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- PDB-4r76: Structure of the m17 leucyl aminopeptidase from malaria complexed... -

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Basic information

Entry
Database: PDB / ID: 4r76
TitleStructure of the m17 leucyl aminopeptidase from malaria complexed with a hydroxamic acid-based inhibitor
ComponentsM17 family aminopeptidase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / PROTEASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Dipeptidases / leucyl aminopeptidase / metallodipeptidase activity / peptide catabolic process / metalloaminopeptidase activity / carboxypeptidase activity / peptidase activity / manganese ion binding / proteolysis / zinc ion binding ...Hydrolases; Acting on peptide bonds (peptidases); Dipeptidases / leucyl aminopeptidase / metallodipeptidase activity / peptide catabolic process / metalloaminopeptidase activity / carboxypeptidase activity / peptidase activity / manganese ion binding / proteolysis / zinc ion binding / identical protein binding / metal ion binding / cytosol / 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
CARBONATE ION / Chem-R5X / Leucine aminopeptidase
Similarity search - Component
Biological speciesPlasmodium falciparum fcb1/columbia (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsDrinkwater, N. / Mcgowan, S.
CitationJournal: J.Med.Chem. / Year: 2014
Title: Two-Pronged Attack: Dual Inhibition of Plasmodium falciparum M1 and M17 Metalloaminopeptidases by a Novel Series of Hydroxamic Acid-Based Inhibitors.
Authors: Mistry, S.N. / Drinkwater, N. / Ruggeri, C. / Sivaraman, K.K. / Loganathan, S. / Fletcher, S. / Drag, M. / Paiardini, A. / Avery, V.M. / Scammells, P.J. / McGowan, S.
History
DepositionAug 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 26, 2014Group: Database references
Revision 1.2Sep 20, 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 / 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_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_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 / _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: M17 family aminopeptidase
B: M17 family aminopeptidase
C: M17 family aminopeptidase
D: M17 family aminopeptidase
E: M17 family aminopeptidase
F: M17 family aminopeptidase
G: M17 family aminopeptidase
H: M17 family aminopeptidase
I: M17 family aminopeptidase
J: M17 family aminopeptidase
K: M17 family aminopeptidase
L: M17 family aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)715,26182
Polymers704,50812
Non-polymers10,75370
Water32,3551796
1
A: M17 family aminopeptidase
B: M17 family aminopeptidase
C: M17 family aminopeptidase
D: M17 family aminopeptidase
E: M17 family aminopeptidase
F: M17 family aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)357,65542
Polymers352,2546
Non-polymers5,40136
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32670 Å2
ΔGint-502 kcal/mol
Surface area96690 Å2
MethodPISA
2
G: M17 family aminopeptidase
H: M17 family aminopeptidase
I: M17 family aminopeptidase
J: M17 family aminopeptidase
K: M17 family aminopeptidase
L: M17 family aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)357,60540
Polymers352,2546
Non-polymers5,35134
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32100 Å2
ΔGint-431 kcal/mol
Surface area96850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.041, 177.408, 231.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsthe biological unit is a hexamer, there are 2 biological units in the asymmetric unit

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Components

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Protein , 1 types, 12 molecules ABCDEFGHIJKL

#1: Protein
M17 family aminopeptidase


Mass: 58708.973 Da / Num. of mol.: 12 / Fragment: unp residues 84-611 / Mutation: D152N, D515N, D516N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum fcb1/columbia (eukaryote)
Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8IL11*PLUS

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Non-polymers , 6 types, 1866 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


Mass: 60.009 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: CO3
#4: Chemical
ChemComp-R5X / 3-amino-N-{(1R)-2-(hydroxyamino)-2-oxo-1-[4-(1H-pyrazol-1-yl)phenyl]ethyl}benzamide


Mass: 351.359 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C18H17N5O3
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1796 / 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: 2.54 Å3/Da / Density % sol: 51.56 %
Crystal growTemperature: 298 K / pH: 8.5
Details: 40% (v/v) PEG 400, 0.1 M Tris pH 8.5, 0.2 M Li2SO4, 1 mM TCEP, vapor diffusion, hanging drop, temperature 298K

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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: Mar 6, 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→46.59 Å / Num. obs: 210997 / Redundancy: 7.2 % / Biso Wilson estimate: 23.39 Å2

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.15data extraction
GDAdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KQZ

