data_5LBV # _model_server_result.job_id IG--lgQmY-UpEk0dn5mzZw _model_server_result.datetime_utc '2024-11-27 05:54:45' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 5lbv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":506}' # _entry.id 5LBV # _exptl.entry_id 5LBV _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 22.99 _entity.id 3 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 'SODIUM ION' _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 5LBV _cell.length_a 64.628 _cell.length_b 213.566 _cell.length_c 124.024 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5LBV _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _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 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 2 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 2 4 3 MAN BMA C1 O1 . O3 HO3 . sing 4 ? 2 5 1 FUC NAG C1 O1 . O6 HO6 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n C NAG 1 C 1 NAG B 1154 NAG 2 n C NAG 2 C 2 NAG B 1155 NAG 2 n C BMA 3 C 3 BMA B 1156 BMA 2 n C MAN 4 C 4 MAN B 1158 MAN 2 n C FUC 5 C 5 FUC B 1157 FUC # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.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.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _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_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order disulf ? disulf1 A SG CYS 3 A CYS 3 1_555 A SG CYS 30 A CYS 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf2 A SG CYS 60 A CYS 60 1_555 A SG CYS 121 A CYS 121 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? disulf ? disulf3 A SG CYS 74 A CYS 74 1_555 A SG CYS 105 A CYS 105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf4 A SG CYS 92 A CYS 92 1_555 A SG CYS 116 A CYS 116 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? disulf ? disulf5 A SG CYS 190 A CYS 190 1_555 A SG CYS 291 A CYS 291 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf6 A SG CYS 308 A CYS 308 1_555 A SG CYS 339 A CYS 339 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf7 B SG CYS 3 B CYS 3 1_555 B SG CYS 30 B CYS 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf8 B SG CYS 60 B CYS 60 1_555 B SG CYS 121 B CYS 121 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? disulf ? disulf9 B SG CYS 74 B CYS 74 1_555 B SG CYS 105 B CYS 105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf10 B SG CYS 92 B CYS 92 1_555 B SG CYS 116 B CYS 116 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf11 B SG CYS 190 B CYS 190 1_555 B SG CYS 291 B CYS 291 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? disulf ? disulf12 B SG CYS 308 B CYS 308 1_555 B SG CYS 339 B CYS 339 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? covale ? covale1 B ND2 ASN 154 B ASN 154 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale2 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.394 ? covale ? covale3 C O6 NAG . C NAG 1 1_555 C C1 FUC . C FUC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.416 ? covale ? covale4 C O4 NAG . C NAG 2 1_555 C C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.407 ? covale ? covale5 C O3 BMA . C BMA 3 1_555 C C1 MAN . C MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.415 ? metalc ? metalc1 B O HIS 158 B HIS 158 1_555 D NA NA . B NA 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.927 ? metalc ? metalc2 B O ASP 161 B ASP 161 1_555 D NA NA . B NA 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.575 ? metalc ? metalc3 B O ARG 164 B ARG 164 1_555 D NA NA . B NA 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.373 ? # _chem_comp.formula 'Na 1' _chem_comp.formula_weight 22.99 _chem_comp.id NA _chem_comp.mon_nstd_flag . _chem_comp.name 'SODIUM ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 5LBV _atom_sites.fract_transf_matrix[1][1] 0.015473 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.004682 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.008063 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code D 3 NA B 1 506 1 NA NA . E 4 HOH A 1 501 509 HOH HOH . E 4 HOH A 2 502 504 HOH HOH . E 4 HOH A 3 503 510 HOH HOH . E 4 HOH A 4 504 502 HOH HOH . E 4 HOH A 5 505 507 HOH HOH . E 4 HOH A 6 506 506 HOH HOH . E 4 HOH A 7 507 503 HOH HOH . E 4 HOH A 8 508 508 HOH HOH . E 4 HOH A 9 509 524 HOH HOH . E 4 HOH A 10 510 512 HOH HOH . E 4 HOH A 11 511 516 HOH HOH . E 4 HOH A 12 512 514 HOH HOH . E 4 HOH A 13 513 505 HOH HOH . E 4 HOH A 14 514 512 HOH HOH . E 4 HOH A 15 515 515 HOH HOH . E 4 HOH A 16 516 501 HOH HOH . E 4 HOH A 17 517 513 HOH HOH . F 4 HOH B 1 601 507 HOH HOH . F 4 HOH B 2 602 511 HOH HOH . F 4 HOH B 3 603 501 HOH HOH . F 4 HOH B 4 604 508 HOH HOH . F 4 HOH B 5 605 502 HOH HOH . F 4 HOH B 6 606 520 HOH HOH . F 4 HOH B 7 607 509 HOH HOH . F 4 HOH B 8 608 504 HOH HOH . F 4 HOH B 9 609 513 HOH HOH . F 4 HOH B 10 610 515 HOH HOH . F 4 HOH B 11 611 506 HOH HOH . F 4 HOH B 12 612 518 HOH HOH . F 4 HOH B 13 613 522 HOH HOH . F 4 HOH B 14 614 521 HOH HOH . F 4 HOH B 15 615 505 HOH HOH . F 4 HOH B 16 616 503 HOH HOH . F 4 HOH B 17 617 519 HOH HOH . F 4 HOH B 18 618 511 HOH HOH . F 4 HOH B 19 619 517 HOH HOH . F 4 HOH B 20 620 525 HOH HOH . F 4 HOH B 21 621 523 HOH HOH . F 4 HOH B 22 622 514 HOH HOH . F 4 HOH B 23 623 516 HOH HOH . F 4 HOH B 24 624 510 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol NA _atom_site.label_atom_id NA _atom_site.label_comp_id NA _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id D _atom_site.label_entity_id 3 _atom_site.Cartn_x -10.494 _atom_site.Cartn_y 13.635 _atom_site.Cartn_z 49.72 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 51.49 _atom_site.pdbx_formal_charge 1 _atom_site.auth_atom_id NA _atom_site.auth_comp_id NA _atom_site.auth_seq_id 506 _atom_site.auth_asym_id B _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 274 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 1 #