data_6KJM # _model_server_result.job_id vyHTtjnzmNDFWrehnPgVhA _model_server_result.datetime_utc '2024-10-10 14:25:58' _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 6kjm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":402}' # _entry.id 6KJM # _exptl.entry_id 6KJM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 347.221 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'ADENOSINE MONOPHOSPHATE' _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 120 _cell.entry_id 6KJM _cell.length_a 95.728 _cell.length_b 95.728 _cell.length_c 201.347 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6KJM _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C10 H14 N5 O7 P' _chem_comp.formula_weight 347.221 _chem_comp.id AMP _chem_comp.mon_nstd_flag . _chem_comp.name 'ADENOSINE MONOPHOSPHATE' _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 O1P AMP doub 13 n n P O2P AMP sing 14 n n P O3P AMP sing 15 n n P O5' AMP sing 16 n n O2P HOP2 AMP sing 17 n n O3P HOP3 AMP sing 18 n n O5' C5' AMP sing 19 n n C5' C4' AMP sing 20 n n C5' "H5'1" AMP sing 21 n n C5' "H5'2" AMP sing 22 n n C4' O4' AMP sing 23 n n C4' C3' AMP sing 24 n n C4' H4' AMP sing 25 n n O4' C1' AMP sing 26 n n C3' O3' AMP sing 27 n n C3' C2' AMP sing 28 n n C3' H3' AMP sing 29 n n O3' HO3' AMP sing 30 n n C2' O2' AMP sing 31 n n C2' C1' AMP sing 32 n n C2' H2' AMP sing 33 n n O2' HO2' AMP sing 34 n n C1' N9 AMP sing 35 n n C1' H1' AMP sing 36 n n N9 C8 AMP sing 37 n y N9 C4 AMP sing 38 n y C8 N7 AMP doub 39 n y C8 H8 AMP sing 40 n n N7 C5 AMP sing 41 n y C5 C6 AMP sing 42 n y C5 C4 AMP doub 43 n y C6 N6 AMP sing 44 n n C6 N1 AMP doub 45 n y N6 HN61 AMP sing 46 n n N6 HN62 AMP sing 47 n n N1 C2 AMP sing 48 n y C2 N3 AMP doub 49 n y C2 H2 AMP sing 50 n n N3 C4 AMP sing 51 n y # _atom_sites.entry_id 6KJM _atom_sites.fract_transf_matrix[1][1] 0.010446 _atom_sites.fract_transf_matrix[1][2] 0.006031 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012062 _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] 0.004967 _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 B 2 NMN A 1 401 401 NMN NMN . C 3 AMP A 1 402 501 AMP AMP . D 4 SO4 A 1 403 1 SO4 SO4 . E 4 SO4 A 1 404 2 SO4 SO4 . F 4 SO4 A 1 405 3 SO4 SO4 . G 4 SO4 A 1 406 5 SO4 SO4 . H 5 HOH A 1 501 165 HOH HOH . H 5 HOH A 2 502 27 HOH HOH . H 5 HOH A 3 503 14 HOH HOH . H 5 HOH A 4 504 158 HOH HOH . H 5 HOH A 5 505 88 HOH HOH . H 5 HOH A 6 506 38 HOH HOH . H 5 HOH A 7 507 9 HOH HOH . H 5 HOH A 8 508 8 HOH HOH . H 5 HOH A 9 509 24 HOH HOH . H 5 HOH A 10 510 18 HOH HOH . H 5 HOH A 11 511 59 HOH HOH . H 5 HOH A 12 512 16 HOH HOH . H 5 HOH A 13 513 134 HOH HOH . H 5 HOH A 14 514 80 HOH HOH . H 5 HOH A 15 515 11 HOH HOH . H 5 HOH A 16 516 147 HOH HOH . H 5 HOH A 17 517 63 