data_5MP8 # _model_server_result.job_id B15SlGQ0rS_IGLqoa1KdPw _model_server_result.datetime_utc '2024-11-24 03:38:25' _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 5mp8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":404}' # _entry.id 5MP8 # _exptl.entry_id 5MP8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 2 _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 5MP8 _cell.length_a 65.17 _cell.length_b 68.34 _cell.length_c 331.45 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5MP8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,F,G,H,I,O 1 1 B,J,K,L,M,N,P 2 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 ? 3 F N N ? 3 K 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 ASN 184 A ASN 161 1_555 I MG MG . A MG 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.497 ? metalc ? metalc2 A OD2 ASP 198 A ASP 175 1_555 I MG MG . A MG 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? metalc ? metalc3 F O1B ADP . A ADP 404 1_555 I MG MG . A MG 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.64 ? metalc ? metalc4 F O1A ADP . A ADP 404 1_555 I MG MG . A MG 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.517 ? # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id ADP _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-5'-DIPHOSPHATE" _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 PB O1B ADP doub 7 n n PB O2B ADP sing 8 n n PB O3B ADP sing 9 n n PB O3A ADP sing 10 n n O2B HOB2 ADP sing 11 n n O3B HOB3 ADP sing 12 n n PA O1A ADP doub 13 n n PA O2A ADP sing 14 n n PA O3A ADP sing 15 n n PA O5' ADP sing 16 n n O2A HOA2 ADP sing 17 n n O5' C5' ADP sing 18 n n C5' C4' ADP sing 19 n n C5' "H5'1" ADP sing 20 n n C5' "H5'2" ADP sing 21 n n C4' O4' ADP sing 22 n n C4' C3' ADP sing 23 n n C4' H4' ADP sing 24 n n O4' C1' ADP sing 25 n n C3' O3' ADP sing 26 n n C3' C2' ADP sing 27 n n C3' H3' ADP sing 28 n n O3' HO3' ADP sing 29 n n C2' O2' ADP sing 30 n n C2' C1' ADP sing 31 n n C2' H2' ADP sing 32 n n O2' HO2' ADP sing 33 n n C1' N9 ADP sing 34 n n C1' H1' ADP sing 35 n n N9 C8 ADP sing 36 n y N9 C4 ADP sing 37 n y C8 N7 ADP doub 38 n y C8 H8 ADP sing 39 n n N7 C5 ADP sing 40 n y C5 C6 ADP sing 41 n y C5 C4 ADP doub 42 n y C6 N6 ADP sing 43 n n C6 N1 ADP doub 44 n y N6 HN61 ADP sing 45 n n N6 HN62 ADP sing 46 n n N1 C2 ADP sing 47 n y C2 N3 ADP doub 48 n y C2 H2 ADP sing 49 n n N3 C4 ADP sing 50 n y # _atom_sites.entry_id 5MP8 _atom_sites.fract_transf_matrix[1][1] 0.015344 _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] 0.014633 _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] 0.003017 _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 2 PO4 A 1 401 1 PO4 PO4 . D 2 PO4 A 1 402 2 PO4 