data_8RIV # _model_server_result.job_id h67blF7mALB133ItR-e2VQ _model_server_result.datetime_utc '2025-01-10 12:54:03' _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 8riv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"X","auth_seq_id":402}' # _entry.id 8RIV # _exptl.entry_id 8RIV _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 24.305 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'MAGNESIUM ION' _entity.pdbx_number_of_molecules 5 _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 8RIV _cell.length_a 104.933 _cell.length_b 156.362 _cell.length_c 183.083 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8RIV _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall 'P 2ac 2ab' _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA _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 H N N ? 6 K N N ? 6 Q N N ? 6 T N N ? 6 X 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 metalc ? metalc1 A OD1 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.218 ? metalc ? metalc2 A OG1 THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.446 ? metalc ? metalc3 A O GLY 44 A GLY 44 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.009 ? metalc ? metalc4 A OE1 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.224 ? metalc ? metalc5 G O1G GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.916 ? metalc ? metalc6 G O1B GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.494 ? metalc ? metalc7 H MG MG . A MG 502 1_555 Y O HOH . A HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.156 ? metalc ? metalc8 H MG MG . A MG 502 1_555 Y O HOH . A HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.816 ? metalc ? metalc9 H MG MG . A MG 502 1_555 Y O HOH . A HOH 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.945 ? metalc ? metalc10 B OE1 GLN 11 B GLN 11 1_555 K MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.249 ? metalc ? metalc11 J O1A GDP . B GDP 501 1_555 K MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.785 ? metalc ? metalc12 K MG MG . B MG 502 1_555 Z O HOH . B HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.873 ? metalc ? metalc13 K MG MG . B MG 502 1_555 Z O HOH . B HOH 622 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.613 ? metalc ? metalc14 C OD1 ASP 39 C ASP 39 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.457 ? metalc ? metalc15 C OD2 ASP 39 C ASP 39 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.38 ? metalc ? metalc16 C O THR 41 C THR 41 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.466 ? metalc ? metalc17 C OG1 THR 41 C THR 41 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.123 ? metalc ? metalc18 C O GLY 44 C GLY 44 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.428 ? metalc ? metalc19 C OE1 GLU 55 C GLU 55 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.534 ? metalc ? metalc20 C OE2 GLU 55 C GLU 55 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.191 ? metalc ? metalc21 C OE2 GLU 71 C GLU 71 1_555 Q MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.848 ? metalc ? metalc22 P O1G GTP . C GTP 501 1_555 Q MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.16 ? metalc ? metalc23 P O1B GTP . C GTP 501 1_555 Q MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.24 ? metalc ? metalc24 Q MG MG . C MG 502 1_555 AA O HOH . C HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? metalc ? metalc25 Q MG MG . C MG 502 1_555 AA O HOH . C HOH 609 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.314 ? metalc ? metalc26 Q MG MG . C MG 502 1_555 AA O HOH . C HOH 628 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.401 ? metalc ? metalc27 Q MG MG . C MG 502 1_555 AA O HOH . C HOH 637 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? metalc ? metalc28 D OE1 GLN 11 D GLN 11 1_555 T MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.882 ? metalc ? metalc29 T MG MG . D MG 502 1_555 BA O HOH . D HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? metalc ? metalc30 E OD2 ASP 42 E ASP 44 1_555 V CA CA . E CA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.153 ? # _chem_comp.formula 'Mg 2' _chem_comp.formula_weight 24.305 _chem_comp.id MG _chem_comp.mon_nstd_flag . _chem_comp.name 'MAGNESIUM ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 8RIV _atom_sites.fract_transf_matrix[1][1] 0.00953 _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] 0.006395 _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] 0.005462 _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 G 5 GTP A 1 501 501 GTP GTP . H 6 MG A 1 502 502 MG MG . I 7 CA A 1 503 503 CA CA . J 8 GDP B 1 501 501 GDP GDP . K 6 MG B 1 502 502 MG MG . L 9 MES B 1 503 504 MES MES . M 10 A1H01 B 1 504 505 A1H01 LIG . N 11 IMD B 1 505 506 IMD IMD . O 11 IMD B 1 506 507 IMD IMD . P 5 GTP C 1 501 501 GTP GTP . Q 6 MG C 1 502 502 MG MG . R 7 CA C 1 503 503 CA CA . S 8 GDP D 1 501 501 GDP GDP . T 6 MG D 1 502 502 MG MG . U 10 A1H01 D 1 503 505 A1H01 LIG . V 7 CA E 1 201 504 CA CA . W 12 ACP F 1 401 401 ACP ACP . X 6 MG F 1 402 402 MG MG . Y 13 HOH A 1 601 33 HOH HOH . Y 13 HOH A 2 602 31 HOH HOH . Y 13 HOH A 3 603 19 HOH HOH . Y 13 HOH A 4 604 20 HOH HOH . Y 13 HOH A 5 605 28 HOH HOH . Y 13 HOH A 6 606 167 HOH HOH . Y 13 HOH A 7 607 166 HOH HOH . Y 13 HOH A 8 608 23 HOH HOH . Y 13 HOH A 9 609 161 HOH HOH . Y 13 HOH A 10 610 179 HOH HOH . Y 13 HOH A 11 611 154 HOH HOH . Z 13 HOH B 1 601 78 HOH HOH . Z 13 HOH B 2 602 32 HOH HOH . Z 13 HOH B 3 603 196 HOH HOH . Z 13 HOH B 4 604 26 HOH HOH . Z 13 HOH B 5 605 110 HOH HOH . Z 13 HOH B 6 606 84 HOH HOH . Z 13 HOH B 7 607 17 HOH HOH . Z 13 HOH B 8 608 94 HOH HOH . Z 13 HOH B 9 609 163 HOH HOH . Z 13 HOH B 10 610 8 HOH HOH . Z 13 HOH B 11 611 48 HOH HOH . Z 13 HOH B 12 612 126 HOH HOH . Z 13 HOH B 13 613 93 HOH HOH . Z 13 HOH B 14 614 16 HOH HOH . Z 13 HOH B 15 615 182 HOH HOH . Z 13 HOH B 16 616 160 HOH HOH . Z 13 HOH B 17 617 43 HOH HOH . Z 13 HOH B 18 618 90 HOH HOH . Z 13 HOH B 19 619 92 HOH HOH . Z 13 HOH B 20 620 195 HOH HOH . Z 13 HOH B 21 621 103 HOH HOH . Z 13 HOH B 22 622 173 HOH HOH . Z 13 HOH B 23 623 142 HOH HOH . Z 13 HOH B 24 624 186 HOH HOH . Z 13 HOH B 25 625 185 HOH HOH . Z 13 HOH B 26 626 149 HOH HOH . AA 13 HOH C 1 601 13 HOH HOH . AA 13 HOH C 2 602 5 HOH HOH . AA 13 HOH C 3 603 141 