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- PDB-6mhm: Crystal structure of human acid ceramidase in covalent complex wi... -

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Basic information

Entry
Database: PDB / ID: 6mhm
TitleCrystal structure of human acid ceramidase in covalent complex with carmofur
Components(Acid ceramidase subunit ...) x 2
KeywordsHYDROLASE / acid ceramidase / acid ceramidase inhibitors / benzoxazolone carboxamides / carmofur
Function / homology
Function and homology information


regulation of programmed necrotic cell death / : / Glycosphingolipid metabolism / ceramidase / N-acylsphingosine amidohydrolase activity / ceramidase activity / ceramide catabolic process / fatty acid amide hydrolase activity / regulation of steroid biosynthetic process / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides ...regulation of programmed necrotic cell death / : / Glycosphingolipid metabolism / ceramidase / N-acylsphingosine amidohydrolase activity / ceramidase activity / ceramide catabolic process / fatty acid amide hydrolase activity / regulation of steroid biosynthetic process / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / sphingosine biosynthetic process / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / ceramide biosynthetic process / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / keratinocyte differentiation / lysosomal lumen / fatty acid metabolic process / nuclear receptor binding / transcription corepressor activity / tertiary granule lumen / cellular response to tumor necrosis factor / ficolin-1-rich granule lumen / lysosome / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / nucleus
Similarity search - Function
Acid ceramidase-like / Acid ceramidase, N-terminal / beta subunit of N-acylethanolamine-hydrolyzing acid amidase / Choloylglycine hydrolase/NAAA C-terminal / Linear amide C-N hydrolases, choloylglycine hydrolase family
Similarity search - Domain/homology
triacetyl-beta-chitotriose / hexylcarbamic acid / Acid ceramidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.743 Å
AuthorsDementiev, A. / Joachimiak, A. / Doan, N.
CitationJournal: J. Med. Chem. / Year: 2019
Title: Molecular Mechanism of Inhibition of Acid Ceramidase by Carmofur.
Authors: Dementiev, A. / Joachimiak, A. / Nguyen, H. / Gorelik, A. / Illes, K. / Shabani, S. / Gelsomino, M. / Ahn, E.E. / Nagar, B. / Doan, N.
History
DepositionSep 18, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_validate_close_contact / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / 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.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 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: Acid ceramidase subunit alpha
B: Acid ceramidase subunit beta
C: Acid ceramidase subunit alpha
D: Acid ceramidase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,45226
Polymers88,1454
Non-polymers4,30722
Water1,42379
1
A: Acid ceramidase subunit alpha
B: Acid ceramidase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,06712
Polymers44,0732
Non-polymers1,99510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Acid ceramidase subunit alpha
D: Acid ceramidase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,38514
Polymers44,0732
Non-polymers2,31212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)153.718, 68.650, 98.386
Angle α, β, γ (deg.)90.000, 120.730, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Acid ceramidase subunit ... , 2 types, 4 molecules ACBD

#1: Protein Acid ceramidase subunit alpha / Acid CDase / Acylsphingosine deacylase / N-acylsphingosine amidohydrolase / Putative 32 kDa heart ...Acid CDase / Acylsphingosine deacylase / N-acylsphingosine amidohydrolase / Putative 32 kDa heart protein / PHP32


Mass: 15079.450 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ASAH1, ASAH, HSD-33, HSD33 / Production host: unidentified baculovirus / References: UniProt: Q13510, ceramidase
#2: Protein Acid ceramidase subunit beta / Acid CDase / Acylsphingosine deacylase / N-acylsphingosine amidohydrolase / Putative 32 kDa heart ...Acid CDase / Acylsphingosine deacylase / N-acylsphingosine amidohydrolase / Putative 32 kDa heart protein / PHP32


Mass: 28993.139 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ASAH1, ASAH, HSD-33, HSD33 / Production host: unidentified baculovirus / References: UniProt: Q13510, ceramidase

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Sugars , 3 types, 7 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / triacetyl-beta-chitotriose


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 627.594 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: oligosaccharide / References: triacetyl-beta-chitotriose
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}}LINUCSPDB-CARE
#4: 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: obtained synthetically
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
#6: 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.: 3 / Source method: obtained synthetically / 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 , 3 types, 94 molecules

#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-JRY / hexylcarbamic acid


Mass: 145.199 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C7H15NO2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.66 Å3/Da / Density % sol: 53.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.3
Details: 0.2 M sodium-phosphate-citrate, pH 4.3, 0.275 M lithium sulfate, and 18% polyethylene glycol 1000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9793 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 31, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.74→50 Å / Num. obs: 23259 / % possible obs: 100 % / Redundancy: 4.9 % / Biso Wilson estimate: 53.81 Å2 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.055 / Rrim(I) all: 0.124 / Χ2: 1.687 / Net I/σ(I): 7.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.74-2.7940.6811860.7230.3830.7841.14999.9
2.79-2.844.30.61111230.7720.330.6971.227100
2.84-2.894.50.47811550.8130.2510.5421.269100
2.89-2.954.80.48411520.8380.2460.5441.34100
2.95-3.025.20.411450.8990.1960.4471.298100
3.02-3.0950.34211500.9290.1690.3831.362100
3.09-3.165.10.26811730.9550.1320.2991.443100
3.16-3.255.10.22611560.9610.110.2511.468100
3.25-3.345.10.19611420.9720.0960.2191.573100
3.34-3.455.10.16811460.9750.0820.1871.7100
3.45-3.585.10.15211570.9790.0740.1691.735100
3.58-3.725.10.11911620.9880.0580.1331.766100
3.72-3.895.10.10111630.990.0490.1131.928100
3.89-4.095.10.09111730.9930.0440.1011.919100
4.09-4.355.10.08111580.9930.0390.091.964100
4.35-4.6850.0711830.9950.0330.0772.159100
4.68-5.1650.06811570.9960.0330.0761.894100
5.16-5.950.07111810.9950.0340.0791.835100
5.9-7.4350.07111840.9950.0340.0791.897100
7.43-504.70.05912130.9930.030.0672.53899.5

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-3000data reduction
HKL-3000data scaling
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5U7Z

5u7z


Resolution: 2.743→48.647 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.95
RfactorNum. reflection% reflection
Rfree0.2616 2000 8.6 %
Rwork0.2141 --
obs0.2182 23252 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 113.8 Å2 / Biso mean: 51.0869 Å2 / Biso min: 20.61 Å2
Refinement stepCycle: final / Resolution: 2.743→48.647 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5864 0 265 79 6208
Biso mean--69.9 45.25 -
Num. residues----734
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066288
X-RAY DIFFRACTIONf_angle_d1.0068568
X-RAY DIFFRACTIONf_chiral_restr0.046967
X-RAY DIFFRACTIONf_plane_restr0.0041060
X-RAY DIFFRACTIONf_dihedral_angle_d5.6843630
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7435-2.84150.36711940.29572059225398
2.8415-2.95530.34841990.267321172316100
2.9553-3.08970.3411990.280721162315100
3.0897-3.25260.28222000.237621252325100
3.2526-3.45630.30071980.220121002298100
3.4563-3.72310.28111990.213821192318100
3.7231-4.09760.25312010.187521382339100
4.0976-4.69010.22822020.177421432345100
4.6901-5.90740.23422010.192921362337100
5.9074-48.65510.22092070.223721992406100

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