PO4 . E 2 PO4 A 1 403 4 PO4 PO4 . F 3 ADP A 1 404 1 ADP ADP . G 4 ACT A 1 405 2 ACT ACT . H 5 RKN A 1 406 1 RKN C03 . I 6 MG A 1 407 1 MG MG . J 2 PO4 B 1 401 3 PO4 PO4 . K 3 ADP B 1 402 2 ADP ADP . L 4 ACT B 1 403 1 ACT ACT . M 4 ACT B 1 404 3 ACT ACT . N 5 RKN B 1 405 2 RKN C03 . O 7 HOH A 1 501 248 HOH HOH . O 7 HOH A 2 502 249 HOH HOH . O 7 HOH A 3 503 28 HOH HOH . O 7 HOH A 4 504 13 HOH HOH . O 7 HOH A 5 505 24 HOH HOH . O 7 HOH A 6 506 172 HOH HOH . O 7 HOH A 7 507 245 HOH HOH . O 7 HOH A 8 508 53 HOH HOH . O 7 HOH A 9 509 36 HOH HOH . O 7 HOH A 10 510 99 HOH HOH . O 7 HOH A 11 511 48 HOH HOH . O 7 HOH A 12 512 242 HOH HOH . O 7 HOH A 13 513 219 HOH HOH . O 7 HOH A 14 514 30 HOH HOH . O 7 HOH A 15 515 119 HOH HOH . O 7 HOH A 16 516 20 HOH HOH . O 7 HOH A 17 517 49 HOH HOH . O 7 HOH A 18 518 176 HOH HOH . O 7 HOH A 19 519 215 HOH HOH . O 7 HOH A 20 520 42 HOH HOH . O 7 HOH A 21 521 206 HOH HOH . O 7 HOH A 22 522 18 HOH HOH . O 7 HOH A 23 523 3 HOH HOH . O 7 HOH A 24 524 122 HOH HOH . O 7 HOH A 25 525 5 HOH HOH . O 7 HOH A 26 526 65 HOH HOH . O 7 HOH A 27 527 19 HOH HOH . O 7 HOH A 28 528 121 HOH HOH . O 7 HOH A 29 529 88 HOH HOH . O 7 HOH A 30 530 102 HOH HOH . O 7 HOH A 31 531 68 HOH HOH . O 7 HOH A 32 532 45 HOH HOH . O 7 HOH A 33 533 92 HOH HOH . O 7 HOH A 34 534 223 HOH HOH . O 7 HOH A 35 535 138 HOH HOH . O 7 HOH A 36 536 100 HOH HOH . O 7 HOH A 37 537 237 HOH HOH . O 7 HOH A 38 538 40 HOH HOH . O 7 HOH A 39 539 93 HOH HOH . O 7 HOH A 40 540 29 HOH HOH . O 7 HOH A 41 541 6 HOH HOH . O 7 HOH A 42 542 37 HOH HOH . O 7 HOH A 43 543 143 HOH HOH . O 7 HOH A 44 544 10 HOH HOH . O 7 HOH A 45 545 209 HOH HOH . O 7 HOH A 46 546 35 HOH HOH . O 7 HOH A 47 547 27 HOH HOH . O 7 HOH A 48 548 210 HOH HOH . O 7 HOH A 49 549 11 HOH HOH . O 7 HOH A 50 550 12 HOH HOH . O 7 HOH A 51 551 4 HOH HOH . O 7 HOH A 52 552 23 HOH HOH . O 7 HOH A 53 553 34 HOH HOH . O 7 HOH A 54 554 22 HOH HOH . O 7 HOH A 55 555 147 HOH HOH . O 7 HOH A 56 556 67 HOH HOH . O 7 HOH A 57 557 145 HOH HOH . O 7 HOH A 58 558 41 HOH HOH . O 7 HOH A 59 559 8 HOH HOH . O 7 HOH A 60 560 243 HOH HOH . O 7 HOH A 61 561 189 HOH HOH . O 7 HOH A 62 562 222 HOH HOH . O 7 HOH A 63 563 184 HOH HOH . O 7 HOH A 64 564 46 HOH HOH . O 7 HOH A 65 565 128 HOH HOH . O 7 HOH A 66 566 96 HOH HOH . O 7 HOH A 67 567 69 HOH HOH . O 7 HOH A 68 568 200 HOH HOH . O 7 HOH A 69 569 194 HOH HOH . O 7 HOH A 70 570 82 HOH HOH . O 7 HOH A 71 571 60 HOH HOH . O 7 HOH A 72 572 50 HOH HOH . O 7 HOH A 73 573 202 HOH HOH . O 7 HOH A 74 574 86 HOH HOH . O 7 HOH A 75 575 232 HOH HOH . O 7 HOH A 76 576 146 HOH HOH . O 7 HOH A 77 577 191 HOH HOH . O 7 HOH A 78 578 17 HOH HOH . O 7 HOH A 79 579 43 HOH HOH . O 7 HOH A 80 580 75 HOH HOH . O 7 HOH A 81 581 187 HOH HOH . O 7 HOH A 82 582 130 HOH HOH . O 7 HOH A 83 583 150 HOH HOH . O 7 HOH A 84 584 124 HOH HOH . O 7 HOH A 85 585 94 HOH HOH . O 7 HOH A 86 586 66 HOH HOH . O 7 HOH A 87 587 225 HOH HOH . O 7 HOH A 88 588 134 HOH HOH . O 7 HOH A 89 589 108 HOH HOH . O 7 HOH A 90 590 126 HOH HOH . O 7 HOH A 91 591 218 HOH HOH . O 7 HOH A 92 592 123 HOH HOH . O 7 HOH A 93 593 203 HOH HOH . O 7 HOH A 94 594 111 HOH HOH . O 7 HOH A 95 595 141 HOH HOH . O 7 HOH A 96 596 166 HOH HOH . O 7 HOH A 97 597 58 HOH HOH . O 7 HOH A 98 598 112 HOH HOH . O 7 HOH A 99 599 113 HOH HOH . O 7 HOH A 100 600 161 HOH HOH . O 7 HOH A 101 601 205 HOH HOH . O 7 HOH A 102 602 182 HOH HOH . O 7 HOH A 103 603 91 HOH HOH . O 7 HOH A 104 604 180 HOH HOH . O 7 HOH A 105 605 107 HOH HOH . O 7 HOH A 106 606 231 HOH HOH . O 7 HOH A 107 607 240 HOH HOH . O 7 HOH A 108 608 98 HOH HOH . O 7 HOH A 109 609 103 HOH HOH . O 7 HOH A 110 610 83 HOH HOH . O 7 HOH A 111 611 229 HOH HOH . O 7 HOH A 112 612 109 HOH HOH . O 7 HOH A 113 613 201 HOH HOH . O 7 HOH A 114 614 79 HOH HOH . O 7 HOH A 115 615 136 HOH HOH . O 7 HOH A 116 616 227 HOH HOH . O 7 HOH A 117 617 236 HOH HOH . O 7 HOH A 118 618 199 HOH HOH . O 7 HOH A 119 619 144 HOH HOH . O 7 HOH A 120 620 156 HOH HOH . P 7 HOH B 1 501 80 HOH HOH . P 7 HOH B 2 502 52 HOH HOH . P 7 HOH B 3 503 246 HOH HOH . P 7 HOH B 4 504 125 HOH HOH . P 7 HOH B 5 505 195 HOH HOH . P 7 HOH B 6 506 44 HOH HOH . P 7 HOH B 7 507 78 HOH HOH . P 7 HOH B 8 508 174 HOH HOH . P 7 HOH B 9 509 171 HOH HOH . P 7 HOH B 10 510 33 HOH HOH . P 7 HOH B 11 511 179 HOH HOH . P 7 HOH B 12 512 168 HOH HOH . P 7 HOH B 13 513 129 HOH HOH . P 7 HOH B 14 514 181 HOH HOH . P 7 HOH B 15 515 175 HOH HOH . P 7 HOH B 16 516 220 HOH HOH . P 7 HOH B 17 517 154 HOH HOH . P 7 HOH B 18 518 71 HOH HOH . P 7 HOH B 19 519 226 HOH HOH . P 7 HOH B 20 520 115 HOH HOH . P 7 HOH B 21 521 211 HOH HOH . P 7 HOH B 22 522 31 HOH HOH . P 7 HOH B 23 523 170 HOH HOH . P 7 HOH B 24 524 204 HOH HOH . P 7 HOH B 25 525 238 HOH HOH . P 7 HOH B 26 526 101 HOH HOH . P 7 HOH B 27 527 217 HOH HOH . P 7 HOH B 28 528 221 HOH HOH . P 7 HOH B 29 529 25 HOH HOH . P 7 HOH B 30 530 47 HOH HOH . P 7 HOH B 31 531 135 HOH HOH . P 7 HOH B 32 532 55 HOH HOH . P 7 HOH B 33 533 183 HOH HOH . P 7 HOH B 34 534 127 HOH HOH . P 7 HOH B 35 535 59 HOH HOH . P 7 HOH B 36 536 140 HOH HOH . P 7 HOH B 37 537 196 HOH HOH . P 7 HOH B 38 538 62 HOH HOH . P 7 HOH B 39 539 224 HOH HOH . P 7 HOH B 40 540 244 HOH HOH . P 7 HOH B 41 541 159 HOH HOH . P 7 HOH B 42 542 56 HOH HOH . P 7 HOH B 43 543 110 HOH HOH . P 7 HOH B 44 544 114 HOH HOH . P 7 HOH B 45 545 208 HOH HOH . P 7 HOH B 46 546 95 HOH HOH . P 7 HOH B 47 547 117 HOH HOH . P 7 HOH B 48 