HOH HOH . H 5 HOH A 18 518 7 HOH HOH . H 5 HOH A 19 519 62 HOH HOH . H 5 HOH A 20 520 19 HOH HOH . H 5 HOH A 21 521 44 HOH HOH . H 5 HOH A 22 522 32 HOH HOH . H 5 HOH A 23 523 93 HOH HOH . H 5 HOH A 24 524 26 HOH HOH . H 5 HOH A 25 525 102 HOH HOH . H 5 HOH A 26 527 39 HOH HOH . H 5 HOH A 27 528 130 HOH HOH . H 5 HOH A 28 529 6 HOH HOH . H 5 HOH A 29 530 86 HOH HOH . H 5 HOH A 30 531 5 HOH HOH . H 5 HOH A 31 532 49 HOH HOH . H 5 HOH A 32 533 77 HOH HOH . H 5 HOH A 33 534 98 HOH HOH . H 5 HOH A 34 535 28 HOH HOH . H 5 HOH A 35 536 64 HOH HOH . H 5 HOH A 36 537 82 HOH HOH . H 5 HOH A 37 538 42 HOH HOH . H 5 HOH A 38 539 121 HOH HOH . H 5 HOH A 39 540 45 HOH HOH . H 5 HOH A 40 541 4 HOH HOH . H 5 HOH A 41 542 31 HOH HOH . H 5 HOH A 42 543 54 HOH HOH . H 5 HOH A 43 544 75 HOH HOH . H 5 HOH A 44 545 70 HOH HOH . H 5 HOH A 45 546 17 HOH HOH . H 5 HOH A 46 547 35 HOH HOH . H 5 HOH A 47 548 73 HOH HOH . H 5 HOH A 48 549 68 HOH HOH . H 5 HOH A 49 550 20 HOH HOH . H 5 HOH A 50 552 36 HOH HOH . H 5 HOH A 51 553 12 HOH HOH . H 5 HOH A 52 554 72 HOH HOH . H 5 HOH A 53 555 114 HOH HOH . H 5 HOH A 54 556 83 HOH HOH . H 5 HOH A 55 557 53 HOH HOH . H 5 HOH A 56 558 90 HOH HOH . H 5 HOH A 57 559 47 HOH HOH . H 5 HOH A 58 560 141 HOH HOH . H 5 HOH A 59 561 116 HOH HOH . H 5 HOH A 60 562 34 HOH HOH . H 5 HOH A 61 563 43 HOH HOH . H 5 HOH A 62 564 183 HOH HOH . H 5 HOH A 63 565 128 HOH HOH . H 5 HOH A 64 566 122 HOH HOH . H 5 HOH A 65 567 85 HOH HOH . H 5 HOH A 66 568 52 HOH HOH . H 5 HOH A 67 569 184 HOH HOH . H 5 HOH A 68 570 136 HOH HOH . H 5 HOH A 69 571 69 HOH HOH . H 5 HOH A 70 572 182 HOH HOH . H 5 HOH A 71 573 57 HOH HOH . H 5 HOH A 72 574 135 HOH HOH . H 5 HOH A 73 575 21 HOH HOH . H 5 HOH A 74 576 125 HOH HOH . H 5 HOH A 75 577 87 HOH HOH . H 5 HOH A 76 578 100 HOH HOH . H 5 HOH A 77 579 171 HOH HOH . H 5 HOH A 78 580 76 HOH HOH . H 5 HOH A 79 581 110 HOH HOH . H 5 HOH A 80 582 143 HOH HOH . H 5 HOH A 81 583 67 HOH HOH . H 5 HOH A 82 584 159 HOH HOH . H 5 HOH A 83 585 176 HOH HOH . H 5 HOH A 84 586 23 HOH HOH . H 5 HOH A 85 587 65 HOH HOH . H 5 HOH A 86 588 10 HOH HOH . H 5 HOH A 87 589 3 HOH HOH . H 5 HOH A 88 590 50 HOH HOH . H 5 HOH A 89 591 160 HOH HOH . H 5 HOH A 90 593 60 HOH HOH . H 5 HOH A 91 594 58 HOH HOH . H 5 HOH A 92 596 81 HOH HOH . H 5 HOH A 93 597 163 HOH HOH . H 5 HOH A 94 598 169 HOH HOH . H 5 HOH A 95 599 48 HOH HOH . H 5 HOH A 96 600 33 HOH HOH . H 5 HOH A 97 601 97 HOH HOH . H 5 HOH A 98 602 91 HOH HOH . H 5 HOH A 99 603 140 HOH HOH . H 5 HOH A 100 604 22 HOH HOH . H 5 HOH A 101 605 46 HOH HOH . H 5 HOH A 102 606 115 HOH HOH . H 5 HOH A 103 607 55 HOH HOH . H 5 HOH A 104 608 161 HOH HOH . H 5 HOH A 105 609 99 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 AMP . . . C 3 -14.681 43.786 