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- PDB-1les: LENTIL LECTIN COMPLEXED WITH SUCROSE -

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Basic information

Entry
Database: PDB / ID: 1les
TitleLENTIL LECTIN COMPLEXED WITH SUCROSE
Components(LENTIL LECTIN) x 2
KeywordsLECTIN / PROTEIN-SUGAR INTERACTIONS
Function / homology
Function and homology information


carbohydrate mediated signaling / mannose binding / manganese ion binding / carbohydrate binding / calcium ion binding
Similarity search - Function
Legume lectin / Legume lectin, alpha chain, conserved site / Legume lectins alpha-chain signature. / Legume lectins beta-chain signature. / Legume lectin domain / Legume lectin, beta chain, Mn/Ca-binding site / Legume lectin domain / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls ...Legume lectin / Legume lectin, alpha chain, conserved site / Legume lectins alpha-chain signature. / Legume lectins beta-chain signature. / Legume lectin domain / Legume lectin, beta chain, Mn/Ca-binding site / Legume lectin domain / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
sucrose / : / : / Lectin
Similarity search - Component
Biological speciesLens culinaris (lentil)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsHamelryck, T. / Loris, R.
Citation
Journal: J.Biol.Chem. / Year: 1995
Title: NMR, molecular modeling, and crystallographic studies of lentil lectin-sucrose interaction.
Authors: Casset, F. / Hamelryck, T. / Loris, R. / Brisson, J.R. / Tellier, C. / Dao-Thi, M.H. / Wyns, L. / Poortmans, F. / Perez, S. / Imberty, A.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Conserved Waters in Legume Lectin Crystal Structures: The Importance of Bound Waters for the Sequence-Structure Relationship within the Legume Lectin Family
Authors: Loris, R. / Stas, P.P.G. / Wyns, L.
#2: Journal: Biochemistry / Year: 1993
Title: Crystal Structure Determination and Refinement at 2.3 Angstroms Resolution of the Lentil Lectin
Authors: Loris, R. / Steyaert, J. / Maes, D. / Lisgarten, J. / Pickersgill, R. / Wyns, L.
#3: Journal: J.Mol.Biol. / Year: 1992
Title: Two Crystal Forms of the Lentil Lectin Diffract to High Resolution
Authors: Loris, R. / Lisgarten, J. / Maes, D. / Pickersgill, R. / Koerber, F. / Reynolds, C. / Wyns, L.
History
DepositionAug 23, 1995Processing site: BNL
Revision 1.0Dec 7, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...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_struct_conn_angle / 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_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_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_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.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.0Oct 14, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / pdbx_branch_scheme / pdbx_entity_branch_link / pdbx_molecule_features / struct_conn
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_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.pdbx_synonyms / _pdbx_branch_scheme.pdb_asym_id / _pdbx_entity_branch_link.atom_id_1 / _pdbx_entity_branch_link.atom_id_2 / _pdbx_entity_branch_link.comp_id_1 / _pdbx_entity_branch_link.comp_id_2 / _pdbx_entity_branch_link.entity_branch_list_num_1 / _pdbx_entity_branch_link.entity_branch_list_num_2 / _pdbx_entity_branch_link.leaving_atom_id_1 / _pdbx_entity_branch_link.leaving_atom_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_atom_id
Revision 3.1Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _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: LENTIL LECTIN
C: LENTIL LECTIN
B: LENTIL LECTIN
D: LENTIL LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,18510
Polymers51,3114
Non-polymers8756
Water4,107228
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18830 Å2
ΔGint-110 kcal/mol
Surface area17200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.030, 124.800, 50.020
Angle α, β, γ (deg.)90.00, 111.80, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: ALA A 80 - ASP A 81 OMEGA = 0.57 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
2: ALA C 80 - ASP C 81 OMEGA = 0.33 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
3: GLY B 47 - HIS B 47 OMEGA = 0.02 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
4: GLY D 47 - HIS D 47 OMEGA = 0.02 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.3718, 0.0008, -0.9283), (0.0001, -1, -0.0008), (-0.9283, -0.0002, -0.3718)
Vector: 15.7303, -0.0271, 23.2268)
DetailsTHE LENTIL LECTIN MOLECULE NORMALLY EXISTS AS A DIMER. THE TWO MONOMERS IN THIS ENTRY ARE RELATED BY A PSEUDO TWO-FOLD AXIS. EACH MONOMER CONSISTS OF TWO SEPARATE POLYPEPTIDE CHAINS, ALPHA AND BETA. THE ALPHA CHAIN CONSISTS OF 181 RESIDUES AND THE BETA CHAIN CONSISTS OF 52 RESIDUES. THE ALPHA AND BETA CHAINS OF MONOMER 1 HAVE BEEN ASSIGNED CHAIN IDENTIFIERS *A* AND *B*, RESPECTIVELY, IN THIS ENTRY. THE ALPHA AND BETA CHAINS OF MONOMER 2 HAVE BEEN ASSIGNED CHAIN IDENTIFIERS *C* AND *D*, RESPECTIVELY, IN THIS ENTRY. THIS NUMBERING SCHEME IS THE SAME AS THAT USED FOR PEA LECTIN BY EINSPAHR ET AL. (ENTRY 2LTN). THE MONOMERS ARE RELATED BY A NON-CRYSTALLOGRAPHIC TWO-FOLD AXIS PARALLEL TO THE CRYSTALLOGRAPHIC B-AXIS. THE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAINS *C* AND *D* WHEN APPLIED TO CHAINS *A* AND *B*, RESPECTIVELY. THE RMS BETWEEN THE BACKBONE COORDINATES IS 0.12 ANGSTROMS.