3kqz


Resolution: 2.5→36.21 Å / SU ML: 0.3 / Phase error: 29.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.248 10411 4.94 %
Rwork0.207 --
obs0.209 210675 85.4 %
Solvent computationSolvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.72 Å2
Refinement stepCycle: LAST / Resolution: 2.5→36.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms46790 0 568 1796 49154
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00348254
X-RAY DIFFRACTIONf_angle_d0.6565440
X-RAY DIFFRACTIONf_dihedral_angle_d12.06217217
X-RAY DIFFRACTIONf_chiral_restr0.0267516
X-RAY DIFFRACTIONf_plane_restr0.0038294
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.52850.33552550.28715203X-RAY DIFFRACTION67
2.5285-2.55820.31922750.27515369X-RAY DIFFRACTION69
2.5582-2.58940.3172940.27995475X-RAY DIFFRACTION71
2.5894-2.62220.32313130.27455571X-RAY DIFFRACTION73
2.6222-2.65670.32262640.27055791X-RAY DIFFRACTION74
2.6567-2.69310.30043010.27855878X-RAY DIFFRACTION76
2.6931-2.73150.3372790.27626085X-RAY DIFFRACTION78
2.7315-2.77230.29482870.27836162X-RAY DIFFRACTION79
2.7723-2.81560.31573380.26276300X-RAY DIFFRACTION81
2.8156-2.86170.31463160.24976471X-RAY DIFFRACTION83
2.8617-2.91110.28933600.25466491X-RAY DIFFRACTION84
2.9111-2.9640.26813790.24386640X-RAY DIFFRACTION86
2.964-3.0210.28313550.24326763X-RAY DIFFRACTION87
3.021-3.08260.30233730.24976864X-RAY DIFFRACTION88
3.0826-3.14960.30063420.25296960X-RAY DIFFRACTION89
3.1496-3.22280.28223890.23827070X-RAY DIFFRACTION91
3.2228-3.30330.2693180.22427133X-RAY DIFFRACTION91
3.3033-3.39260.26113950.21197178X-RAY DIFFRACTION92
3.3926-3.49230.27643830.2077226X-RAY DIFFRACTION93
3.4923-3.6050.24143920.19657278X-RAY DIFFRACTION93
3.605-3.73370.24873880.19117334X-RAY DIFFRACTION94
3.7337-3.8830.21133430.17617349X-RAY DIFFRACTION93
3.883-4.05950.22733910.17257292X-RAY DIFFRACTION93
4.0595-4.27320.20823860.16447270X-RAY DIFFRACTION93
4.2732-4.54050.16964010.1487237X-RAY DIFFRACTION92
4.5405-4.89030.18043800.14627214X-RAY DIFFRACTION92
4.8903-5.3810.2073790.16137220X-RAY DIFFRACTION91
5.381-6.15630.22013510.18247218X-RAY DIFFRACTION91
6.1563-7.74380.22153880.17987165X-RAY DIFFRACTION90
7.7438-36.21760.18173960.16227057X-RAY DIFFRACTION86
Refinement TLS params.Method: refined / Origin x: 89.3334 Å / Origin y: 56.1982 Å / Origin z: 80.0074 Å
111213212223313233
T0.1611 Å20.0307 Å20.0021 Å2-0.2555 Å20.029 Å2--0.2707 Å2
L-0.0004 °20.0151 °2-0.0067 °2-0.0268 °20.0176 °2--0.1156 °2
S-0.0073 Å °-0.0292 Å °-0.052 Å °0.0053 Å °0.0121 Å °-0.0182 Å °0.0064 Å °0.0012 Å °-0.0033 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA86 - 1003
2X-RAY DIFFRACTION1allB86 - 1003
3X-RAY DIFFRACTION1allC86 - 1003
4X-RAY DIFFRACTION1allD86 - 1003
5X-RAY DIFFRACTION1allE86 - 1003
6X-RAY DIFFRACTION1allF86 - 1003
7X-RAY DIFFRACTION1allG86 - 1003
8X-RAY DIFFRACTION1allH86 - 1003
9X-RAY DIFFRACTION1allI86 - 1003
10X-RAY DIFFRACTION1allJ86 - 1003
11X-RAY DIFFRACTION1allK86 - 1003
12X-RAY DIFFRACTION1allL86 - 1003
13X-RAY DIFFRACTION1allB1 - 1004
14X-RAY DIFFRACTION1allJ - E2 - 1004
15X-RAY DIFFRACTION1allI7 - 1004
16X-RAY DIFFRACTION1allF8 - 1004
17X-RAY DIFFRACTION1allL9 - 1004
18X-RAY DIFFRACTION1allA10 - 1004
19X-RAY DIFFRACTION1allC11 - 1004
20X-RAY DIFFRACTION1allG12 - 1004
21X-RAY DIFFRACTION1allC2 - 1921
22X-RAY DIFFRACTION1allK1 - 1005
23X-RAY DIFFRACTION1allF2 - 1005
24X-RAY DIFFRACTION1allG3 - 1005
25X-RAY DIFFRACTION1allA4 - 1005
26X-RAY DIFFRACTION1allG1 - 1006
27X-RAY DIFFRACTION1allG2 - 1007
28X-RAY DIFFRACTION1allE3 - 1005
29X-RAY DIFFRACTION1allJ4 - 1005
30X-RAY DIFFRACTION1allI5 - 1005
31X-RAY DIFFRACTION1allB6 - 1005
32X-RAY DIFFRACTION1allK7 - 1006
33X-RAY DIFFRACTION1allL8 - 1005
34X-RAY DIFFRACTION1allB9 - 1006
35X-RAY DIFFRACTION1allH10 - 1005
36X-RAY DIFFRACTION1allI11 - 1006
37X-RAY DIFFRACTION1allF12 - 1006
38X-RAY DIFFRACTION1allF13 - 1007
39X-RAY DIFFRACTION1allF - E14 - 1006
40X-RAY DIFFRACTION1allE1 - 1007
41X-RAY DIFFRACTION1allA1 - 1006
42X-RAY DIFFRACTION1allF1 - 1009

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