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- PDB-4do5: Pharmacological chaperones for human alpha-N-acetylgalactosaminidase -

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Basic information

Entry
Database: PDB / ID: 4do5
TitlePharmacological chaperones for human alpha-N-acetylgalactosaminidase
ComponentsAlpha-N-acetylgalactosaminidase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / PHARMACOLOGICAL CHAPERONE / BETA/ALPHA)8 BARREL / GLYCOSIDASE / CARBOHYDRATE-BINDING PROTEIN / GLYCOPROTEIN / LYSOSOME / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


alpha-N-acetylgalactosaminidase / alpha-N-acetylgalactosaminidase activity / glycolipid catabolic process / alpha-galactosidase activity / oligosaccharide metabolic process / glycoside catabolic process / carbohydrate catabolic process / lysosome / protein homodimerization activity / extracellular exosome / cytoplasm
Similarity search - Function
Alpha galactosidase A, C-terminal beta-sandwich domain / Alpha galactosidase A C-terminal beta sandwich domain / Alpha galactosidase A / Glycoside hydrolase, family 27 / Glycoside hydrolase family 27/36, conserved site / Alpha-galactosidase signature. / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Aldolase class I / Aldolase-type TIM barrel ...Alpha galactosidase A, C-terminal beta-sandwich domain / Alpha galactosidase A C-terminal beta sandwich domain / Alpha galactosidase A / Glycoside hydrolase, family 27 / Glycoside hydrolase family 27/36, conserved site / Alpha-galactosidase signature. / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Aldolase class I / Aldolase-type TIM barrel / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / Chem-DGJ / Alpha-N-acetylgalactosaminidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.51 Å
AuthorsClark, N.E. / Garman, S.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Pharmacological chaperones for human alpha-N-acetylgalactosaminidase
Authors: Clark, N.E. / Metcalf, M.C. / Best, D. / Fleet, G.W. / Garman, S.C.
History
DepositionFeb 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2012Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_PDB_caveat / 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_special_symmetry / struct_asym / struct_conn / struct_ref_seq_dif / 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.type_symbol / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_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_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-N-acetylgalactosaminidase
B: Alpha-N-acetylgalactosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,27926
Polymers91,1662
Non-polymers5,11324
Water18,4111022
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9380 Å2
ΔGint35 kcal/mol
Surface area31890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.352, 114.513, 68.553
Angle α, β, γ (deg.)90.000, 95.640, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-692-

HOH

21A-1148-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Alpha-N-acetylgalactosaminidase / Alpha-galactosidase B


Mass: 45582.867 Da / Num. of mol.: 2 / Fragment: UNP residues 18-411 / Mutation: N201Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NAGA / Plasmid: pIB/V5-His-TOPO TA / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): HI-FIVE
References: UniProt: P17050, alpha-N-acetylgalactosaminidase

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Sugars , 3 types, 6 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: 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.: 2
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 , 4 types, 1040 molecules

#5: Chemical ChemComp-DGJ / (2R,3S,4R,5S)-2-(hydroxymethyl)piperidine-3,4,5-triol / 1-deoxygalactonojirimycin


Mass: 163.172 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: medication, Galafold*YM
#6: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1022 / 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: 3.31 Å3/Da / Density % sol: 62.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.4
Details: 8-16% PEG3350, 70mM citric acid, 30mM Bis-Tris propane, pH 3.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 12, 2008 / Details: TOROIDAL FOCUSING MIRROR
RadiationMonochromator: SI(111) CHANNEL CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 178912 / % possible obs: 96.1 % / Redundancy: 4 % / Rmerge(I) obs: 0.046 / Rsym value: 0.046 / Χ2: 1.01 / Net I/σ(I): 15.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.5-1.552.90.644135880.993173.2
1.55-1.623.50.538172591.005192.8
1.62-1.694.10.436182351.019198.4
1.69-1.784.20.286183481.03198.7
1.78-1.894.20.187184321.045199.1
1.89-2.044.20.106184741.109199.3
2.04-2.244.20.065185011.117199.6
2.24-2.564.20.048186081.07199.8
2.56-3.234.20.032186631.009199.9
3.23-504.20.024188040.689199.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 3H53

3h53


Resolution: 1.51→31.89 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.971 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.839 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.059 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1779 9021 5.1 %RANDOM
Rwork0.1592 ---
obs0.1601 178628 95.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 142.75 Å2 / Biso mean: 29.5642 Å2 / Biso min: 9.87 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20.18 Å2
2---0.05 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.51→31.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6279 0 338 1022 7639
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0216921
X-RAY DIFFRACTIONr_bond_other_d0.0010.024672
X-RAY DIFFRACTIONr_angle_refined_deg1.36129435
X-RAY DIFFRACTIONr_angle_other_deg0.886311326
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2915813
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.25724.065310
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.461151078
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3421540
X-RAY DIFFRACTIONr_chiral_restr0.0830.21027
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217527
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021369
X-RAY DIFFRACTIONr_mcbond_it2.627124007
X-RAY DIFFRACTIONr_mcbond_other1.047121610
X-RAY DIFFRACTIONr_mcangle_it3.859166478
X-RAY DIFFRACTIONr_scbond_it5.924202914
X-RAY DIFFRACTIONr_scangle_it8.533242957
LS refinement shellResolution: 1.51→1.544 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 454 -
Rwork0.311 8577 -
all-9031 -
obs--65.61 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.08320.0782-0.1640.3359-0.12960.40280.02960.02270.11450.02810.02320.0138-0.02530.0359-0.05280.0605-0.0077-0.00680.0457-0.01080.02156.9588-1.222810.1632
21.4161-0.0773-0.30541.5984-0.27140.80930.0550.04740.1630.09610.10050.3325-0.1109-0.1662-0.15550.04020.02830.02010.06820.06240.126826.25693.256410.9694
31.14640.3842-0.52751.6086-0.53630.8008-0.05370.08170.00770.12120.19480.39510.0079-0.14-0.1410.0791-0.00640.00040.08870.07280.130421.9069-31.573821.924
42.17080.3362-0.68081.7057-0.2341.0984-0.142-0.0647-0.4222-0.013-0.0206-0.43990.1560.2030.16270.07020.03120.00180.06460.020.181151.6099-37.164616.4726
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A18 - 310
2X-RAY DIFFRACTION2A311 - 404
3X-RAY DIFFRACTION3B18 - 310
4X-RAY DIFFRACTION4B311 - 404

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