data_6FD9 # _model_server_result.job_id 4kQc3AkFvwkObzoiM4ZJSg _model_server_result.datetime_utc '2024-11-09 02:35:34' _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 6fd9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":500}' # _entry.id 6FD9 # _exptl.entry_id 6FD9 _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 105.36 _cell.angle_gamma 90 _cell.entry_id 6FD9 _cell.length_a 70.82 _cell.length_b 33.94 _cell.length_c 92.407 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6FD9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 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 6FD9 _atom_sites.fract_transf_matrix[1][1] 0.01412 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003878 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.029464 _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] 0.011222 _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 1 500 500 AMP AMP . C 3 HOH A 1 601 63 HOH HOH . C 3 HOH A 2 602 54 HOH HOH . C 3 HOH A 3 603 87 HOH HOH . C 3 HOH A 4 604 81 HOH HOH . C 3 HOH A 5 605 60 HOH HOH . C 3 HOH A 6 606 50 HOH HOH . C 3 HOH A 7 607 70 HOH HOH . C 3 HOH A 8 608 41 HOH HOH . C 3 HOH A 9 609 71 HOH HOH . C 3 HOH A 10 610 84 HOH HOH . C 3 HOH A 11 611 22 HOH HOH . C 3 HOH A 12 612 39 HOH HOH . C 3 HOH A 13 613 8 HOH HOH . C 3 HOH A 14 614 58 HOH HOH . C 3 HOH A 15 615 2 HOH HOH . C 3 HOH A 16 616 16 HOH HOH . C 3 HOH A 17 617 57 HOH HOH . C 3 HOH A 18 618 61 HOH HOH . C 3 HOH A 19 619 5 HOH HOH . C 3 HOH A 20 620 13 HOH HOH . C 3 HOH A 21 621 24 HOH HOH . C 3 HOH A 22 622 12 HOH HOH . C 3 HOH A 23 623 44 HOH HOH . C 3 HOH A 24 624 75 HOH HOH . C 3 HOH A 25 625 83 HOH HOH . C 3 HOH A 26 626 26 HOH HOH . C 3 HOH A 27 627 59 HOH HOH . C 3 HOH A 28 628 37 HOH HOH . C 3 HOH A 29 629 1 HOH HOH . C 3 HOH A 30 630 76 HOH HOH . C 3 HOH A 31 631 11 HOH HOH . C 3 HOH A 32 632 53 HOH HOH . C 3 HOH A 33 633 43 HOH HOH . C 3 HOH A 34 634 78 HOH HOH . C 3 HOH A 35 635 14 HOH HOH . C 3 HOH A 36 636 10 HOH HOH . C 3 HOH A 37 637 49 HOH HOH . C 3 HOH A 38 638 19 HOH HOH . C 3 HOH A 39 639 23 HOH HOH . C 3 HOH A 40 640 30 HOH HOH . C 3 HOH A 41 641 7 HOH HOH . C 3 HOH A 42 642 85 HOH HOH . C 3 HOH A 43 643 9 HOH HOH . C 3 HOH A 44 644 86 HOH HOH . C 3 HOH A 45 645 65 HOH HOH . C 3 HOH A 46 646 34 HOH HOH . C 3 HOH A 47 647 21 HOH HOH . C 3 HOH A 48 648 38 HOH HOH . C 3 HOH A 49 649 3 HOH HOH . C 3 HOH A 50 650 79 HOH HOH . C 3 HOH A 51 651 48 HOH HOH . C 3 HOH A 52 652 18 HOH HOH . C 3 HOH A 53 653 35 HOH HOH . C 3 HOH A 54 654 29 HOH HOH . C 3 HOH A 55 655 64 HOH HOH . C 3 HOH A 56 656 62 HOH HOH . C 3 HOH A 57 657 28 HOH HOH . C 3 HOH A 58 658 15 HOH HOH . C 3 HOH A 59 659 40 HOH HOH . C 3 HOH A 60 660 52 HOH HOH . C 3 HOH A 61 661 25 HOH HOH . C 3 HOH A 62 662 73 HOH HOH . C 3 HOH A 63 663 31 HOH HOH . C 3 HOH A 64 664 51 HOH HOH . C 3 HOH A 65 665 17 HOH HOH . C 3 HOH A 66 666 27 HOH HOH . C 3 HOH A 67 667 88 HOH HOH . C 3 HOH A 68 668 20 HOH HOH . C 3 HOH A 69 669 68 HOH HOH . C 3 HOH A 70 670 66 HOH HOH . C 3 HOH A 71 671 4 HOH HOH . C 3 HOH A 72 672 56 HOH HOH . C 3 HOH A 73 673 67 HOH HOH . C 3 HOH A 74 674 72 HOH HOH . C 3 HOH A 75 675 55 HOH HOH . C 3 HOH A 76 676 45 HOH HOH . C 3 HOH A 77 677 32 HOH HOH . C 3 HOH A 78 678 6 HOH HOH . C 3 HOH A 79 679 33 HOH HOH . C 3 HOH A 80 680 82 HOH HOH . C 3 HOH A 81 681 46 HOH HOH . C 3 HOH A 82 682 36 HOH HOH . C 3 HOH A 83 683 80 HOH HOH . C 3 HOH A 84 684 69 HOH HOH . C 3 HOH A 85 685 77 HOH HOH . C 3 HOH A 86 686 47 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 -6.769 -8.456 -14.978 1 28.87 ? P AMP 500 A 1 HETATM 2 O O1P AMP . . . B 2 -7.197 -9.709 -15.719 1 28.11 ? O1P AMP 500 A 1 HETATM 3 O O2P AMP . . . B 2 -5.442 -7.911 -15.483 1 28.43 ? O2P AMP 500 A 1 HETATM 4 O O3P AMP . . . B 2 -7.864 -7.406 -14.899 1 28.12 ? O3P AMP 500 A 1 HETATM 5 O O5' AMP . . . B 2 -6.51 -8.942 -13.463 1 33.9 ? O5' AMP 500 A 1 HETATM 6 C C5' AMP . . . B 2 -5.721 -8.118 -12.569 1 37.29 ? C5' AMP 500 A 1 HETATM 7 C C4' AMP . . . B 2 -5.12 -8.996 -11.499 1 42.41 ? C4' AMP 500 A 1 HETATM 8 O O4' AMP . . . B 2 -6.127 -9.274 -10.49 1 46.02 ? O4' AMP 500 A 1 HETATM 9 C C3' AMP . . . B 2 -4.594 -10.366 -11.951 1 44.93 ? C3' AMP 500 A 1 HETATM 10 O O3' AMP . . . B 2 -3.398 -10.7 -11.253 1 45.17 ? O3' AMP 500 A 1 HETATM 11 C C2' AMP . . . B 2 -5.75 -11.323 -11.629 1 46.5 ? C2' AMP 500 A 1 HETATM 12 O O2' AMP . . . B 2 -5.282 -12.613 -11.292 1 46.52 ? O2' AMP 500 A 1 HETATM 13 C C1' AMP . . . B 2 -6.447 -10.648 -10.446 1 46.86 ? C1' AMP 500 A 1 HETATM 14 N N9 AMP . . . B 2 -7.917 -10.746 -10.461 1 49.38 ? N9 AMP 500 A 1 HETATM 15 C C8 AMP . . . B 2 -8.767 -10.333 -11.464 1 48.99 ? C8 AMP 500 A 1 HETATM 16 N N7 AMP . . . B 2 -10.03 -10.543 -11.172 1 48.9 ? N7 AMP 500 A 1 HETATM 17 C C5 AMP . . . B 2 -10.013 -11.119 -9.91 1 47.66 ? C5 AMP 500 A 1 HETATM 18 C C6 AMP . . . B 2 -11.043 -11.568 -9.061 1 47.1 ? C6 AMP 500 A 1 HETATM 19 N N6 AMP . . . B 2 -12.335 -11.501 -9.369 1 44.95 ? N6 AMP 500 A 1 HETATM 20 N N1 AMP . . . B 2 -10.679 -12.099 -7.868 1 46.76 ? N1 AMP 500 A 1 HETATM 21 C C2 AMP . . . B 2 -9.372 -12.16 -7.568 1 48.56 ? C2 AMP 500 A 1 HETATM 22 N N3 AMP . . . B 2 -8.321 -11.76 -8.283 1 48.71 ? N3 AMP 500 A 1 HETATM 23 C C4 AMP . . . B 2 -8.715 -11.244 -9.461 1 48.51 ? C4 AMP 500 A 1 # _model_server_stats.io_time_ms 23 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 292 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 23 #