data_6KDU # _model_server_result.job_id w9GPVslru2lf78w0Mt-_Qg _model_server_result.datetime_utc '2025-08-31 21:11:48' _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 6kdu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 6KDU # _exptl.entry_id 6KDU _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 347.221 _entity.id 2 _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 6KDU _cell.length_a 96.168 _cell.length_b 96.168 _cell.length_c 200.835 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6KDU _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 _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 2 _struct_asym.id B _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 6KDU _atom_sites.fract_transf_matrix[1][1] 0.010398 _atom_sites.fract_transf_matrix[1][2] 0.006004 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012007 _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] 0.004979 _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 AMP A 1 401 1 AMP AMP . C 3 NMN A 1 402 2 NMN LIG . D 4 SO4 A 1 403 2 SO4 SO4 . E 4 SO4 A 1 404 3 SO4 SO4 . F 4 SO4 A 1 405 4 SO4 SO4 . G 5 HOH A 1 501 47 HOH HOH . G 5 HOH A 2 502 51 HOH HOH . G 5 HOH A 3 503 31 HOH HOH . G 5 HOH A 4 504 118 HOH HOH . G 5 HOH A 5 505 16 HOH HOH . G 5 HOH A 6 506 21 HOH HOH . G 5 HOH A 7 507 70 HOH HOH . G 5 HOH A 8 508 23 HOH HOH . G 5 HOH A 9 509 99 HOH HOH . G 5 HOH A 10 510 20 HOH HOH . G 5 HOH A 11 511 43 HOH HOH . G 5 HOH A 12 512 50 HOH HOH . G 5 HOH A 13 513 32 HOH HOH . G 5 HOH A 14 514 156 HOH HOH . G 5 HOH A 15 515 144 HOH HOH . G 5 HOH A 16 516 54 HOH HOH . G 5 HOH A 17 517 68 HOH HOH . G 5 HOH A 18 518 49 HOH HOH . G 5 HOH A 19 519 36 HOH HOH . G 5 HOH A 20 520 5 HOH HOH . G 5 HOH A 21 521 17 HOH HOH . G 5 HOH A 22 522 14 HOH HOH . G 5 HOH A 23 523 193 HOH HOH . G 5 HOH A 24 524 10 HOH HOH . G 5 HOH A 25 525 188 HOH HOH . G 5 HOH A 26 526 40 HOH HOH . G 5 HOH A 27 527 15 HOH HOH . G 5 HOH A 28 528 11 HOH HOH . G 5 HOH A 29 529 38 HOH HOH . G 5 HOH A 30 530 121 HOH HOH . G 5 HOH A 31 531 96 HOH HOH . G 5 HOH A 32 532 110 HOH HOH . G 5 HOH A 33 533 27 HOH HOH . G 5 HOH A 34 534 4 HOH HOH . G 5 HOH A 35 535 124 HOH HOH . G 5 HOH A 36 536 19 HOH HOH . G 5 HOH A 37 537 63 HOH HOH . G 5 HOH A 38 538 85 HOH HOH . G 5 HOH A 39 539 28 HOH HOH . G 5 HOH A 40 540 56 HOH HOH . G 5 HOH A 41 541 154 HOH HOH . G 5 HOH A 42 542 44 HOH HOH . G 5 HOH A 43 543 46 HOH HOH . G 5 HOH A 44 544 133 HOH HOH . G 5 HOH A 45 545 102 HOH HOH . G 5 HOH A 46 546 136 HOH HOH . G 5 HOH A 47 547 37 HOH HOH . G 5 HOH A 48 548 97 HOH HOH . G 5 HOH A 49 549 115 HOH HOH . G 5 HOH A 50 550 8 HOH HOH . G 5 HOH A 51 551 69 HOH HOH . G 5 HOH A 52 552 53 HOH HOH . G 5 HOH A 53 553 134 HOH HOH . G 5 HOH A 54 554 42 HOH HOH . G 5 HOH A 55 555 34 HOH HOH . G 5 HOH A 56 556 45 HOH HOH . G 5 HOH A 57 557 6 HOH HOH . G 5 HOH A 58 558 159 HOH HOH . G 5 HOH A 59 559 66 HOH HOH . G 5 HOH A 60 560 33 HOH HOH . G 5 HOH A 61 561 86 HOH HOH . G 5 HOH A 62 562 48 HOH HOH . G 5 HOH A 63 563 61 HOH HOH . G 5 HOH A 64 564 12 HOH HOH . G 5 HOH A 65 565 64 HOH HOH . G 5 HOH A 66 566 83 HOH HOH . G 5 HOH A 67 567 157 HOH HOH . G 5 HOH A 68 568 94 HOH HOH . G 5 HOH A 69 569 84 HOH HOH . G 5 HOH A 70 570 79 HOH HOH . G 5 HOH A 71 571 74 HOH HOH . G 5 HOH A 72 572 131 HOH HOH . G 5 HOH A 73 573 101 HOH HOH . G 5 HOH A 74 574 3 HOH HOH . G 5 HOH A 75 575 41 HOH HOH . G 5 HOH A 76 576 25 HOH HOH . G 5 HOH A 77 577 73 HOH HOH . G 5 HOH A 78 578 29 HOH HOH . G 5 HOH A 79 579 92 HOH HOH . G 5 HOH A 80 580 130 HOH HOH . G 5 HOH A 81 