data_3X01 # _model_server_result.job_id 09_MH7VX-rkychCUwJhWPA _model_server_result.datetime_utc '2024-11-25 11:19:55' _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 3x01 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":502}' # _entry.id 3X01 # _exptl.entry_id 3X01 _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 4 _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 3X01 _cell.length_a 108.385 _cell.length_b 181.79 _cell.length_c 107.619 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3X01 _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _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,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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 D N N ? 2 E N N ? 2 F N 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 3X01 _atom_sites.fract_transf_matrix[1][1] 0.009226 _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] 0.005501 _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] 0.009292 _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 AMP A 1 501 501 AMP AMP . D 2 AMP A 1 502 502 AMP AMP . E 2 AMP A 1 503 503 AMP AMP . F 2 AMP B 1 501 501 AMP AMP . G 3 HOH A 1 601 601 HOH HOH . G 3 HOH A 2 602 602 HOH HOH . G 3 HOH A 3 603 603 HOH HOH . G 3 HOH A 4 604 604 HOH HOH . G 3 HOH A 5 605 605 HOH HOH . G 3 HOH A 6 606 606 HOH HOH . G 3 HOH A 7 607 607 HOH HOH . G 3 HOH A 8 608 608 HOH HOH . G 3 HOH A 9 609 609 HOH HOH . G 3 HOH A 10 610 610 HOH HOH . G 3 HOH A 11 611 611 HOH HOH . G 3 HOH A 12 612 612 HOH HOH . G 3 HOH A 13 613 613 HOH HOH . G 3 HOH A 14 614 614 HOH HOH . G 3 HOH A 15 615 615 HOH HOH . G 3 HOH A 16 616 616 HOH HOH . G 3 HOH A 17 617 617 HOH HOH . G 3 HOH A 18 618 618 HOH HOH . G 3 HOH A 19 619 619 HOH HOH . G 3 HOH A 20 620 620 HOH HOH . G 3 HOH A 21 621 621 HOH HOH . G 3 HOH A 22 622 622 HOH HOH . G 3 HOH A 23 623 623 HOH HOH . G 3 HOH A 24 624 624 HOH HOH . G 3 HOH A 25 625 625 HOH HOH . G 3 HOH A 26 626 626 HOH HOH . G 3 HOH A 27 627 627 HOH HOH . G 3 HOH A 28 628 628 HOH HOH . G 3 HOH A 29 629 629 HOH HOH . G 3 HOH A 30 630 630 HOH HOH . G 3 HOH A 31 631 631 HOH HOH . G 3 HOH A 32 632 632 HOH HOH . G 3 HOH A 33 633 633 HOH HOH . G 3 HOH A 34 634 634 HOH HOH . G 3 HOH A 35 635 635 HOH HOH . G 3 HOH A 36 636 636 HOH HOH . G 3 HOH A 37 637 637 HOH HOH . G 3 HOH A 38 638 638 HOH HOH . G 3 HOH A 39 639 639 HOH HOH . G 3 HOH A 40 640 640 HOH HOH . G 3 HOH A 41 641 641 HOH HOH . G 3 HOH A 42 642 642 HOH HOH . G 3 HOH A 43 643 643 HOH HOH . G 3 HOH A 44 644 644 HOH HOH . G 3 HOH A 45 645 645 HOH HOH . G 3 HOH A 46 646 646 HOH HOH . G 3 HOH A 47 647 647 HOH HOH . G 3 HOH A 48 648 648 HOH HOH . G 3 HOH A 49 649 649 HOH HOH . G 3 HOH A 50 650 650 HOH HOH . G 3 HOH A 51 651 651 HOH HOH . G 3 HOH A 52 652 652 HOH HOH . G 3 HOH A 53 653 653 HOH HOH . G 3 HOH A 54 654 654 HOH HOH . G 3 HOH A 55 655 655 HOH HOH . H 3 HOH B 1 601 601 HOH HOH . H 3 HOH B 2 602 602 HOH HOH . H 3 HOH B 3 603 603 HOH HOH . H 3 HOH B 4 604 604 HOH HOH . H 3 HOH B 5 605 605 HOH HOH . H 3 HOH B 6 606 606 HOH HOH . H 3 HOH B 7 607 607 HOH HOH . H 3 HOH B 8 608 608 HOH HOH . H 3 HOH B 9 609 609 HOH HOH . H 3 HOH B 10 610 610 HOH HOH . H 3 HOH B 11 611 611 HOH HOH . H 3 HOH B 12 612 612 HOH HOH . H 3 HOH B 13 613 613 HOH HOH . H 3 HOH B 14 614 614 HOH HOH . H 3 HOH B 15 615 615 HOH HOH . H 3 HOH B 16 616 616 HOH HOH . H 3 HOH B 17 617 617 HOH HOH . H 3 HOH B 18 618 618 HOH HOH . H 3 HOH B 19 619 619 HOH HOH . H 3 HOH B 20 620 620 HOH HOH . H 3 HOH B 21 621 621 HOH HOH . H 3 HOH B 22 622 622 HOH HOH . H 3 HOH B 23 623 623 HOH HOH . H 3 HOH B 24 624 624 HOH HOH . H 3 HOH B 25 625 625 HOH HOH . H 3 HOH B 26 626 626 HOH