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- PDB-3lpp: Crystal complex of N-terminal sucrase-isomaltase with kotalanol -

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Basic information

Entry
Database: PDB / ID: 3lpp
TitleCrystal complex of N-terminal sucrase-isomaltase with kotalanol
ComponentsSucrase-isomaltase
KeywordsHYDROLASE / Glycoside hydrolase family 31 / isomaltase / alpha-glucosidase / Cell membrane / Disease mutation / Disulfide bond / Glycoprotein / Glycosidase / Membrane / Multifunctional enzyme / Polymorphism / Signal-anchor / Sulfation / Transmembrane
Function / homology
Function and homology information


Intestinal saccharidase deficiencies / sucrose alpha-glucosidase / oligo-1,6-glucosidase activity / oligo-1,6-glucosidase / sucrose alpha-glucosidase activity / alpha-1,4-glucosidase activity / polysaccharide digestion / Digestion of dietary carbohydrate / brush border / hydrolase activity, hydrolyzing O-glycosyl compounds ...Intestinal saccharidase deficiencies / sucrose alpha-glucosidase / oligo-1,6-glucosidase activity / oligo-1,6-glucosidase / sucrose alpha-glucosidase activity / alpha-1,4-glucosidase activity / polysaccharide digestion / Digestion of dietary carbohydrate / brush border / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / apical plasma membrane / carbohydrate metabolic process / Golgi apparatus / extracellular exosome / integral component of membrane / plasma membrane
Similarity search - Function
Galactose mutarotase, N-terminal barrel / N-terminal barrel of NtMGAM and CtMGAM, maltase-glucoamylase / Spasmolytic Protein, domain 1 / Spasmolytic Protein; domain 1 / P-type 'Trefoil' domain signature. / P-type trefoil, conserved site / Trefoil (P-type) domain / P-type 'Trefoil' domain profile. / P-type trefoil domain / P or trefoil or TFF domain ...Galactose mutarotase, N-terminal barrel / N-terminal barrel of NtMGAM and CtMGAM, maltase-glucoamylase / Spasmolytic Protein, domain 1 / Spasmolytic Protein; domain 1 / P-type 'Trefoil' domain signature. / P-type trefoil, conserved site / Trefoil (P-type) domain / P-type 'Trefoil' domain profile. / P-type trefoil domain / P or trefoil or TFF domain / Glycosyl hydrolases family 31 signature 2. / Glycosyl hydrolases family 31, conserved site / Glycosyl hydrolases family 31 active site. / Glycosyl hydrolases family 31, active site / glycosyl hydrolase (family 31) / Glycoside hydrolase family 31 / Glycosyl hydrolases family 31 / Galactose mutarotase-like domain superfamily / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Irregular / Few Secondary Structures / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
beta-D-mannopyranose / Chem-KTL / DI(HYDROXYETHYL)ETHER / Sucrase-isomaltase, intestinal
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 Å
AuthorsSim, L. / Rose, D.R.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structural basis for substrate selectivity in human maltase-glucoamylase and sucrase-isomaltase N-terminal domains.
Authors: Sim, L. / Willemsma, C. / Mohan, S. / Naim, H.Y. / Pinto, B.M. / Rose, D.R.
History
DepositionFeb 5, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _software.classification ..._pdbx_unobs_or_zero_occ_atoms.label_asym_id / _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 / 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_unobs_or_zero_occ_atoms / 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 / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sucrase-isomaltase
B: Sucrase-isomaltase
C: Sucrase-isomaltase
D: Sucrase-isomaltase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)417,30025
Polymers411,4694
Non-polymers5,83121
Water31,1121727
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A: Sucrase-isomaltase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,7468
Polymers102,8671
Non-polymers1,8797
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sucrase-isomaltase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,2236
Polymers102,8671
Non-polymers1,3565
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Sucrase-isomaltase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,5087
Polymers102,8671
Non-polymers1,6416
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Sucrase-isomaltase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,8224
Polymers102,8671
Non-polymers9553
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)69.403, 165.763, 341.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Sucrase-isomaltase / / Sucrase / Isomaltase


Mass: 102867.148 Da / Num. of mol.: 4 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SI / Plasmid: pMT-TEVA / Cell (production host): S2 cells / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P14410, oligo-1,6-glucosidase

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Sugars , 4 types, 12 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: 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.: 3
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
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6
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
#8: Sugar ChemComp-BMA / beta-D-mannopyranose / Mannose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-mannopyranoseCOMMON NAMEGMML 1.0
b-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 1736 molecules

#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Chemical ChemComp-KTL / (1S,2R,3R,4S)-1-{(1S)-2-[(2R,3S,4S)-3,4-dihydroxy-2-(hydroxymethyl)tetrahydrothiophenium-1-yl]-1-hydroxyethyl}-2,3,4,5-tetrahydroxypentyl sulfate


Mass: 424.442 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H24O12S2
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1727 / 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: 2.39 Å3/Da / Density % sol: 48.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7
Details: 0.5M NaCl, 0.1M Bis-Tris propane, 18% PEG 4000, pH 7.0, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9175 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 9, 2009
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9175 Å / Relative weight: 1
ReflectionResolution: 2.15→20 Å / Num. obs: 202547 / % possible obs: 95 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.165 / Net I/σ(I): 11.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
2.15-2.193.10.47484.6
2.19-2.233.20.46687.9
2.23-2.273.30.4590.4
2.27-2.323.40.40292.5
2.32-2.373.50.36293.1
2.37-2.423.60.32492.9
2.42-2.483.70.29393.1
2.48-2.553.70.27193.7
2.55-2.623.80.24294.2
2.62-2.713.90.22694.6
2.71-2.840.20695.3
2.8-2.924.10.1996.3
2.92-3.054.30.18397.3
3.05-3.214.70.17598.3
3.21-3.415.40.19598.8
3.41-3.675.50.17199.2
3.67-4.045.50.14699.3
4.04-4.615.70.12298.1
4.61-5.796.20.124100
5.79-206.40.1599.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→19.95 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.926 / Occupancy max: 1 / Occupancy min: 1 / SU B: 10.114 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.255 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22263 10150 5 %RANDOM
Rwork0.17693 ---
obs0.1792 192262 94.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.936 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20 Å2
2--0.02 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.15→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27961 0 376 1727 30064
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02229165
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3041.94439797
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.35953458
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.96124.3521459
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.901154506
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.10115148
X-RAY DIFFRACTIONr_chiral_restr0.0920.24322
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0222576
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1980.213667
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.219914
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.22040
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2010.2133
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1520.230
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6271.517757
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.99228116
X-RAY DIFFRACTIONr_scbond_it1.625313262
X-RAY DIFFRACTIONr_scangle_it2.5454.511681
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.208 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 700 -
Rwork0.209 12186 -
obs--83.35 %

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