data_1NBM # _model_server_result.job_id sTMsMEeG_Ax-qPI6XGbCYg _model_server_result.datetime_utc '2024-11-24 08:44:09' _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 1nbm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"P","auth_seq_id":602}' # _entry.id 1NBM # _exptl.entry_id 1NBM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 94.971 _entity.id 8 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHATE 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 1NBM _cell.length_a 281 _cell.length_b 106.6 _cell.length_c 138.8 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1NBM _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details heptameric _pdbx_struct_assembly.oligomeric_count 7 _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 _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 8 _struct_asym.id P _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 covale ? covale1 E C ILE 314 E ILE 310 1_555 E N TYN 315 E TYN 311 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale2 E C TYN 315 E TYN 311 1_555 E N VAL 316 E VAL 312 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? metalc ? metalc1 A OG1 THR 176 A THR 176 1_555 H MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.645 ? metalc ? metalc2 A OE1 GLN 208 A GLN 208 1_555 H MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.846 ? metalc ? metalc3 I O2G ATP . A ATP 600 1_555 H MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.858 ? metalc ? metalc4 B OG1 THR 176 B THR 176 1_555 J MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.658 ? metalc ? metalc5 B OE1 GLN 208 B GLN 208 1_555 J MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.088 ? metalc ? metalc6 K O2G ATP . B ATP 600 1_555 J MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.092 ? metalc ? metalc7 K O2B ATP . B ATP 600 1_555 J MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.612 ? metalc ? metalc8 C OG1 THR 176 C THR 176 1_555 L MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.621 ? metalc ? metalc9 M O2G ATP . C ATP 600 1_555 L MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.763 ? metalc ? metalc10 M O2B ATP . C ATP 600 1_555 L MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.793 ? metalc ? metalc11 D OG1 THR 167 D THR 163 1_555 N MG MG . D MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.641 ? metalc ? metalc12 O O2B ADP . D ADP 600 1_555 N MG MG . D MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.696 ? metalc ? metalc13 N MG MG . D MG 601 1_555 V O HOH . D HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.666 ? metalc ? metalc14 F OG1 THR 167 F THR 163 1_555 Q MG MG . F MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.621 ? metalc ? metalc15 R O2G ATP . F ATP 600 1_555 Q MG MG . F MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.856 ? metalc ? metalc16 R O2B ATP . F ATP 600 1_555 Q MG MG . F MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.256 ? # _chem_comp.formula 'O4 P -3' _chem_comp.formula_weight 94.971 _chem_comp.id PO4 _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHATE ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag P O1 PO4 doub 353 n n P O2 PO4 sing 354 n n P O3 PO4 sing 355 n n P O4 PO4 sing 356 n n # _atom_sites.entry_id 1NBM _atom_sites.fract_transf_matrix[1][1] 0.003559 _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] 0.009381 _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] 0.007205 _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 H 5 MG A 1 601 601 MG MG . I 6 ATP A 1 600 600 ATP ATP . J 5 MG B 1 601 601 MG MG . K 6 ATP B 1 600 600 ATP ATP . L 5 MG C 1 601 601 MG MG . M 6 ATP C 1 600 600 ATP ATP . N 5 MG D 1 601 601 MG MG . O 7 ADP D 1 600 600 ADP ADP . P 8 PO4 E 1 602 602 PO4 PO4 . Q 5 MG F 1 601 601 MG MG . R 6 ATP F 1 600 600 ATP ATP . S 9 HOH A 1 602 1 HOH HOH . S 9 HOH A 2 603 3 HOH HOH . S 9 HOH A 3 604 4 HOH HOH . S 9 HOH A 4 605 5 HOH HOH . S 9 HOH A 5 606 6 HOH HOH . S 9 HOH A 6 607 7 HOH HOH . S 9 HOH A 7 608 8 HOH HOH . S 9 HOH A 8 609 10 HOH HOH . S 9 HOH A 9 610 11 HOH HOH . S 9 HOH A 10 611 12 HOH HOH . S 9 HOH A 11 612 13 HOH HOH . S 9 HOH A 12 613 14 HOH HOH . S 9 HOH A 13 614 15 HOH HOH . S 9 HOH A 14 615 16 HOH HOH . S 9 HOH A 15 616 18 HOH HOH . S 9 HOH A 16 617 19 HOH HOH . S 9 HOH A 17 618 20 HOH HOH . S 9 HOH A 18 619 21 HOH HOH . S 9 HOH A 19 620 97 HOH HOH . S 9 HOH A 20 621 98 HOH HOH . S 9 HOH A 21 622 99 HOH HOH . S 9 HOH A 22 623 100 HOH HOH . S 9 HOH A 23 624 101 HOH HOH . S 9 HOH A 24 625 102 HOH HOH . S 9 HOH A 25 626 103 HOH HOH . S 9 HOH A 26 627 121 HOH HOH . S 9 HOH A 27 628 129 HOH HOH . S 9 HOH A 28 629 130 HOH HOH . S 9 HOH A 29 630 131 HOH HOH . S 9 HOH A 30 631 132 HOH HOH . S 9 HOH A 31 632 133 HOH HOH . S 9 HOH A 32 633 138 HOH HOH . S 9 HOH A 33 634 149 HOH HOH . S 9 HOH A 34 635 157 HOH HOH . S 9 HOH A 35 636 163 HOH HOH . T 9 HOH B 1 602 42 HOH HOH . T 9 HOH B 2 603 43 HOH HOH . T 9 HOH B 3 604 44 HOH HOH . T 9 HOH B 4 605 45 HOH HOH . T 9 HOH B 5 606 46 HOH HOH . T 9 HOH B 6 607 48 HOH HOH . T 9 HOH B 7 608 50 HOH HOH . T 9 HOH B 8 609 51 HOH HOH . T 9 HOH B 9 610 53 HOH HOH . T 9 HOH B 10 611 54 HOH HOH . T 9 HOH B 11 612 55 HOH HOH . T 9 HOH B 12 613 56 HOH HOH . T 9 HOH B 13 614 57 HOH HOH . T 9 HOH B 14 615 58 HOH HOH . T 9 HOH B 15 616 59 HOH HOH . T 9 HOH B 16 617 60 HOH HOH . T 9 HOH B 17 618 61 HOH HOH . T 9 HOH B 18 619 80 HOH HOH . T 9 HOH B 19 620 105 HOH HOH . T 9 HOH B 20 621 106 HOH HOH . T 9 HOH B 21 622 107 HOH HOH . T 9 HOH B 22 623 108 HOH HOH . T 9 HOH B 23 624 109 HOH HOH . T 9 HOH B 24 625 110 HOH HOH . T 9 HOH B 25 626 111 HOH HOH . T 9 HOH B 26 627 112 HOH HOH . T 9 HOH B 27 628 134 HOH HOH . T 9 HOH B 28 629 135 HOH HOH . T 9 HOH B 29 630 136 HOH HOH . T 9 HOH B 30 631 137 HOH HOH . T 9 HOH B 31 632 150 HOH HOH . T 9 HOH B 32 633 158 HOH HOH . T 9 HOH B 33 634 160 HOH HOH . T 9 HOH B 34 635 164 HOH HOH . U 9 HOH C 1 602 23 HOH HOH . U 9 HOH C 2 603 24 HOH HOH . U 9 HOH C 3 604 26 HOH HOH . U 9 HOH C 4 605 27 HOH HOH . U 9 HOH C 5 606 29 HOH HOH . U 9 HOH C 6 607 30 HOH HOH . U 9 HOH C 7 608 31 HOH HOH . U 9 HOH C 8 609 32 HOH HOH . U 9 HOH C 9 610 33 HOH HOH . U 9 HOH C 10 611 34 HOH HOH . U 9 HOH