data_4WDB # _model_server_result.job_id Ov5jRDJBsiR5aiBMNG4EuA _model_server_result.datetime_utc '2024-11-15 15:50:42' _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 4wdb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 4WDB # _exptl.entry_id 4WDB _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-2'-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 90 _cell.entry_id 4WDB _cell.length_a 38.88 _cell.length_b 47.89 _cell.length_c 107.41 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4WDB _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 monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D _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 2AM _chem_comp.mon_nstd_flag . _chem_comp.name "ADENOSINE-2'-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 2AM doub 1 n n P O2P 2AM sing 2 n n P O3P 2AM sing 3 n n P O2' 2AM sing 4 n n O2P HOP2 2AM sing 5 n n O3P HOP3 2AM sing 6 n n C5' O5' 2AM sing 7 n n C5' C4' 2AM sing 8 n n C5' "H5'1" 2AM sing 9 n n C5' "H5'2" 2AM sing 10 n n O5' HO5' 2AM sing 11 n n C4' O4' 2AM sing 12 n n C4' C3' 2AM sing 13 n n C4' H4' 2AM sing 14 n n O4' C1' 2AM sing 15 n n C3' O3' 2AM sing 16 n n C3' C2' 2AM sing 17 n n C3' H3' 2AM sing 18 n n O3' HO3' 2AM sing 19 n n C2' O2' 2AM sing 20 n n C2' C1' 2AM sing 21 n n C2' H2' 2AM sing 22 n n C1' N9 2AM sing 23 n n C1' H1' 2AM sing 24 n n N9 C8 2AM sing 25 n y N9 C4 2AM sing 26 n y C8 N7 2AM doub 27 n y C8 H8 2AM sing 28 n n N7 C5 2AM sing 29 n y C5 C6 2AM sing 30 n y C5 C4 2AM doub 31 n y C6 N6 2AM sing 32 n n C6 N1 2AM doub 33 n y N6 HN61 2AM sing 34 n n N6 HN62 2AM sing 35 n n N1 C2 2AM sing 36 n y C2 N3 2AM doub 37 n y C2 H2 2AM sing 38 n n N3 C4 2AM sing 39 n y # _atom_sites.entry_id 4WDB _atom_sites.fract_transf_matrix[1][1] 0.02572 _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] 0.020881 _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] 0.00931 _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 2AM A 1 401 1 2AM 2AM . C 3 CL A 1 402 1 CL CL . D 4 HOH A 1 501 22 HOH HOH . D 4 HOH A 2 502 99 HOH HOH . D 4 HOH A 3 503 122 HOH HOH . D 4 HOH A 4 504 102 HOH HOH . D 4 HOH A 5 505 83 HOH HOH . D 4 HOH A 6 506 77 HOH HOH . D 4 HOH A 7 507 28 HOH HOH . D 4 HOH A 8 508 7 HOH HOH . D 4 HOH A 9 509 24 HOH HOH . D 4 HOH A 10 510 38 HOH HOH . D 4 HOH A 11 511 53 HOH HOH . D 4 HOH A 12 512 18 HOH HOH . D 4 HOH A 13 513 12 HOH HOH . D 4 HOH A 14 514 69 HOH HOH . D 4 HOH A 15 515 80 HOH HOH . D 4 HOH A 16 516 94 HOH HOH . D 4 HOH A 17 517 65 HOH HOH . D 4 HOH A 18 518 41 HOH HOH . D 4 HOH A 19 519 78 HOH HOH . D 4 HOH A 20 520 29 HOH HOH . D 4 HOH A 21 521 79 HOH HOH . D 4 HOH A 22 522 100 HOH HOH . D 4 HOH A 23 523 66 HOH HOH . D 4 HOH A 24 524 136 HOH HOH . D 4 HOH A 25 525 14 HOH HOH . D 4 HOH A 26 526 40 HOH HOH . D 4 HOH A 27 527 82 HOH HOH . D 4 HOH A 28 528 85 HOH HOH . D 4 HOH A 29 529 46 HOH HOH . D 4 HOH A 30 530 45 HOH HOH . D 4 HOH A 31 531 96 HOH HOH . D 4 HOH A 32 532 49 HOH HOH . D 4 HOH A 33 533 76 HOH HOH . D 4 HOH A 34 534 50 HOH HOH . D 4 HOH A 35 535 11 HOH HOH . D 4 HOH A 36 536 71 HOH HOH . D 4 HOH A 37 537 68 HOH HOH . D 4 HOH A 38 538 67 HOH HOH . D 4 HOH A 39 539 126 HOH HOH . D 4 HOH A 40 540 114 HOH HOH . D 4 HOH A 41 541 127 HOH HOH . D 4 HOH A 42 542 132 HOH HOH . D 4 HOH A 43 543 89 HOH HOH . D 4 HOH A 44 544 124 HOH HOH . D 4 HOH A 45 545 116 HOH HOH . D 4 HOH A 46 546 101 HOH HOH . D 4 HOH A 47 547 125 HOH HOH . D 4 HOH A 48 548 135 HOH HOH . D 4 HOH A 49 549 54 HOH HOH . D 4 HOH A 50 550 111 HOH HOH . D 4 HOH A 51 551 1 HOH HOH . D 4 HOH A 52 552 2 HOH HOH . D 4 HOH A 53 553 3 HOH HOH . D 4 HOH A 54 554 4 HOH HOH . D 4 HOH A 55 555 5 HOH HOH . D 4 HOH A 56 556 6 HOH HOH . D 4 HOH A 57 557 8 HOH HOH . D 4 HOH A 58 558 9 HOH HOH . D 4 HOH A 59 559 10 HOH HOH . D 4 HOH A 60 560 13 HOH HOH . D 4 HOH A 61 561 15 HOH HOH . D 4 HOH A 62 562 16 HOH HOH . D 4 HOH A 63 563 17 HOH HOH . D 4 HOH A 64 564 19 HOH HOH . D 4 HOH A 65 565 20 HOH HOH . D 4 HOH A 66 566 21 HOH HOH . D 4 HOH A 67 567 25 HOH HOH . D 4 HOH A 68 568 26 HOH HOH . D 4 HOH A 69 569 27 HOH HOH . D 4 HOH A 70 570 31 HOH HOH . D 4 HOH A 71 571 32 HOH HOH . D 4 HOH A 72 572 33 HOH HOH . D 4 HOH A 73 573 35 HOH HOH . D 4 HOH A 74 574 36 HOH HOH . D 4 HOH A 75 575 37 HOH HOH . D 4 HOH A 76 576 39 HOH HOH . D 4 HOH A 77 577 42 HOH HOH . D 4 HOH A 78 578 43 HOH HOH . D 4 HOH A 79 579 44 HOH HOH . D 4 HOH A 80 580 47 HOH HOH . D 4 HOH A 81 581 48 HOH HOH . D 4 HOH A 82 582 51 HOH HOH . D 4 HOH A 83 583 55 HOH HOH . D 4 HOH A 84 584 56 HOH HOH . D 4 HOH A 85 585 57 HOH HOH . D 4 HOH A 86 586 59 HOH HOH . D 4 HOH