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- PDB-4zy0: X-ray crystal structure of PfA-M17 in complex with hydroxamic aci... -

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Basic information

Entry
Database: PDB / ID: 4zy0
TitleX-ray crystal structure of PfA-M17 in complex with hydroxamic acid-based inhibitor 10q
ComponentsProbable M17 family aminopeptidase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / M17 LEUCYL-AMINOPEPTIDASE / PROTEASE / INHIBITOR / HYDROXAMIC ACID / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


leucyl aminopeptidase / metalloaminopeptidase activity / manganese ion binding / proteolysis / 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-4TM / CARBONATE ION / leucyl aminopeptidase
Similarity search - Component
Biological speciesPlasmodium falciparum FcB1/Columbia (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 / 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_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)710,178109
Polymers695,78712
Non-polymers14,39197
Water59,2873291
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)355,37556
Polymers347,8936
Non-polymers7,48250
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27520 Å2
ΔGint-130 kcal/mol
Surface area95480 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)354,80353
Polymers347,8936
Non-polymers6,90947
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27600 Å2
ΔGint-127 kcal/mol
Surface area96290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.717, 176.072, 230.579
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: A0A024V0B1, leucyl aminopeptidase

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Non-polymers , 7 types, 3388 molecules

#2: Chemical
ChemComp-4TM / N-{(1R)-2-(hydroxyamino)-2-oxo-1-[4-(thiophen-3-yl)phenyl]ethyl}-2,2-dimethylpropanamide


Mass: 332.417 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C17H20N2O3S
#3: Chemical...
ChemComp-ZN / ZINC ION


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


Mass: 60.009 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: CO3
#5: Chemical...
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3291 / 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: 2.55 Å3/Da / Density % sol: 51.81 %
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: Sep 26, 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: 2.2→48.63 Å / Num. obs: 355767 / % possible obs: 100 % / Redundancy: 6.1 % / Biso Wilson estimate: 24.24 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.406 / Rpim(I) all: 0.163 / Net I/σ(I): 5.6 / Num. measured all: 2155326 / Scaling rejects: 887
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.2-2.2462.9981.5105371174530.5871.208100
12.05-48.635.60.077141329223560.9890.03498.5

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Processing

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

3kqz


Resolution: 2.2→48.63 Å / FOM work R set: 0.7603 / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2439 17735 5 %
Rwork0.1984 336894 -
obs0.2007 354629 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114.18 Å2 / Biso mean: 29.99 Å2 / Biso min: 10.8 Å2
Refinement stepCycle: final / Resolution: 2.2→48.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms46981 0 719 3291 50991
Biso mean--41.61 35.41 -
Num. residues----6173
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00448570
X-RAY DIFFRACTIONf_angle_d0.7865857
X-RAY DIFFRACTIONf_chiral_restr0.037551
X-RAY DIFFRACTIONf_plane_restr0.0038330
X-RAY DIFFRACTIONf_dihedral_angle_d12.87917358
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 (%)
2.2-2.2250.36365640.30461114111705100
2.225-2.25120.36475660.30171116211728100
2.2512-2.27860.33655250.28511116711692100
2.2786-2.30750.32325670.28411115211719100
2.3075-2.33780.31615030.26651121911722100
2.3378-2.36990.31316130.27071115211765100
2.3699-2.40370.33055800.26761112711707100
2.4037-2.43960.29035750.25081116011735100
2.4396-2.47770.30875730.25081119811771100
2.4777-2.51830.30926240.24941114711771100
2.5183-2.56180.29855750.24281117911754100
2.5618-2.60830.31435650.23721116711732100
2.6083-2.65850.2735950.22441118311778100
2.6585-2.71280.27215910.22111120911800100
2.7128-2.77170.27426350.21921109011725100
2.7717-2.83620.26446060.20661118411790100
2.8362-2.90710.27815550.20281124711802100
2.9071-2.98570.25735920.20421122811820100
2.9857-3.07360.25096610.1981116311824100
3.0736-3.17280.2586320.20691119211824100
3.1728-3.28610.25225870.20351123311820100
3.2861-3.41770.23095580.18321130611864100
3.4177-3.57320.22496180.17991120911827100
3.5732-3.76150.20945560.16781134811904100
3.7615-3.9970.19475930.15751128511878100
3.997-4.30550.18436380.14571128211920100
4.3055-4.73840.17245940.13951136011954100
4.7384-5.42330.18966040.14711139712001100
5.4233-6.82980.19486210.16951146312084100
6.8298-48.64170.20936690.1724115441221398
Refinement TLS params.Method: refined / Origin x: 175.9693 Å / Origin y: 231.8708 Å / Origin z: -35.5712 Å
111213212223313233
T0.1119 Å2-0.0054 Å2-0.0023 Å2-0.1076 Å20.0336 Å2--0.172 Å2
L0.0552 °2-0.0147 °2-0.0261 °2-0.05 °20.0198 °2--0.1129 °2
S-0.0038 Å °-0.0102 Å °-0.0337 Å °-0.0012 Å °0.0051 Å °-0.0097 Å °0.0016 Å °-0.0025 Å °-0.0015 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 - 76
14X-RAY DIFFRACTION1allS1 - 3323
15X-RAY DIFFRACTION1allN1 - 23

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