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- PDB-6g46: Red kidney bean purple acid phosphatase in complex with 2-(Naphth... -

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Basic information

Entry
Database: PDB / ID: 6g46
TitleRed kidney bean purple acid phosphatase in complex with 2-(Naphthalen-1-yl)thiazole-4-carboxylic acid
ComponentsFe(3+)-Zn(2+) purple acid phosphatase
KeywordsMETAL BINDING PROTEIN / Phosphatase / Metallohydrolase / Hydrolase / Metalloprotein / purple acid phosphatase / PAP / red kidney bean / rkbPAP / drug design / drug discovery / rational drug design / osteoporosis
Function / homology
Function and homology information


acid phosphatase / acid phosphatase activity / ferric iron binding / zinc ion binding / extracellular region
Similarity search - Function
Purple acid phosphatase-like, N-terminal / Purple acid phosphatase-like / Purple acid phosphatase, N-terminal / Iron/zinc purple acid phosphatase-like C-terminal domain / Purple acid phosphatase, metallophosphatase domain / Iron/zinc purple acid phosphatase-like protein C / Purple acid Phosphatase, N-terminal domain / Purple acid phosphatase-like, N-terminal / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 ...Purple acid phosphatase-like, N-terminal / Purple acid phosphatase-like / Purple acid phosphatase, N-terminal / Iron/zinc purple acid phosphatase-like C-terminal domain / Purple acid phosphatase, metallophosphatase domain / Iron/zinc purple acid phosphatase-like protein C / Purple acid Phosphatase, N-terminal domain / Purple acid phosphatase-like, N-terminal / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / 4-Layer Sandwich / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
2-naphthalen-1-yl-1,3-thiazole-4-carboxylic acid / : / ISOPROPYL ALCOHOL / Fe(3+)-Zn(2+) purple acid phosphatase
Similarity search - Component
Biological speciesPhaseolus vulgaris (French bean)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsFeder, D.F.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research CouncilDP0986292 Australia
Australian Research CouncilDP150104358 Australia
CitationJournal: Eur J Med Chem / Year: 2018
Title: Purple acid phosphatase inhibitors as leads for osteoporosis chemotherapeutics.
Authors: Hussein, W.M. / Feder, D. / Schenk, G. / Guddat, L.W. / McGeary, R.P.
History
DepositionMar 26, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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_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_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 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fe(3+)-Zn(2+) purple acid phosphatase
B: Fe(3+)-Zn(2+) purple acid phosphatase
D: Fe(3+)-Zn(2+) purple acid phosphatase
C: Fe(3+)-Zn(2+) purple acid phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,71550
Polymers198,2224
Non-polymers8,49346
Water22,0681225
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20970 Å2
ΔGint-197 kcal/mol
Surface area61100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.208, 126.208, 297.119
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 4 molecules ABDC

#1: Protein
Fe(3+)-Zn(2+) purple acid phosphatase / PAP / Iron(III)-zinc(II) purple acid phosphatase


Mass: 49555.398 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Phaseolus vulgaris (French bean) / Variant: red kidney bean / References: UniProt: P80366, acid phosphatase

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Sugars , 3 types, 16 molecules

#2: Polysaccharide
alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta- ...alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-3[DGlcpNAcb1-4]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2-1/a3-b1_a4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-3DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#7: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 9 types, 1255 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-ELH / 2-naphthalen-1-yl-1,3-thiazole-4-carboxylic acid


Mass: 255.292 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H9NO2S
#9: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#10: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Na
#11: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#12: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1225 / 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: 3.46 Å3/Da / Density % sol: 64.45 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 2 M ammonium sulfate and 0.1 M sodium acetate, pH 4.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.4→43.27 Å / Num. obs: 107272 / % possible obs: 99.4 % / Redundancy: 4.36 % / Rmerge(I) obs: 0.083 / Rrim(I) all: 0.094 / Net I/σ(I): 10.9
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 2.93 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 3.4 / Rrim(I) all: 0.338 / Χ2: 1.25 / % possible all: 97.5

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
CrystalClear2data reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DHL

4dhl


Resolution: 2.4→43.262 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 21.68
RfactorNum. reflection% reflection
Rfree0.223 5324 4.99 %
Rwork0.1721 --
obs0.1747 106611 98.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.4→43.262 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13980 0 523 1225 15728
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00915029
X-RAY DIFFRACTIONf_angle_d0.95720486
X-RAY DIFFRACTIONf_dihedral_angle_d17.3725439
X-RAY DIFFRACTIONf_chiral_restr0.0592134
X-RAY DIFFRACTIONf_plane_restr0.0062586
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4001-2.42730.31231730.21253178X-RAY DIFFRACTION93
2.4273-2.45590.27781620.20983302X-RAY DIFFRACTION99
2.4559-2.48580.29421680.20483357X-RAY DIFFRACTION99
2.4858-2.51730.28061650.20593370X-RAY DIFFRACTION99
2.5173-2.55040.27091880.19483317X-RAY DIFFRACTION99
2.5504-2.58530.29211620.19313396X-RAY DIFFRACTION99
2.5853-2.62230.22761560.1973355X-RAY DIFFRACTION99
2.6223-2.66140.29051590.20393390X-RAY DIFFRACTION99
2.6614-2.7030.30141860.21843320X-RAY DIFFRACTION99
2.703-2.74730.31071900.21243374X-RAY DIFFRACTION99
2.7473-2.79470.26251840.1973336X-RAY DIFFRACTION99
2.7947-2.84550.24791860.19673335X-RAY DIFFRACTION99
2.8455-2.90020.27041760.19333371X-RAY DIFFRACTION99
2.9002-2.95940.24831740.19533371X-RAY DIFFRACTION99
2.9594-3.02370.25721760.20223346X-RAY DIFFRACTION99
3.0237-3.0940.25071700.19153360X-RAY DIFFRACTION99
3.094-3.17140.24091880.19513347X-RAY DIFFRACTION99
3.1714-3.25710.26351730.18653379X-RAY DIFFRACTION99
3.2571-3.35290.22721910.17123329X-RAY DIFFRACTION99
3.3529-3.46110.21161600.16043410X-RAY DIFFRACTION99
3.4611-3.58470.19121800.15153383X-RAY DIFFRACTION99
3.5847-3.72820.20621910.15163365X-RAY DIFFRACTION99
3.7282-3.89780.19211800.14713380X-RAY DIFFRACTION99
3.8978-4.10310.18491910.14483414X-RAY DIFFRACTION99
4.1031-4.360.17911980.13643382X-RAY DIFFRACTION99
4.36-4.69620.15451880.13523408X-RAY DIFFRACTION99
4.6962-5.16810.20261920.14083430X-RAY DIFFRACTION99
5.1681-5.91430.18741780.15273480X-RAY DIFFRACTION99
5.9143-7.44530.20751910.17883478X-RAY DIFFRACTION99
7.4453-43.26850.24321480.20833624X-RAY DIFFRACTION97

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