C 11 612 35 HOH HOH . U 9 HOH C 12 613 37 HOH HOH . U 9 HOH C 13 614 38 HOH HOH . U 9 HOH C 14 615 39 HOH HOH . U 9 HOH C 15 616 40 HOH HOH . U 9 HOH C 16 617 41 HOH HOH . U 9 HOH C 17 618 64 HOH HOH . U 9 HOH C 18 619 91 HOH HOH . U 9 HOH C 19 620 113 HOH HOH . U 9 HOH C 20 621 114 HOH HOH . U 9 HOH C 21 622 115 HOH HOH . U 9 HOH C 22 623 139 HOH HOH . U 9 HOH C 23 624 140 HOH HOH . U 9 HOH C 24 625 142 HOH HOH . U 9 HOH C 25 626 143 HOH HOH . U 9 HOH C 26 627 144 HOH HOH . U 9 HOH C 27 628 145 HOH HOH . U 9 HOH C 28 629 153 HOH HOH . V 9 HOH D 1 602 25 HOH HOH . V 9 HOH D 2 603 28 HOH HOH . V 9 HOH D 3 604 62 HOH HOH . V 9 HOH D 4 605 63 HOH HOH . V 9 HOH D 5 606 65 HOH HOH . V 9 HOH D 6 607 66 HOH HOH . V 9 HOH D 7 608 67 HOH HOH . V 9 HOH D 8 609 68 HOH HOH . V 9 HOH D 9 610 69 HOH HOH . V 9 HOH D 10 611 104 HOH HOH . V 9 HOH D 11 612 116 HOH HOH . V 9 HOH D 12 613 117 HOH HOH . V 9 HOH D 13 614 118 HOH HOH . V 9 HOH D 14 615 119 HOH HOH . V 9 HOH D 15 616 120 HOH HOH . V 9 HOH D 16 617 146 HOH HOH . V 9 HOH D 17 618 147 HOH HOH . V 9 HOH D 18 619 148 HOH HOH . V 9 HOH D 19 620 162 HOH HOH . W 9 HOH E 1 603 2 HOH HOH . W 9 HOH E 2 604 9 HOH HOH . W 9 HOH E 3 605 17 HOH HOH . W 9 HOH E 4 606 52 HOH HOH . W 9 HOH E 5 607 70 HOH HOH . W 9 HOH E 6 608 71 HOH HOH . W 9 HOH E 7 609 72 HOH HOH . W 9 HOH E 8 610 73 HOH HOH . W 9 HOH E 9 611 74 HOH HOH . W 9 HOH E 10 612 75 HOH HOH . W 9 HOH E 11 613 76 HOH HOH . W 9 HOH E 12 614 77 HOH HOH . W 9 HOH E 13 615 78 HOH HOH . W 9 HOH E 14 616 79 HOH HOH . W 9 HOH E 15 617 81 HOH HOH . W 9 HOH E 16 618 122 HOH HOH . W 9 HOH E 17 619 123 HOH HOH . W 9 HOH E 18 620 124 HOH HOH . W 9 HOH E 19 621 151 HOH HOH . W 9 HOH E 20 622 159 HOH HOH . W 9 HOH E 21 623 161 HOH HOH . X 9 HOH F 1 602 22 HOH HOH . X 9 HOH F 2 603 36 HOH HOH . X 9 HOH F 3 604 47 HOH HOH . X 9 HOH F 4 605 49 HOH HOH . X 9 HOH F 5 606 82 HOH HOH . X 9 HOH F 6 607 83 HOH HOH . X 9 HOH F 7 608 84 HOH HOH . X 9 HOH F 8 609 85 HOH HOH . X 9 HOH F 9 610 86 HOH HOH . X 9 HOH F 10 611 87 HOH HOH . X 9 HOH F 11 612 88 HOH HOH . X 9 HOH F 12 613 89 HOH HOH . X 9 HOH F 13 614 90 HOH HOH . X 9 HOH F 14 615 92 HOH HOH . X 9 HOH F 15 616 93 HOH HOH . X 9 HOH F 16 617 94 HOH HOH . X 9 HOH F 17 618 95 HOH HOH . X 9 HOH F 18 619 96 HOH HOH . X 9 HOH F 19 620 125 HOH HOH . X 9 HOH F 20 621 126 HOH HOH . X 9 HOH F 21 622 127 HOH HOH . X 9 HOH F 22 623 128 HOH HOH . X 9 HOH F 23 624 141 HOH HOH . X 9 HOH F 24 625 152 HOH HOH . X 9 HOH F 25 626 154 HOH HOH . X 9 HOH F 26 627 155 HOH HOH . Y 9 HOH G 1 273 156 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 P P PO4 . . . P 8 99.207 98.35 50.59 1 100 ? P PO4 602 E 1 HETATM 2 O O1 PO4 . . . P 8 99.955 99.618 50.45 1 100 ? O1 PO4 602 E 1 HETATM 3 O O2 PO4 . . . P 8 99.953 97.253 49.94 1 95.18 ? O2 PO4 602 E 1 HETATM 4 O O3 PO4 . . . P 8 99.03 98.043 52.027 1 100 ? O3 PO4 602 E 1 HETATM 5 O O4 PO4 . . . P 8 97.877 98.488 49.958 1 100 ? O4 PO4 602 E 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 45 _model_server_stats.query_time_ms 286 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 5 #