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein LENTIL LECTIN / LENS CULINARIS LECTIN


Mass: 19906.982 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Lens culinaris (lentil) / Organ: SEED / References: PIR: LNLWBA, UniProt: P02870*PLUS
#2: Protein LENTIL LECTIN / LENS CULINARIS LECTIN


Mass: 5748.350 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Lens culinaris (lentil) / Organ: SEED / References: UniProt: P02870

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Sugars , 1 types, 2 molecules

#3: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose /


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 3 types, 232 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 228 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsEACH MONOMER HAS A BOUND CALCIUM, MANGANESE, AND SUCROSE MOLECULE. THE CALCIUM AND MANGANESE IONS ...EACH MONOMER HAS A BOUND CALCIUM, MANGANESE, AND SUCROSE MOLECULE. THE CALCIUM AND MANGANESE IONS ARE ESSENTIAL FOR STABILIZING AN UNUSUAL ALA-ASP CIS PEPTIDE BOND THAT IS AN ESSENTIAL FEATURE OF THE CARBOHYDRATE RECOGNITION SITE OF THIS LECTIN. THESE SITES ARE PRESENTED ON *SITE* RECORDS BELOW. THE ELECTRON DENSITY OF ONE BOUND SUCROSE MOLECULE WAS CLEARLY VISIBLE IN EACH SUGAR BINDING SITE. THE GLUCOSE MOIETY IS DIRECTLY BOUND IN THE BINDING SITE, WHILE THE CONTACT WITH THE FRUCTOSE MOIETY IS MEDIATED BY WATER MOLECULES. BOTH CARBOHYDRATE BINDING SITES INTERACT WITH EACH OTHER THROUGH CRYSTAL CONTACTS.

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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: 2.82 Å3/Da / Density % sol: 56.46 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16.25 mg/mlprotein 1drop
250 mMcacodylate1drop
325 mMsucrose1drop
420 %(v/v)MPD1drop
540 %(v/v)MPD1reservoir
6100 mMcacodylate1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418 Å
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Jun 24, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.79→15 Å / Num. obs: 43108 / % possible obs: 69.9 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.073
Reflection
*PLUS
Highest resolution: 1.9 Å / Num. measured all: 114331 / Rmerge(I) obs: 0.073
Reflection shell
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 1.96 Å / % possible obs: 75.1 % / Rmerge(I) obs: 0.295

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
MADNESdata reduction
X-PLOR3.1phasing
RefinementResolution: 1.9→6 Å / σ(F): 0 /
Rfactor% reflection
Rwork0.188 -
obs0.188 75.1 %
Displacement parametersBiso mean: 23.51 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.9→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3560 0 50 228 3838
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.231
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.84
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.925
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.84
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.925

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