HOH HOH . AA 13 HOH C 4 604 47 HOH HOH . AA 13 HOH C 5 605 25 HOH HOH . AA 13 HOH C 6 606 108 HOH HOH . AA 13 HOH C 7 607 21 HOH HOH . AA 13 HOH C 8 608 7 HOH HOH . AA 13 HOH C 9 609 193 HOH HOH . AA 13 HOH C 10 610 159 HOH HOH . AA 13 HOH C 11 611 143 HOH HOH . AA 13 HOH C 12 612 60 HOH HOH . AA 13 HOH C 13 613 69 HOH HOH . AA 13 HOH C 14 614 42 HOH HOH . AA 13 HOH C 15 615 98 HOH HOH . AA 13 HOH C 16 616 9 HOH HOH . AA 13 HOH C 17 617 80 HOH HOH . AA 13 HOH C 18 618 41 HOH HOH . AA 13 HOH C 19 619 57 HOH HOH . AA 13 HOH C 20 620 37 HOH HOH . AA 13 HOH C 21 621 61 HOH HOH . AA 13 HOH C 22 622 38 HOH HOH . AA 13 HOH C 23 623 82 HOH HOH . AA 13 HOH C 24 624 130 HOH HOH . AA 13 HOH C 25 625 175 HOH HOH . AA 13 HOH C 26 626 3 HOH HOH . AA 13 HOH C 27 627 121 HOH HOH . AA 13 HOH C 28 628 192 HOH HOH . AA 13 HOH C 29 629 6 HOH HOH . AA 13 HOH C 30 630 129 HOH HOH . AA 13 HOH C 31 631 45 HOH HOH . AA 13 HOH C 32 632 91 HOH HOH . AA 13 HOH C 33 633 83 HOH HOH . AA 13 HOH C 34 634 165 HOH HOH . AA 13 HOH C 35 635 134 HOH HOH . AA 13 HOH C 36 636 29 HOH HOH . AA 13 HOH C 37 637 15 HOH HOH . AA 13 HOH C 38 638 148 HOH HOH . AA 13 HOH C 39 639 14 HOH HOH . AA 13 HOH C 40 640 12 HOH HOH . AA 13 HOH C 41 641 10 HOH HOH . AA 13 HOH C 42 642 30 HOH HOH . AA 13 HOH C 43 643 58 HOH HOH . AA 13 HOH C 44 644 73 HOH HOH . AA 13 HOH C 45 645 106 HOH HOH . AA 13 HOH C 46 646 127 HOH HOH . AA 13 HOH C 47 647 59 HOH HOH . AA 13 HOH C 48 648 71 HOH HOH . AA 13 HOH C 49 649 204 HOH HOH . AA 13 HOH C 50 650 44 HOH HOH . AA 13 HOH C 51 651 112 HOH HOH . AA 13 HOH C 52 652 18 HOH HOH . AA 13 HOH C 53 653 102 HOH HOH . AA 13 HOH C 54 654 138 HOH HOH . AA 13 HOH C 55 655 115 HOH HOH . AA 13 HOH C 56 656 151 HOH HOH . AA 13 HOH C 57 657 75 HOH HOH . AA 13 HOH C 58 658 51 HOH HOH . AA 13 HOH C 59 659 70 HOH HOH . AA 13 HOH C 60 660 125 HOH HOH . AA 13 HOH C 61 661 203 HOH HOH . AA 13 HOH C 62 662 95 HOH HOH . AA 13 HOH C 63 663 117 HOH HOH . AA 13 HOH C 64 664 65 HOH HOH . AA 13 HOH C 65 665 49 HOH HOH . AA 13 HOH C 66 666 147 HOH HOH . AA 13 HOH C 67 667 24 HOH HOH . AA 13 HOH C 68 668 197 HOH HOH . AA 13 HOH C 69 669 172 HOH HOH . AA 13 HOH C 70 670 145 HOH HOH . AA 13 HOH C 71 671 34 HOH HOH . AA 13 HOH C 72 672 140 HOH HOH . AA 13 HOH C 73 673 67 HOH HOH . BA 13 HOH D 1 601 198 HOH HOH . BA 13 HOH D 2 602 199 HOH HOH . CA 13 HOH E 1 301 116 HOH HOH . CA 13 HOH E 2 302 35 HOH HOH . CA 13 HOH E 3 303 100 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol MG _atom_site.label_atom_id MG _atom_site.label_comp_id MG _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id X _atom_site.label_entity_id 6 _atom_site.Cartn_x 9.602 _atom_site.Cartn_y 43.929 _atom_site.Cartn_z 92.954 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 174.98 _atom_site.pdbx_formal_charge 2 _atom_site.auth_atom_id MG _atom_site.auth_comp_id MG _atom_site.auth_seq_id 402 _atom_site.auth_asym_id F _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 86 _model_server_stats.parse_time_ms 25 _model_server_stats.create_model_time_ms 58 _model_server_stats.query_time_ms 395 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 1 #