HOH . H 3 HOH B 27 627 627 HOH HOH . H 3 HOH B 28 628 628 HOH HOH . H 3 HOH B 29 629 629 HOH HOH . H 3 HOH B 30 630 630 HOH HOH . H 3 HOH B 31 631 631 HOH HOH . H 3 HOH B 32 632 632 HOH HOH . H 3 HOH B 33 633 633 HOH HOH . H 3 HOH B 34 634 634 HOH HOH . H 3 HOH B 35 635 635 HOH HOH . H 3 HOH B 36 636 636 HOH HOH . H 3 HOH B 37 637 637 HOH HOH . H 3 HOH B 38 638 638 HOH HOH . H 3 HOH B 39 639 639 HOH HOH . H 3 HOH B 40 640 640 HOH HOH . H 3 HOH B 41 641 641 HOH HOH . H 3 HOH B 42 642 642 HOH HOH . H 3 HOH B 43 643 643 HOH HOH . H 3 HOH B 44 644 644 HOH HOH . H 3 HOH B 45 645 645 HOH HOH . H 3 HOH B 46 646 646 HOH HOH . H 3 HOH B 47 647 647 HOH HOH . H 3 HOH B 48 648 648 HOH HOH . H 3 HOH B 49 649 649 HOH HOH . H 3 HOH B 50 650 650 HOH HOH . H 3 HOH B 51 651 651 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 . . . D 2 47.597 47.577 -23.516 1 50.67 ? P AMP 502 A 1 HETATM 2 O O1P AMP . . . D 2 46.229 48.209 -23.461 1 42.34 ? O1P AMP 502 A 1 HETATM 3 O O2P AMP . . . D 2 48.029 46.903 -24.798 1 58.91 ? O2P AMP 502 A 1 HETATM 4 O O3P AMP . . . D 2 47.769 46.542 -22.424 1 50.56 ? O3P AMP 502 A 1 HETATM 5 O O5' AMP . . . D 2 48.674 48.658 -23.082 1 49.89 ? O5' AMP 502 A 1 HETATM 6 C C5' AMP . . . D 2 48.277 49.809 -22.342 1 55.76 ? C5' AMP 502 A 1 HETATM 7 C C4' AMP . . . D 2 49.396 50.804 -22.249 1 54.85 ? C4' AMP 502 A 1 HETATM 8 O O4' AMP . . . D 2 50.516 50.177 -21.559 1 44.85 ? O4' AMP 502 A 1 HETATM 9 C C3' AMP . . . D 2 49.942 51.264 -23.596 1 53.19 ? C3' AMP 502 A 1 HETATM 10 O O3' AMP . . . D 2 50.504 52.565 -23.465 1 60.88 ? O3' AMP 502 A 1 HETATM 11 C C2' AMP . . . D 2 51.045 50.251 -23.857 1 50.97 ? C2' AMP 502 A 1 HETATM 12 O O2' AMP . . . D 2 52.032 50.671 -24.77 1 59.62 ? O2' AMP 502 A 1 HETATM 13 C C1' AMP . . . D 2 51.615 50.052 -22.448 1 52.71 ? C1' AMP 502 A 1 HETATM 14 N N9 AMP . . . D 2 52.225 48.74 -22.241 1 49.74 ? N9 AMP 502 A 1 HETATM 15 C C8 AMP . . . D 2 51.572 47.563 -22.261 1 51.04 ? C8 AMP 502 A 1 HETATM 16 N N7 AMP . . . D 2 52.441 46.534 -22.063 1 48 ? N7 AMP 502 A 1 HETATM 17 C C5 AMP . . . D 2 53.671 47.057 -21.933 1 42.12 ? C5 AMP 502 A 1 HETATM 18 C C6 AMP . . . D 2 55.025 46.53 -21.686 1 44.16 ? C6 AMP 502 A 1 HETATM 19 N N6 AMP . . . D 2 55.252 45.2 -21.548 1 45.88 ? N6 AMP 502 A 1 HETATM 20 N N1 AMP . . . D 2 56.025 47.417 -21.607 1 43.16 ? N1 AMP 502 A 1 HETATM 21 C C2 AMP . . . D 2 55.828 48.741 -21.732 1 46.29 ? C2 AMP 502 A 1 HETATM 22 N N3 AMP . . . D 2 54.619 49.282 -21.949 1 53.22 ? N3 AMP 502 A 1 HETATM 23 C C4 AMP . . . D 2 53.522 48.505 -22.055 1 45.55 ? C4 AMP 502 A 1 HETATM 24 H "H5'1" AMP . . . D 2 47.974 49.508 -21.337 1 66.87 ? "H5'1" AMP 502 A 1 HETATM 25 H "H5'2" AMP . . . D 2 47.416 50.274 -22.826 1 66.87 ? "H5'2" AMP 502 A 1 HETATM 26 H H4' AMP . . . D 2 49.049 51.681 -21.686 1 65.78 ? H4' AMP 502 A 1 HETATM 27 H H3' AMP . . . D 2 49.168 51.216 -24.375 1 63.79 ? H3' AMP 502 A 1 HETATM 28 H HO3' AMP . . . D 2 50.85 52.854 -24.32 1 73.01 ? HO3' AMP 502 A 1 HETATM 29 H H2' AMP . . . D 2 50.592 49.308 -24.195 1 61.12 ? H2' AMP 502 A 1 HETATM 30 H HO2' AMP . . . D 2 51.624 50.839 -25.631 1 71.5 ? HO2' AMP 502 A 1 HETATM 31 H H1' AMP . . . D 2 52.35 50.844 -22.248 1 63.21 ? H1' AMP 502 A 1 HETATM 32 H H8 AMP . . . D 2 50.505 47.451 -22.409 1 61.21 ? H8 AMP 502 A 1 HETATM 33 H HN61 AMP . . . D 2 56.19 44.861 -21.39 1 55.01 ? HN61 AMP 502 A 1 HETATM 34 H HN62 AMP . . . D 2 54.484 44.547 -21.614 1 55.01 ? HN62 AMP 502 A 1 HETATM 35 H H2 AMP . . . D 2 56.684 49.4 -21.659 1 55.5 ? H2 AMP 502 A 1 # _model_server_stats.io_time_ms 58 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 342 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 35 #