data_5YLV # _model_server_result.job_id F0b3hEKOh2_d0IDxEZJ4-w _model_server_result.datetime_utc '2024-11-15 03:18:06' _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 5ylv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":1106}' # _entry.id 5YLV # _exptl.entry_id 5YLV _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 85.468 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'RUBIDIUM ION' _entity.pdbx_number_of_molecules 3 _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 120 _cell.entry_id 5YLV _cell.length_a 105.05 _cell.length_b 105.05 _cell.length_c 368.54 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YLV _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall 'P 31 2"' _symmetry.space_group_name_H-M 'P 31 2 1' # _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,G,H,I,J,K,L,M,N,O _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 6 F N N ? 6 G N N ? 6 H N N # 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 B SG CYS 130 B CYS 131 1_555 B SG CYS 151 B CYS 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf2 B SG CYS 161 B CYS 162 1_555 B SG CYS 177 B CYS 178 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf3 B SG CYS 200 B CYS 201 1_555 B SG CYS 261 B CYS 262 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? covale ? covale1 A C SER 385 A SER 384 1_555 A N BFD 386 A BFD 385 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale2 A C BFD 386 A BFD 385 1_555 A N LYS 387 A LYS 386 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.31 ? covale ? covale3 B ND2 ASN 98 B ASN 99 1_555 I C1 NAG . B NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale4 B ND2 ASN 129 B ASN 130 1_555 J C1 NAG . B NAG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.493 ? covale ? covale5 B OE1 GLN 138 B GLN 139 1_555 B CG LYS 148 B LYS 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.129 ? covale ? covale6 B OE1 GLN 138 B GLN 139 1_555 B CD LYS 148 B LYS 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.495 ? covale ? covale7 B ND2 ASN 160 B ASN 161 1_555 K C1 NAG . B NAG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? metalc ? metalc1 A O ASP 184 A ASP 183 1_555 H RB RB . A RB 1106 6_655 ? ? ? ? ? ? ? ? ? ? ? ? 3.068 ? metalc ? metalc2 A OD2 ASP 186 A ASP 185 1_555 H RB RB . A RB 1106 6_655 ? ? ? ? ? ? ? ? ? ? ? ? 2.998 ? metalc ? metalc3 A O VAL 342 A VAL 341 1_555 F RB RB . A RB 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.888 ? metalc ? metalc4 A OD2 BFD 386 A BFD 385 1_555 D MG MG . A MG 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.492 ? metalc ? metalc5 A O THR 388 A THR 387 1_555 D MG MG . A MG 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.596 ? metalc ? metalc6 A O SER 409 A SER 408 1_555 H RB RB . A RB 1106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.868 ? metalc ? metalc7 A OG SER 409 A SER 408 1_555 H RB RB . A RB 1106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.946 ? metalc ? metalc8 A O GLN 419 A GLN 418 1_555 H RB RB . A RB 1106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.166 ? metalc ? metalc9 A O THR 420 A THR 419 1_555 H RB RB . A RB 1106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.129 ? metalc ? metalc10 A OD1 ASP 727 A ASP 726 1_555 D MG MG . A MG 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.192 ? metalc ? metalc11 A O LYS 736 A LYS 735 1_555 G RB RB . A RB 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.698 ? metalc ? metalc12 A O ALA 738 A ALA 737 1_555 G RB RB . A RB 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.921 ? metalc ? metalc13 A OD1 ASP 757 A ASP 756 1_555 G RB RB . A RB 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.654 ? # _chem_comp.formula 'Rb 1' _chem_comp.formula_weight 85.468 _chem_comp.id RB _chem_comp.mon_nstd_flag . _chem_comp.name 'RUBIDIUM ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 5YLV _atom_sites.fract_transf_matrix[1][1] 0.009519 _atom_sites.fract_transf_matrix[1][2] 0.005496 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010992 _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] 0.002713 _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 C 3 8WX A 1 1101 1101 8WX 8WX . D 4 MG A 1 1102 1102 MG MG . E 5 CE1 A 1 1103 1103 CE1 CE1 . F 6 RB A 1 1104 1104 RB RB . G 6 RB A 1 1105 1105 RB RB . H 6 RB A 1 1106 1106 RB RB . I 7 NAG B 1 301 301 NAG NAG . J 7 NAG B 1 302 302 NAG NAG . K 7 NAG B 1 303 303 NAG NAG . L 8 PCW B 1 304 304 PCW PCW . M 5 CE1 B 1 305 305 CE1 CE1 . N 9 HOH A 1 1201 1201 HOH HOH . N 9 HOH A 2 1202 1202 HOH HOH . N 9 HOH A 3 1203 1203 HOH HOH . N 9 HOH A 4 1204 1204 HOH HOH . N 9 HOH A 5 1205 1205 HOH HOH . N 9 HOH A 6 1206 1206 HOH HOH . N 9 HOH A 7 1207 1207 HOH HOH . N 9 HOH A 8 1208 1208 HOH HOH . N 9 HOH A 9 1209 1209 HOH HOH . N 9 HOH A 10 1210 1210 HOH HOH . N 9 HOH A 11 1211 1211 HOH HOH . N 9 HOH A 12 1212 1212 HOH HOH . N 9 HOH A 13 1213 1213 HOH HOH . N 9 HOH A 14 1214 1214 HOH HOH . N 9 HOH A 15 1215 1215 HOH HOH . N 9 HOH A 16 1216 1216 HOH HOH . N 9 HOH A 17 1217 1217 HOH HOH . N 9 HOH A 18 1218 1218 HOH HOH . N 9 HOH A 19 1219 1219 HOH HOH . N 9 HOH A 20 1220 1220 HOH HOH . N 9 HOH A 21 1221 1221 HOH HOH . N 9 HOH A 22 1222 1222 HOH HOH . O 9 HOH B 1 401 401 HOH HOH . O 9 HOH B 2 402 402 HOH HOH . O 9 HOH B 3 403 403 HOH HOH . O 9 HOH B 4 404 404 HOH HOH . O 9 HOH B 5 405 405 HOH HOH . O 9 HOH B 6 406 406 HOH HOH . O 9 HOH B 7 407 407 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol RB _atom_site.label_atom_id RB _atom_site.label_comp_id RB _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id H _atom_site.label_entity_id 6 _atom_site.Cartn_x 69.323 _atom_site.Cartn_y -5.523 _atom_site.Cartn_z 63.89 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 60.04 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id RB _atom_site.auth_comp_id RB _atom_site.auth_seq_id 1106 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 249 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 1 #