data_2BVK # _entry.id 2BVK # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.329 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 2BVK PDBE EBI-24674 WWPDB D_1290024674 # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.content_type _pdbx_database_related.details PDB 1HYA unspecified . PDB 2HYA unspecified . PDB 3HYA unspecified . PDB 4HYA unspecified . # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 2BVK _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _pdbx_database_status.SG_entry . _pdbx_database_status.recvd_initial_deposition_date 2005-06-30 _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Almond, A.' 1 'DeAngelis, P.L.' 2 'Blundell, C.D.' 3 # _citation.id primary _citation.title ;Hyaluronan: The Local Solution Conformation Determined by NMR and Computer Modeling is Close to a Contracted Left-Handed 4-Fold Helix. ; _citation.journal_abbrev J.Mol.Biol. _citation.journal_volume 358 _citation.page_first 1256 _citation.page_last ? _citation.year 2006 _citation.journal_id_ASTM JMOBAK _citation.country UK _citation.journal_id_ISSN 0022-2836 _citation.journal_id_CSD 0070 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 16584748 _citation.pdbx_database_id_DOI 10.1016/J.JMB.2006.02.077 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Almond, A.' 1 ? primary 'Deangelis, P.L.' 2 ? primary 'Blundell, C.D.' 3 ? # _cell.entry_id 2BVK _cell.length_a 1.000 _cell.length_b 1.000 _cell.length_c 1.000 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2BVK _symmetry.space_group_name_H-M 'P 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 # _entity.id 1 _entity.type branched _entity.src_method man _entity.pdbx_description ;2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid ; _entity.formula_weight 1535.282 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.details ? # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight BDP 'D-saccharide, beta linking' . 'beta-D-glucopyranuronic acid' 'D-GLUCURONIC ACID' 'C6 H10 O7' 194.139 NAG 'D-saccharide, beta linking' . 2-acetamido-2-deoxy-beta-D-glucopyranose ? 'C8 H15 N O6' 221.208 # loop_ _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.type _pdbx_nmr_exptl.solution_id 1 1 '[1H-15N] HSQC' 1 2 1 '[1H-1H-15N] NOESY-H' 1 # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 298 _pdbx_nmr_exptl_sample_conditions.pressure_units ? _pdbx_nmr_exptl_sample_conditions.pressure ? _pdbx_nmr_exptl_sample_conditions.pH 6.0 _pdbx_nmr_exptl_sample_conditions.ionic_strength ? _pdbx_nmr_exptl_sample_conditions.ionic_strength_units ? _pdbx_nmr_exptl_sample_conditions.pH_units pH _pdbx_nmr_exptl_sample_conditions.temperature_units K _pdbx_nmr_exptl_sample_conditions.label ? # _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.model OMEGA _pdbx_nmr_spectrometer.manufacturer GE _pdbx_nmr_spectrometer.field_strength 600 _pdbx_nmr_spectrometer.type ? # _pdbx_nmr_refine.entry_id 2BVK _pdbx_nmr_refine.method 'MOLECULAR DYNAMICS CONFIRMED BY BA CALCULATION OF EXPERIMENTAL NMR PA' _pdbx_nmr_refine.details ? _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_details.entry_id 2BVK _pdbx_nmr_details.text 'IONS AND WATER WERE REMOVED TO GENERATE ATOMIC COORDINATES' # _pdbx_nmr_ensemble.entry_id 2BVK _pdbx_nmr_ensemble.conformers_calculated_total_number 250000 _pdbx_nmr_ensemble.conformers_submitted_total_number 1 _pdbx_nmr_ensemble.conformer_selection_criteria ;AVERAGE CONFORMATION FROM A 50 NAN MOLECULAR DYNAMICS TRAJECTORY THAT EXPLICIT SOLVENT WATER AND CHARGE SODIUM IONS. THE 1-3 AND 1-4 LINKA FIXED AT (50.78, 9.78) AND (47.98, RESPECTIVELY USING THE H1-C1-OX-HX NOMENCLATURE ; # loop_ _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.authors _pdbx_nmr_software.ordinal refinement CHARMM ? 'BROOKS,BRUCCOLERI,OLAFSEN,STATES, SWAMINATHAN, KARPLUS' 1 'structure solution' CHARMM ? ? 