581 35 HOH HOH . G 5 HOH A 82 582 191 HOH HOH . G 5 HOH A 83 583 1 HOH HOH . G 5 HOH A 84 584 78 HOH HOH . G 5 HOH A 85 585 167 HOH HOH . G 5 HOH A 86 586 185 HOH HOH . G 5 HOH A 87 587 175 HOH HOH . G 5 HOH A 88 588 141 HOH HOH . G 5 HOH A 89 589 76 HOH HOH . G 5 HOH A 90 590 132 HOH HOH . G 5 HOH A 91 591 186 HOH HOH . G 5 HOH A 92 592 125 HOH HOH . G 5 HOH A 93 593 146 HOH HOH . G 5 HOH A 94 594 91 HOH HOH . G 5 HOH A 95 595 30 HOH HOH . G 5 HOH A 96 596 71 HOH HOH . G 5 HOH A 97 597 142 HOH HOH . G 5 HOH A 98 598 192 HOH HOH . G 5 HOH A 99 599 72 HOH HOH . G 5 HOH A 100 600 129 HOH HOH . G 5 HOH A 101 601 57 HOH HOH . G 5 HOH A 102 602 190 HOH HOH . G 5 HOH A 103 603 114 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 . . . B 2 -14.855 42.384 67.424 1 103.34 ? P AMP 401 A 1 HETATM 2 O O1P AMP . . . B 2 -14.016 41.698 66.352 1 87.51 ? O1P AMP 401 A 1 HETATM 3 O O2P AMP . . . B 2 -16.036 42.901 66.71 1 76.37 -1 O2P AMP 401 A 1 HETATM 4 O O3P AMP . . . B 2 -15.445 41.561 68.492 1 84.09 ? O3P AMP 401 A 1 HETATM 5 O O5' AMP . . . B 2 -14.092 43.678 68.128 1 92.31 ? O5' AMP 401 A 1 HETATM 6 C C5' AMP . . . B 2 -12.863 44.09 67.562 1 81.59 ? C5' AMP 401 A 1 HETATM 7 C C4' AMP . . . B 2 -11.689 44.016 68.54 1 84.89 ? C4' AMP 401 A 1 HETATM 8 O O4' AMP . . . B 2 -10.678 43.281 68.123 1 78.67 ? O4' AMP 401 A 1 HETATM 9 C C3' AMP . . . B 2 -11.125 45.515 68.599 1 79.2 ? C3' AMP 401 A 1 HETATM 10 O O3' AMP . . . B 2 -11.643 45.949 69.765 1 81.28 ? O3' AMP 401 A 1 HETATM 11 C C2' AMP . . . B 2 -9.842 45.519 68.492 1 83.35 ? C2' AMP 401 A 1 HETATM 12 O O2' AMP . . . B 2 -9.081 46.339 69.386 1 88.82 ? O2' AMP 401 A 1 HETATM 13 C C1' AMP . . . B 2 -9.371 44.034 68.295 1 72.21 ? C1' AMP 401 A 1 HETATM 14 N N9 AMP . . . B 2 -8.701 43.757 67.002 1 60.24 ? N9 AMP 401 A 1 HETATM 15 C C8 AMP . . . B 2 -8.682 42.632 66.362 1 51.7 ? C8 AMP 401 A 1 HETATM 16 N N7 AMP . . . B 2 -7.982 42.739 65.268 1 53.94 ? N7 AMP 401 A 1 HETATM 17 C C5 AMP . . . B 2 -7.556 44.021 65.171 1 56.82 ? C5 AMP 401 A 1 HETATM 18 C C6 AMP . . . B 2 -6.786 44.793 64.236 1 52.54 ? C6 AMP 401 A 1 HETATM 19 N N6 AMP . . . B 2 -6.228 44.249 63.032 1 45.87 ? N6 AMP 401 A 1 HETATM 20 N N1 AMP . . . B 2 -6.543 46.031 64.506 1 52.06 ? N1 AMP 401 A 1 HETATM 21 C C2 AMP . . . B 2 -7.007 46.564 65.593 1 48.92 ? C2 AMP 401 A 1 HETATM 22 N N3 AMP . . . B 2 -7.714 45.904 66.435 1 48.74 ? N3 AMP 401 A 1 HETATM 23 C C4 AMP . . . B 2 -8.007 44.639 66.266 1 50.57 ? C4 AMP 401 A 1 HETATM 24 H "H5'1" AMP . . . B 2 -12.667 43.525 66.799 1 97.91 ? "H5'1" AMP 401 A 1 HETATM 25 H "H5'2" AMP . . . B 2 -12.953 45.006 67.256 1 97.91 ? "H5'2" AMP 401 A 1 HETATM 26 H H4' AMP . . . B 2 -11.984 43.728 69.419 1 101.87 ? H4' AMP 401 A 1 HETATM 27 H H3' AMP . . . B 2 -11.505 46.027 67.868 1 95.04 ? H3' AMP 401 A 1 HETATM 28 H HO3' AMP . . . B 2 -11.784 45.285 70.278 1 97.53 ? HO3' AMP 401 A 1 HETATM 29 H H2' AMP . . . B 2 -9.691 45.929 67.626 1 100.01 ? H2' AMP 401 A 1 HETATM 30 H HO2' AMP . . . B 2 -8.282 46.053 69.42 1 106.58 ? HO2' AMP 401 A 1 HETATM 31 H H1' AMP . . . B 2 -8.865 43.704 69.054 1 86.66 ? H1' AMP 401 A 1 HETATM 32 H H8 AMP . . . B 2 -9.086 41.848 66.657 1 62.04 ? H8 AMP 401 A 1 HETATM 33 H HN61 AMP . . . B 2 -6.697 43.719 62.543 1 55.05 ? HN61 AMP 401 A 1 HETATM 34 H HN62 AMP . . . B 2 -5.425 44.452 62.798 1 55.05 ? HN62 AMP 401 A 1 HETATM 35 H H2 AMP . . . B 2 -6.839 47.464 65.759 1 58.7 ? H2 AMP 401 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 429 _model_server_stats.encode_time_ms 53 _model_server_stats.element_count 35 #