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- PDB-4zy2: X-ray crystal structure of PfA-M17 in complex with hydroxamic aci... -

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Basic information

Entry
Database: PDB / ID: 4zy2
TitleX-ray crystal structure of PfA-M17 in complex with hydroxamic acid-based inhibitor 10o
ComponentsProbable M17 family aminopeptidase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / M17 LEUCYL-AMINOPEPTIDASE / PROTEASE / INHIBITOR / HYDROXAMIC ACID / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


metalloexopeptidase activity / aminopeptidase activity / manganese ion binding / cytoplasm
Similarity search - Function
Peptidase M17, leucine aminopeptidase / Cytosol aminopeptidase signature. / Peptidase M17, leucyl aminopeptidase, C-terminal / Peptidase M17, leucine aminopeptidase/peptidase B / Cytosol aminopeptidase family, catalytic domain / Leucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / Zn peptidases / Aminopeptidase / Macro domain-like ...Peptidase M17, leucine aminopeptidase / Cytosol aminopeptidase signature. / Peptidase M17, leucyl aminopeptidase, C-terminal / Peptidase M17, leucine aminopeptidase/peptidase B / Cytosol aminopeptidase family, catalytic domain / Leucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / Zn peptidases / Aminopeptidase / Macro domain-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-4TL / CARBONATE ION / CYTOSOL_AP domain-containing protein
Similarity search - Component
Biological speciesPlasmodium falciparum FcB1/Columbia (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsDrinkwater, N. / McGowan, S.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1063786 Australia
CitationJournal: Eur.J.Med.Chem. / Year: 2016
Title: Potent dual inhibitors of Plasmodium falciparum M1 and M17 aminopeptidases through optimization of S1 pocket interactions.
Authors: Drinkwater, N. / Vinh, N.B. / Mistry, S.N. / Bamert, R.S. / Ruggeri, C. / Holleran, J.P. / Loganathan, S. / Paiardini, A. / Charman, S.A. / Powell, A.K. / Avery, V.M. / McGowan, S. / Scammells, P.J.
History
DepositionMay 21, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations
Category: citation / diffrn_source ...citation / diffrn_source / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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.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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable M17 family aminopeptidase
B: Probable M17 family aminopeptidase
C: Probable M17 family aminopeptidase
D: Probable M17 family aminopeptidase
E: Probable M17 family aminopeptidase
F: Probable M17 family aminopeptidase
G: Probable M17 family aminopeptidase
H: Probable M17 family aminopeptidase
I: Probable M17 family aminopeptidase
J: Probable M17 family aminopeptidase
K: Probable M17 family aminopeptidase
L: Probable M17 family aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)714,858130
Polymers695,78712
Non-polymers19,071118
Water86,5624805
1
A: Probable M17 family aminopeptidase
B: Probable M17 family aminopeptidase
C: Probable M17 family aminopeptidase
D: Probable M17 family aminopeptidase
E: Probable M17 family aminopeptidase
F: Probable M17 family aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)356,93662
Polymers347,8936
Non-polymers9,04356
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27910 Å2
ΔGint-131 kcal/mol
Surface area96270 Å2
MethodPISA
2
G: Probable M17 family aminopeptidase
H: Probable M17 family aminopeptidase
I: Probable M17 family aminopeptidase
J: Probable M17 family aminopeptidase
K: Probable M17 family aminopeptidase
L: Probable M17 family aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)357,92268
Polymers347,8936
Non-polymers10,02862
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27810 Å2
ΔGint-132 kcal/mol
Surface area96300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.060, 177.247, 230.773
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 12 molecules ABCDEFGHIJKL

#1: Protein
Probable M17 family aminopeptidase


Mass: 57982.230 Da / Num. of mol.: 12 / Fragment: UNP residues 84-605 / Mutation: D152N,D515N,D516N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum FcB1/Columbia (eukaryote)
Strain: isolate FcB1 / Columbia / Plasmid: PTRCHIS-2B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A0A0L7M119

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Non-polymers , 7 types, 4923 molecules

#2: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CO3 / CARBONATE ION / Carbonate


Mass: 60.009 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: CO3
#4: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: SO4
#5: Chemical...
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 39 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Chemical
ChemComp-4TL / N-[(1R)-2-(hydroxyamino)-2-oxo-1-(3',4',5'-trifluorobiphenyl-4-yl)ethyl]-2,2-dimethylpropanamide


Mass: 380.361 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C19H19F3N2O3
#7: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4805 / 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: 2.58 Å3/Da / Density % sol: 52.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 40% (v/v) PEG 400, 0.1 M Tris pH 8.5, 0.2 M Li2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 17, 2014
RadiationMonochromator: DOUBLE CRYSTAL SILICON 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.1→48.54 Å / Num. obs: 412225 / % possible obs: 100 % / Redundancy: 6.3 % / Biso Wilson estimate: 22.27 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.311 / Rpim(I) all: 0.131 / Net I/σ(I): 5.2 / Num. measured all: 2613407 / Scaling rejects: 1095
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.1-2.146.421.4128611202430.5650.845100
11.5-48.5460.05812.51610227010.9930.02698