2 # loop_ _exptl.entry_id _exptl.method _exptl.crystals_number 2BVK 'SOLUTION NMR' ? 2BVK 'THEORETICAL MODEL' ? # _struct.entry_id 2BVK _struct.title ;Hyaluronan: the local solution conformation determined by NMR and computer modelling is close to a contracted left-handed four-fold helix ; _struct.pdbx_descriptor 'CELL ADHESION' _struct.pdbx_model_details ;50 NANOSECOND FREE MOLECULAR DYNAMICS SIMULATION WITH EXPLIC INCLUSION OF WATER MOLECULES AND IONS AND A FORCE-FIELD DERIVED FOR CARBOHYRDRATES. THE DERIVED PDB STRUCTURE WAS THE AVERAGE CONFORMAT OBSERVED DURING THE MOLECULAR DYNAMICS SIMULATION ; _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details 'MINIMIZED AVERAGE' # _struct_keywords.entry_id 2BVK _struct_keywords.pdbx_keywords 'CELL ADHESION' _struct_keywords.text ;CELL ADHESION, HYALURONAN, GLYCOSAMINOGLYCAN, CARBOHYDRATE, N-ACETYL- GLUCOSAMINE, GLUCURONIC ACID, EXTRACELLULAR MATRIX, SIMLUATION, AQUEOUS MOLECULAR DYNAMICS, HYALURONIC ACID, SODIUM HYALURONATE ; # _struct_asym.id A _struct_asym.pdbx_blank_PDB_chainid_flag N _struct_asym.pdbx_modified N _struct_asym.entity_id 1 _struct_asym.details ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale both ? A BDP . O4 ? ? ? 1_555 A NAG . C1 ? ? P BDP 1 P NAG 2 1_555 ? ? ? ? ? ? ? 1.395 ? ? covale2 covale both ? A NAG . O3 ? ? ? 1_555 A BDP . C1 ? ? P NAG 2 P BDP 3 1_555 ? ? ? ? ? ? ? 1.397 ? ? covale3 covale both ? A BDP . O4 ? ? ? 1_555 A NAG . C1 ? ? P BDP 3 P NAG 4 1_555 ? ? ? ? ? ? ? 1.396 ? ? covale4 covale both ? A NAG . O3 ? ? ? 1_555 A BDP . C1 ? ? P NAG 4 P BDP 5 1_555 ? ? ? ? ? ? ? 1.397 ? ? covale5 covale both ? A BDP . O4 ? ? ? 1_555 A NAG . C1 ? ? P BDP 5 P NAG 6 1_555 ? ? ? ? ? ? ? 1.395 ? ? covale6 covale both ? A NAG . O3 ? ? ? 1_555 A BDP . C1 ? ? P NAG 6 P BDP 7 1_555 ? ? ? ? ? ? ? 1.397 ? ? covale7 covale both ? A BDP . O4 ? ? ? 1_555 A NAG . C1 ? ? P BDP 7 P NAG 8 1_555 ? ? ? ? ? ? ? 1.395 ? ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # _database_PDB_matrix.entry_id 2BVK _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _atom_sites.entry_id 2BVK _atom_sites.fract_transf_matrix[1][1] 1.000000 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 1.000000 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 1.000000 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C H N O # loop_ _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2006-10-30 2 'Structure model' 1 1 2011-06-02 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2018-10-03 5 'Structure model' 2 0 2020-07-29 # loop_ _pdbx_audit_revision_details.ordinal _pdbx_audit_revision_details.revision_ordinal _pdbx_audit_revision_details.data_content_type _pdbx_audit_revision_details.provider _pdbx_audit_revision_details.type _pdbx_audit_revision_details.description _pdbx_audit_revision_details.details 1 1 'Structure model' repository 'Initial release' ? ? 2 5 'Structure model' repository Remediation 'Carbohydrate remediation' ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' 'Data collection' 4 5 'Structure model' 'Atomic model' 5 5 'Structure model' 'Data collection' 6 5 'Structure model' 'Derived calculations' 7 5 'Structure model' 'Structure summary' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 4 'Structure model' pdbx_nmr_spectrometer 2 5 'Structure model' atom_site 3 5 'Structure model' chem_comp 4 5 'Structure model' entity 5 5 'Structure model' pdbx_branch_scheme 6 5 'Structure model' pdbx_chem_comp_identifier 7 5 'Structure model' pdbx_entity_branch 8 5 'Structure model' pdbx_entity_branch_descriptor 9 5 'Structure model' pdbx_entity_branch_link 10 5 'Structure model' pdbx_entity_branch_list 11 5 'Structure model' pdbx_entity_nonpoly 12 5 'Structure model' pdbx_nonpoly_scheme 13 5 'Structure model' pdbx_struct_assembly_gen 14 5 'Structure model' struct_asym 