A 87 587 60 HOH HOH . D 4 HOH A 88 588 61 HOH HOH . D 4 HOH A 89 589 62 HOH HOH . D 4 HOH A 90 590 63 HOH HOH . D 4 HOH A 91 591 64 HOH HOH . D 4 HOH A 92 592 70 HOH HOH . D 4 HOH A 93 593 72 HOH HOH . D 4 HOH A 94 594 73 HOH HOH . D 4 HOH A 95 595 74 HOH HOH . D 4 HOH A 96 596 75 HOH HOH . D 4 HOH A 97 597 81 HOH HOH . D 4 HOH A 98 598 84 HOH HOH . D 4 HOH A 99 599 86 HOH HOH . D 4 HOH A 100 600 87 HOH HOH . D 4 HOH A 101 601 90 HOH HOH . D 4 HOH A 102 602 91 HOH HOH . D 4 HOH A 103 603 92 HOH HOH . D 4 HOH A 104 604 93 HOH HOH . D 4 HOH A 105 605 98 HOH HOH . D 4 HOH A 106 606 103 HOH HOH . D 4 HOH A 107 607 104 HOH HOH . D 4 HOH A 108 608 107 HOH HOH . D 4 HOH A 109 609 109 HOH HOH . D 4 HOH A 110 610 110 HOH HOH . D 4 HOH A 111 611 112 HOH HOH . D 4 HOH A 112 612 113 HOH HOH . D 4 HOH A 113 613 115 HOH HOH . D 4 HOH A 114 614 117 HOH HOH . D 4 HOH A 115 615 118 HOH HOH . D 4 HOH A 116 616 121 HOH HOH . D 4 HOH A 117 617 123 HOH HOH . D 4 HOH A 118 618 128 HOH HOH . D 4 HOH A 119 619 129 HOH HOH . D 4 HOH A 120 620 130 HOH HOH . D 4 HOH A 121 621 133 HOH HOH . D 4 HOH A 122 622 134 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 2AM . A . B 2 -5.346 5.978 -21.404 0.54 46.89 ? P 2AM 401 A 1 HETATM 2 P P 2AM . B . B 2 -6.108 4.47 -20.73 0.46 50.01 ? P 2AM 401 A 1 HETATM 3 O O1P 2AM . A . B 2 -3.978 6.38 -21.909 0.54 36.8 ? O1P 2AM 401 A 1 HETATM 4 O O1P 2AM . B . B 2 -6.023 3.175 -21.501 0.46 53.89 ? O1P 2AM 401 A 1 HETATM 5 O O2P 2AM . A . B 2 -6.294 7.106 -21.113 0.54 51.08 ? O2P 2AM 401 A 1 HETATM 6 O O2P 2AM . B . B 2 -4.715 4.912 -20.396 0.46 47.54 ? O2P 2AM 401 A 1 HETATM 7 O O3P 2AM . A . B 2 -5.318 5.101 -20.187 0.54 48.21 ? O3P 2AM 401 A 1 HETATM 8 O O3P 2AM . B . B 2 -6.939 4.14 -19.506 0.46 50.15 ? O3P 2AM 401 A 1 HETATM 9 C C5' 2AM . A . B 2 -6.11 6.376 -27.063 0.54 46.4 ? C5' 2AM 401 A 1 HETATM 10 C C5' 2AM . B . B 2 -6.23 6.277 -26.416 0.46 45.19 ? C5' 2AM 401 A 1 HETATM 11 O O5' 2AM . A . B 2 -6.337 4.98 -27.061 0.54 41.52 ? O5' 2AM 401 A 1 HETATM 12 O O5' 2AM . B . B 2 -6.662 4.936 -26.406 0.46 39.93 ? O5' 2AM 401 A 1 HETATM 13 C C4' 2AM . A . B 2 -6.291 6.941 -25.654 0.54 49.12 ? C4' 2AM 401 A 1 HETATM 14 C C4' 2AM . B . B 2 -6.597 6.924 -25.081 0.46 50.94 ? C4' 2AM 401 A 1 HETATM 15 O O4' 2AM . A . B 2 -7.636 6.85 -25.209 0.54 