548 157 HOH HOH . P 7 HOH B 49 549 162 HOH HOH . P 7 HOH B 50 550 165 HOH HOH . P 7 HOH B 51 551 247 HOH HOH . P 7 HOH B 52 552 148 HOH HOH . P 7 HOH B 53 553 192 HOH HOH . P 7 HOH B 54 554 178 HOH HOH . P 7 HOH B 55 555 185 HOH HOH . P 7 HOH B 56 556 188 HOH HOH . P 7 HOH B 57 557 133 HOH HOH . P 7 HOH B 58 558 163 HOH HOH . P 7 HOH B 59 559 239 HOH HOH . P 7 HOH B 60 560 193 HOH HOH . P 7 HOH B 61 561 81 HOH HOH . P 7 HOH B 62 562 105 HOH HOH . P 7 HOH B 63 563 151 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 PB ADP . . . F 3 17.369 130.932 355.462 1 61.28 ? PB ADP 404 A 1 HETATM 2 O O1B ADP . . . F 3 16.802 131.182 354.047 1 57.59 ? O1B ADP 404 A 1 HETATM 3 O O2B ADP . . . F 3 17.964 129.536 355.42 1 65.94 ? O2B ADP 404 A 1 HETATM 4 O O3B ADP . . . F 3 18.458 131.878 355.888 1 59.8 ? O3B ADP 404 A 1 HETATM 5 P PA ADP . . . F 3 14.74 131.652 356.719 1 52.2 ? PA ADP 404 A 1 HETATM 6 O O1A ADP . . . F 3 14.372 132.634 355.643 1 53.42 ? O1A ADP 404 A 1 HETATM 7 O O2A ADP . . . F 3 14.767 132.38 358.005 1 51.99 ? O2A ADP 404 A 1 HETATM 8 O O3A ADP . . . F 3 16.131 130.898 356.475 1 58.3 ? O3A ADP 404 A 1 HETATM 9 O O5' ADP . . . F 3 13.618 130.537 356.649 1 50.46 ? O5' ADP 404 A 1 HETATM 10 C C5' ADP . . . F 3 13.287 129.803 355.452 1 50.51 ? C5' ADP 404 A 1 HETATM 11 C C4' ADP . . . F 3 11.788 129.772 355.305 1 48.36 ? C4' ADP 404 A 1 HETATM 12 O O4' ADP . . . F 3 11.173 129.378 356.555 1 46.22 ? O4' ADP 404 A 1 HETATM 13 C C3' ADP . . . F 3 11.11 131.094 354.966 1 47.85 ? C3' ADP 404 A 1 HETATM 14 O O3' ADP . . . F 3 11.269 131.501 353.61 1 50.11 ? O3' ADP 404 A 1 HETATM 15 C C2' ADP . . . F 3 9.672 130.823 355.409 1 46.6 ? C2' ADP 404 A 1 HETATM 16 O O2' ADP . . . F 3 8.948 130.037 354.461 1 46.59 ? O2' ADP 404 A 1 HETATM 17 C C1' ADP . . . F 3 9.909 130.015 356.691 1 44.43 ? C1' ADP 404 A 1 HETATM 18 N N9 ADP . . . F 3 9.909 130.819 357.913 1 41.14 ? N9 ADP 404 A 1 HETATM 19 C C8 ADP . . . F 3 10.985 131.401 358.532 1 38.45 ? C8 ADP 404 A 1 HETATM 20 N N7 ADP . . . F 3 10.676 132.109 359.592 1 35.51 ? N7 ADP 404 A 1 HETATM 21 C C5 ADP . . . F 3 9.299 131.978 359.683 1 37.65 ? C5 ADP 404 A 1 HETATM 22 C C6 ADP . . . F 3 8.362 132.441 360.63 1 39.4 ? C6 ADP 404 A 1 HETATM 23 N N6 ADP . . . F 3 8.695 133.134 361.72 1 37.3 ? N6 ADP 404 A 1 HETATM 24 N N1 ADP . . . F 3 7.067 132.081 360.461 1 40.46 ? N1 ADP 404 A 1 HETATM 25 C C2 ADP . . . F 3 6.742 131.301 359.422 1 36.36 ? C2 ADP 404 A 1 HETATM 26 N N3 ADP . . . F 3 7.536 130.804 358.472 1 39.1 ? N3 ADP 404 A 1 HETATM 27 C C4 ADP . . . F 3 8.813 131.178 358.657 1 38.61 ? C4 ADP 404 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 221 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 27 #