Da / Density % sol: 49.65 %
Crystal growMethod: microbatch under oil / pH: 7.2
Details: 200 mM sodium formate, 20% PEG 3350, pH 7.2, microbatch under oil

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM
DetectorType: ADSC QUANTUM 210r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.47→50 Å / Num. obs: 60021 / % possible obs: 99.5 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.095 / Χ2: 8.854 / Net I/σ(I): 17.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.47-1.52.60.38529042.824196.1
1.5-1.522.90.33929883.138199.9
1.52-1.553.10.31329943.4681100
1.55-1.583.40.29630024.0771100
1.58-1.623.70.27430184.3671100
1.62-1.663.70.25129905.4731100
1.66-1.73.70.23130256.1061100
1.7-1.743.70.21329766.671100
1.74-1.793.70.19930207.6371100
1.79-1.853.70.18430058.5541100
1.85-1.923.70.174300810.1761100
1.92-23.80.159303611.8971100
2-2.093.80.148299713.5431100
2.09-2.23.80.138301913.9341100
2.2-2.333.80.127301613.947199.9
2.33-2.513.80.117302212.9831100
2.51-2.773.80.103302212.1961100
2.77-3.173.80.088302910.8611100
3.17-3.993.60.07229839.798197.8
3.99-503.50.06829678.578196.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.8 Å31.3 Å
Translation1.8 Å31.3 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.47→31.29 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.954 / WRfactor Rfree: 0.2318 / WRfactor Rwork: 0.2091 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8477 / SU B: 1.225 / SU ML: 0.047 / SU R Cruickshank DPI: 0.0704 / SU Rfree: 0.0706 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.07 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2208 3030 5.1 %RANDOM
Rwork0.1988 ---
obs0.1999 59952 99.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 61.78 Å2 / Biso mean: 22.5781 Å2 / Biso min: 10 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0.01 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.47→31.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2395 0 30 154 2579
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0212506
X-RAY DIFFRACTIONr_angle_refined_deg2.431.9643408
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9635309
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.82623.13115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.0315409
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0411520
X-RAY DIFFRACTIONr_chiral_restr0.180.2370
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0211935
X-RAY DIFFRACTIONr_mcbond_it1.5611.51534
X-RAY DIFFRACTIONr_mcangle_it2.38122491
X-RAY DIFFRACTIONr_scbond_it3.2723972
X-RAY DIFFRACTIONr_scangle_it5.1584.5917
LS refinement shellResolution: 1.468→1.506 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 198 -
Rwork0.327 3934 -
all-4132 -
obs--93.89 %

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