15 5 'Structure model' struct_conn # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 4 'Structure model' '_pdbx_nmr_spectrometer.manufacturer' 2 4 'Structure model' '_pdbx_nmr_spectrometer.model' 3 5 'Structure model' '_atom_site.Cartn_x' 4 5 'Structure model' '_atom_site.Cartn_y' 5 5 'Structure model' '_atom_site.Cartn_z' 6 5 'Structure model' '_atom_site.auth_atom_id' 7 5 'Structure model' '_atom_site.auth_comp_id' 8 5 'Structure model' '_atom_site.auth_seq_id' 9 5 'Structure model' '_atom_site.label_asym_id' 10 5 'Structure model' '_atom_site.label_atom_id' 11 5 'Structure model' '_atom_site.label_comp_id' 12 5 'Structure model' '_atom_site.label_entity_id' 13 5 'Structure model' '_atom_site.type_symbol' 14 5 'Structure model' '_chem_comp.name' 15 5 'Structure model' '_chem_comp.type' 16 5 'Structure model' '_pdbx_struct_assembly_gen.asym_id_list' 17 5 'Structure model' '_struct_conn.pdbx_dist_value' 18 5 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 19 5 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 20 5 'Structure model' '_struct_conn.ptnr1_label_asym_id' 21 5 'Structure model' '_struct_conn.ptnr1_label_atom_id' 22 5 'Structure model' '_struct_conn.ptnr1_label_comp_id' 23 5 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 24 5 'Structure model' '_struct_conn.ptnr2_label_asym_id' 25 5 'Structure model' '_struct_conn.ptnr2_label_atom_id' 26 5 'Structure model' '_struct_conn.ptnr2_label_comp_id' # loop_ _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_mon_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.hetero A 1 BDP 1 P BDP 1 P BDP 8 n A 1 NAG 2 P NAG 2 P NAG 7 n A 1 BDP 3 P BDP 3 P BDP 6 n A 1 NAG 4 P NAG 4 P NAG 5 n A 1 BDP 5 P BDP 5 P BDP 4 n A 1 NAG 6 P NAG 6 P NAG 3 n A 1 BDP 7 P BDP 7 P BDP 2 n A 1 NAG 8 P NAG 8 P NAG 1 n # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version _pdbx_chem_comp_identifier.identifier BDP 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1.0 DGlcpAb BDP 'COMMON NAME' GMML 1.0 'b-D-glucopyranuronic acid' BDP 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1.0 b-D-GlcpA BDP 'SNFG CARBOHYDRATE SYMBOL' GMML 1.0 GlcA NAG 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1.0 DGlcpNAcb NAG 'COMMON NAME' GMML 1.0 N-acetyl-b-D-glucopyranosamine NAG 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1.0 b-D-GlcpNAc NAG 'SNFG CARBOHYDRATE SYMBOL' GMML 1.0 GlcNAc # _pdbx_entity_branch.entity_id 1 _pdbx_entity_branch.type oligosaccharide # loop_ _pdbx_entity_branch_descriptor.ordinal _pdbx_entity_branch_descriptor.entity_id _pdbx_entity_branch_descriptor.descriptor _pdbx_entity_branch_descriptor.type _pdbx_entity_branch_descriptor.program _pdbx_entity_branch_descriptor.program_version 1 1 DGlcpNAcb1-4DGlcpAb1-3DGlcpNAcb1-4DGlcpAb1-3DGlcpNAcb1-4DGlcpAb1-3DGlcpNAcb1-4DGlcpAb1-ROH 'Glycam Condensed Sequence' GMML 1.0 2 1 'WURCS=2.0/2,8,7/[a2122A-1b_1-5][a2122h-1b_1-5_2*NCC/3=O]/1-2-1-2-1-2-1-2/a4-b1_b3-c1_c4-d1_d3-e1_e4-f1_f3-g1_g4-h1' WURCS PDB2Glycan 1.1.0 3 1 ;[][b-D-GlcpA]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-D-GlcpA]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-D-GlcpA]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-D-GlcpA]{[(4+1)][b-D-GlcpNAc]{}}}}}}}} ; LINUCS PDB-CARE ? # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.value_order _pdbx_entity_branch_link.details 1 1 2 NAG C1 O1 1 BDP O4 HO4 sing ? 2 1 3 BDP C1 O1 2 NAG O3 HO3 sing ? 3 1 4 NAG C1 O1 3 BDP O4 HO4 sing ? 4 1 5 BDP C1 O1 4 NAG O3 HO3 sing ? 5 1 6 NAG C1 O1 5 BDP O4 HO4 sing ? 6 1 7 BDP C1 O1 6 NAG O3 HO3 sing ? 7 1 8 NAG C1 O1 7 BDP O4 HO4 sing ? # loop_ _pdbx_entity_branch_list.entity_id _pdbx_entity_branch_list.comp_id _pdbx_entity_branch_list.num _pdbx_entity_branch_list.hetero 1 BDP 1 n 1 NAG 2 n 1 BDP 3 n 1 NAG 4 n 1 BDP 5 n 1 NAG 6 n 1 BDP 7 n 1 NAG 8 n #