68.273 1 58.84 ? P AMP 402 A 1 HETATM 2 O O1P AMP . . . C 3 -15.234 44.798 67.398 1 52.92 ? O1P AMP 402 A 1 HETATM 3 O O2P AMP . . . C 3 -15.212 43.938 69.591 1 53.69 ? O2P AMP 402 A 1 HETATM 4 O O3P AMP . . . C 3 -15.081 42.472 67.733 1 53.62 ? O3P AMP 402 A 1 HETATM 5 O O5' AMP . . . C 3 -13.103 43.915 68.278 1 45.02 ? O5' AMP 402 A 1 HETATM 6 C C5' AMP . . . C 3 -12.23 44.859 68.816 1 40.72 ? C5' AMP 402 A 1 HETATM 7 C C4' AMP . . . C 3 -10.947 44.013 68.894 1 47.33 ? C4' AMP 402 A 1 HETATM 8 O O4' AMP . . . C 3 -10.568 43.51 67.769 1 37.44 ? O4' AMP 402 A 1 HETATM 9 C C3' AMP . . . C 3 -9.655 44.861 69.276 1 47.22 ? C3' AMP 402 A 1 HETATM 10 O O3' AMP . . . C 3 -9.848 45.471 70.485 1 58.7 ? O3' AMP 402 A 1 HETATM 11 C C2' AMP . . . C 3 -8.705 44.039 69.166 1 33.45 ? C2' AMP 402 A 1 HETATM 12 O O2' AMP . . . C 3 -8.348 43.299 70.24 1 43.12 ? O2' AMP 402 A 1 HETATM 13 C C1' AMP . . . C 3 -9.187 43.067 68.042 1 37.55 ? C1' AMP 402 A 1 HETATM 14 N N9 AMP . . . C 3 -8.477 43.072 66.787 1 25.89 ? N9 AMP 402 A 1 HETATM 15 C C8 AMP . . . C 3 -8.281 42.055 66.047 1 25.97 ? C8 AMP 402 A 1 HETATM 16 N N7 AMP . . . C 3 -7.606 42.376 65.032 1 26.16 ? N7 AMP 402 A 1 HETATM 17 C C5 AMP . . . C 3 -7.37 43.661 65.102 1 30.42 ? C5 AMP 402 A 1 HETATM 18 C C6 AMP . . . C 3 -6.708 44.603 64.298 1 31.89 ? C6 AMP 402 A 1 HETATM 19 N N6 AMP . . . C 3 -6.055 44.212 63.094 1 25.03 ? N6 AMP 402 A 1 HETATM 20 N N1 AMP . . . C 3 -6.66 45.832 64.71 1 29.78 ? N1 AMP 402 A 1 HETATM 21 C C2 AMP . . . C 3 -7.203 46.185 65.818 1 28.49 ? C2 AMP 402 A 1 HETATM 22 N N3 AMP . . . C 3 -7.836 45.362 66.552 1 27.96 ? N3 AMP 402 A 1 HETATM 23 C C4 AMP . . . C 3 -7.919 44.102 66.234 1 24.19 ? C4 AMP 402 A 1 HETATM 24 H "H5'1" AMP . . . C 3 -12.118 45.614 68.218 1 48.87 ? "H5'1" AMP 402 A 1 HETATM 25 H "H5'2" AMP . . . C 3 -12.518 45.143 69.698 1 48.87 ? "H5'2" AMP 402 A 1 HETATM 26 H H4' AMP . . . C 3 -11.065 43.301 69.541 1 56.8 ? H4' AMP 402 A 1 HETATM 27 H H3' AMP . . . C 3 -9.535 45.55 68.603 1 56.66 ? H3' AMP 402 A 1 HETATM 28 H HO3' AMP . . . C 3 -9.371 46.174 70.527 1 70.44 ? HO3' AMP 402 A 1 HETATM 29 H H2' AMP . . . C 3 -7.924 44.518 68.847 1 40.14 ? H2' AMP 402 A 1 HETATM 30 H HO2' AMP . . . C 3 -7.908 42.62 69.98 1 51.75 ? HO2' AMP 402 A 1 HETATM 31 H H1' AMP . . . C 3 -9.21 42.163 68.394 1 45.06 ? H1' AMP 402 A 1 HETATM 32 H H8 AMP . . . C 3 -8.575 41.195 66.241 1 31.17 ? H8 AMP 402 A 1 HETATM 33 H HN61 AMP . . . C 3 -6.522 43.99 62.407 1 30.04 ? HN61 AMP 402 A 1 HETATM 34 H HN62 AMP . . . C 3 -5.196 44.197 63.055 1 30.04 ? HN62 AMP 402 A 1 HETATM 35 H H2 AMP . . . C 3 -7.166 47.079 66.075 1 34.19 ? H2 AMP 402 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 266 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 35 #