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimless0.3.8data scaling
PHASERphasing
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KQZ

3kqz


Resolution: 2.1→48.54 Å / FOM work R set: 0.7642 / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2392 20597 5.01 %
Rwork0.1936 390210 -
obs0.1959 410807 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 131.51 Å2 / Biso mean: 26.7 Å2 / Biso min: 3.53 Å2
Refinement stepCycle: final / Resolution: 2.1→48.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms47189 0 879 4805 52873
Biso mean--38.8 36.58 -
Num. residues----6186
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00348928
X-RAY DIFFRACTIONf_angle_d0.68166288
X-RAY DIFFRACTIONf_chiral_restr0.0277555
X-RAY DIFFRACTIONf_plane_restr0.0038357
X-RAY DIFFRACTIONf_dihedral_angle_d12.27317270
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.12390.34156530.30971291113564100
2.1239-2.14890.34746450.30211291113556100
2.1489-2.17510.32977380.2951290313641100
2.1751-2.20260.3197040.27561290413608100
2.2026-2.23160.30277120.27331289713609100
2.2316-2.26210.29476750.26621288413559100
2.2621-2.29450.30166700.25711294113611100
2.2945-2.32870.29916790.25651293713616100
2.3287-2.36510.3096860.24631295913645100
2.3651-2.40390.30366780.24661292513603100
2.4039-2.44530.29757090.23671292713636100
2.4453-2.48980.28916640.2271299313657100
2.4898-2.53770.28786810.22651292913610100
2.5377-2.58950.27767160.21871292813644100
2.5895-2.64580.25536400.20631305713697100
2.6458-2.70730.26046670.20491293313600100
2.7073-2.7750.25287370.1961295913696100
2.775-2.850.2386630.19011303213695100
2.85-2.93390.24656070.19271302813635100
2.9339-3.02860.25056960.18891304513741100
3.0286-3.13680.23826770.18351301213689100
3.1368-3.26240.24847310.18121304113772100
3.2624-3.41080.22427010.17711305313754100
3.4108-3.59060.22376860.16981306113747100
3.5906-3.81540.20287440.15571303813782100
3.8154-4.10990.18536900.14581313113821100
4.1099-4.52320.16276800.13361320313883100
4.5232-5.17710.16956680.1401131681383699
5.1771-6.52010.2197150.17021324513960100
6.5201-48.55530.18196850.1623132551394097
Refinement TLS params.Method: refined / Origin x: 89.2335 Å / Origin y: 56.2323 Å / Origin z: 79.6395 Å
111213212223313233
T0.0337 Å20.0112 Å20.0027 Å2-0.0347 Å20.0353 Å2--0.0411 Å2
L-0.0057 °2-0.0021 °2-0.0019 °2--0.005 °20.0034 °2--0.0203 °2
S-0.0066 Å °-0.0128 Å °-0.0083 Å °-0.0044 Å °0.0106 Å °-0.0273 Å °0.0067 Å °-0.0112 Å °0.003 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA85 - 1004
2X-RAY DIFFRACTION1allB86 - 1004
3X-RAY DIFFRACTION1allC86 - 1004
4X-RAY DIFFRACTION1allD85 - 1004
5X-RAY DIFFRACTION1allE86 - 1004
6X-RAY DIFFRACTION1allF86 - 1004
7X-RAY DIFFRACTION1allG85 - 1004
8X-RAY DIFFRACTION1allH86 - 1004
9X-RAY DIFFRACTION1allI86 - 1004
10X-RAY DIFFRACTION1allJ85 - 1004
11X-RAY DIFFRACTION1allK86 - 1004
12X-RAY DIFFRACTION1allL86 - 1004
13X-RAY DIFFRACTION1allM1 - 45
14X-RAY DIFFRACTION1allM46 - 47
15X-RAY DIFFRACTION1allM48
16X-RAY DIFFRACTION1allM49
17X-RAY DIFFRACTION1allM50
18X-RAY DIFFRACTION1allM51
19X-RAY DIFFRACTION1allM52
20X-RAY DIFFRACTION1allM53
21X-RAY DIFFRACTION1allN1 - 71
22X-RAY DIFFRACTION1allN62 - 69
23X-RAY DIFFRACTION1allP2 - 7050
24X-RAY DIFFRACTION1allO1
25X-RAY DIFFRACTION1allO2 - 12
26X-RAY DIFFRACTION1allR1
27X-RAY DIFFRACTION1allR2
28X-RAY DIFFRACTION1allR3
29X-RAY DIFFRACTION1allQ1
30X-RAY DIFFRACTION1allS1
31X-RAY DIFFRACTION1allT1
32X-RAY DIFFRACTION1allU1
33X-RAY DIFFRACTION1allV1
34X-RAY DIFFRACTION1allW1
35X-RAY DIFFRACTION1allX1
36X-RAY DIFFRACTION1allY1
37X-RAY DIFFRACTION1allZ1
38X-RAY DIFFRACTION1alla1

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