52.23 ? O4' 2AM 401 A 1 HETATM 16 O O4' 2AM . B . B 2 -7.98 6.743 -24.831 0.46 53.17 ? O4' 2AM 401 A 1 HETATM 17 C C3' 2AM . A . B 2 -5.423 6.172 -24.674 0.54 53.85 ? C3' 2AM 401 A 1 HETATM 18 C C3' 2AM . B . B 2 -5.876 6.304 -23.885 0.46 55.25 ? C3' 2AM 401 A 1 HETATM 19 O O3' 2AM . A . B 2 -4.593 7.109 -24.028 0.54 55.76 ? O3' 2AM 401 A 1 HETATM 20 O O3' 2AM . B . B 2 -5.299 7.328 -23.119 0.46 56.11 ? O3' 2AM 401 A 1 HETATM 21 C C2' 2AM . A . B 2 -6.441 5.402 -23.827 0.54 56.11 ? C2' 2AM 401 A 1 HETATM 22 C C2' 2AM . B . B 2 -6.921 5.562 -23.058 0.46 57.44 ? C2' 2AM 401 A 1 HETATM 23 O O2' 2AM . A . B 2 -6.093 5.069 -22.502 0.54 58.45 ? O2' 2AM 401 A 1 HETATM 24 O O2' 2AM . B . B 2 -6.722 5.669 -21.648 0.46 66.53 ? O2' 2AM 401 A 1 HETATM 25 C C1' 2AM . A . B 2 -7.723 6.234 -23.933 0.54 55.08 ? C1' 2AM 401 A 1 HETATM 26 C C1' 2AM . B . B 2 -8.204 6.248 -23.521 0.46 55.35 ? C1' 2AM 401 A 1 HETATM 27 N N9 2AM . A . B 2 -8.963 5.429 -23.82 0.54 54.84 ? N9 2AM 401 A 1 HETATM 28 N N9 2AM . B . B 2 -9.374 5.358 -23.532 0.46 55.02 ? N9 2AM 401 A 1 HETATM 29 C C8 2AM . A . B 2 -9.925 5.552 -22.854 0.54 56.02 ? C8 2AM 401 A 1 HETATM 30 C C8 2AM . B . B 2 -10.388 5.376 -22.619 0.46 55.53 ? C8 2AM 401 A 1 HETATM 31 N N7 2AM . A . B 2 -10.907 4.655 -23.101 0.54 56.06 ? N7 2AM 401 A 1 HETATM 32 N N7 2AM . B . B 2 -11.296 4.438 -22.97 0.46 56.2 ? N7 2AM 401 A 1 HETATM 33 C C5 2AM . A . B 2 -10.587 3.948 -24.211 0.54 54.56 ? C5 2AM 401 A 1 HETATM 34 C C5 2AM . B . B 2 -10.872 3.825 -24.098 0.46 55.16 ? C5 2AM 401 A 1 HETATM 35 C C6 2AM . A . B 2 -11.233 2.918 -24.899 0.54 55.92 ? C6 2AM 401 A 1 HETATM 36 C C6 2AM . B . B 2 -11.416 2.804 -24.873 0.46 55.9 ? C6 2AM 401 A 1 HETATM 37 N N6 2AM . A . B 2 -12.4 2.44 -24.466 0.54 55.45 ? N6 2AM 401 A 1 HETATM 38 N N6 2AM . B . B 2 -12.566 2.249 -24.512 0.46 55.34 ? N6 2AM 401 A 1 HETATM 39 N N1 2AM . A . B 2 -10.649 2.389 -26.031 0.54 54.65 ? N1 2AM 401 A 1 HETATM 40 N N1 2AM . B . B 2 -10.754 2.371 -26.003 0.46 54.43 ? N1 2AM 401 A 1 HETATM 41 C C2 2AM . A . B 2 -9.438 2.877 -26.484 0.54 54.89 ? C2 2AM 401 A 1 HETATM 42 C C2 2AM . B . B 2 -9.555 2.951 -26.369 0.46 54.66 ? C2 2AM 401 A 1 HETATM 43 N N3 2AM . A . B 2 -8.802 3.897 -25.799 0.54 54.48 ? N3 2AM 401 A 1 HETATM 44 N N3 2AM . B . B 2 -9.021 3.966 -25.595 0.46 54.07 ? N3 2AM 401 A 1 HETATM 45 C C4 2AM . A . B 2 -9.369 4.431 -24.681 0.54 55.52 ? C4 2AM 401 A 1 HETATM 46 C C4 2AM . B . B 2 -9.667 4.4 -24.476 0.46 55.63 ? C4 2AM 401 A 1 HETATM 47 H "H5'1" 2AM . A . B 2 -6.809 6.861 -27.745 0.54 55.68 ? "H5'1" 2AM 401 A 1 HETATM 48 H "H5'1" 2AM . B . B 2 -6.71 6.815 -27.234 0.46 54.23 ? "H5'1" 2AM 401 A 1 HETATM 49 H "H5'2" 2AM . A . B 2 -5.098 6.582 -27.413 0.54 55.68 ? "H5'2" 2AM 401 A 1 HETATM 50 H "H5'2" 2AM . B . B 2 -5.151 6.319 -26.565 0.46 54.23 ? "H5'2" 2AM 401 A 1 HETATM 51 H HO5' 2AM . A . B 2 -6.561 4.686 -26.153 0.54 49.82 ? HO5' 2AM 401 A 1 HETATM 52 H HO5' 2AM . B . B 2 -7.093 4.738 -25.549 0.46 47.91 ? HO5' 2AM 401 A 1 HETATM 53 H H4' 2AM . A . B 2 -5.973 7.984 -25.654 0.54 58.95 ? H4' 2AM 401 A 1 HETATM 54 H H4' 2AM . B . B 2 -6.361 7.987 -25.125 0.46 61.12 ? H4' 2AM 401 A 1 HETATM 55 H H3' 2AM . A . B 2 -4.816 5.457 -25.23 0.54 64.62 ? H3' 2AM 401 A 1 HETATM 56 H H3' 2AM . B . B 2 -5.117 5.604 -24.234 0.46 66.3 ? H3' 2AM 401 A 1 HETATM 57 H HO3' 2AM . A . B 2 -4.806 7.128 -23.071 0.54 66.91 ? HO3' 2AM 401 A 1 HETATM 58 H HO3' 2AM . B . B 2 -5.701 7.333 -22.225 0.46 67.34 ? HO3' 2AM 401 A 1 HETATM 59 H H2' 2AM . A . B 2 -6.635 4.468 -24.355 0.54 67.33 ? H2' 2AM 401 A 1 HETATM 60 H H2' 2AM . B . B 2 -6.943 4.516 -23.362 0.46 68.92 ? H2' 2AM 401 A 1 HETATM 61 H H1' 2AM . A . B 2 -7.707 6.997 -23.155 0.54 66.1 ? H1' 2AM 401 A 1 HETATM 62 H H1' 2AM . B . B 2 -8.399 7.085 -22.852 0.46 66.42 ? H1' 2AM 401 A 1 HETATM 63 H H8 2AM . A . B 2 -9.904 6.257 -22.022 0.54 67.22 ? H8 2AM 401 A 1 HETATM 64 H H8 2AM . B . B 2 -10.454 6.035 -21.753 0.46 66.64 ? H8 2AM 401 A 1 HETATM 65 H HN61 2AM . A . B 2 -12.827 2.825 -23.63 0.54 66.54 ? HN61 2AM 401 A 1 HETATM 66 H HN61 2AM . B . B 2 -13.044 2.569 -23.676 0.46 66.41 ? HN61 2AM 401 A 1 HETATM 67 H HN62 2AM . A . B 2 -12.86 1.69 -24.972 0.54 66.54 ? HN62 2AM 401 A 1 HETATM 68 H HN62 2AM . B . B 2 -12.967 1.503 -25.071 0.46 66.41 ? HN62 2AM 401 A 1 HETATM 69 H H2 2AM . A . B 2 -8.983 2.458 -27.381 0.54 65.87 ? H2 2AM 401 A 1 HETATM 70 H H2 2AM . B . B 2 -9.092 2.689 -27.321 0.46 65.59 ? H2 2AM 401 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 30 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 1103 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 70 #