data_1X8J # _model_server_result.job_id ZU9TyM9JxX5proId4DoVLg _model_server_result.datetime_utc '2024-10-18 15:26:15' _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 1x8j # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":602}' # _entry.id 1X8J # _exptl.entry_id 1X8J _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-3'-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 111.17 _cell.angle_gamma 90 _cell.entry_id 1X8J _cell.length_a 81.767 _cell.length_b 66.762 _cell.length_c 84.503 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1X8J _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J _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 ? 3 D N N ? 3 E N N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc ? metalc1 A O GLU 118 A GLU 118 1_555 C CA CA . A CA 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.809 ? metalc ? metalc2 A OD1 ASN 121 A ASN 121 1_555 C CA CA . A CA 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.517 ? metalc ? metalc3 A OD1 ASP 122 A ASP 122 1_555 C CA CA . A CA 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.47 ? metalc ? metalc4 B O GLU 118 B GLU 118 1_555 G CA CA . B CA 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.805 ? metalc ? metalc5 B OD1 ASN 121 B ASN 121 1_555 G CA CA . B CA 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.516 ? metalc ? metalc6 B OD1 ASP 122 B ASP 122 1_555 G CA CA . B CA 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.573 ? # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id A3P _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-3'-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _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 P1 O1P A3P doub 1 n n P1 O2P A3P sing 2 n n P1 O3P A3P sing 3 n n P1 O3' A3P sing 4 n n O2P HOP2 A3P sing 5 n n O3P HOP3 A3P sing 6 n n P2 O4P A3P doub 7 n n P2 O5P A3P sing 8 n n P2 O6P A3P sing 9 n n P2 O5' A3P sing 10 n n O5P HOP5 A3P sing 11 n n O6P HOP6 A3P sing 12 n n O5' C5' A3P sing 13 n n C5' C4' A3P sing 14 n n C5' "H5'1" A3P sing 15 n n C5' "H5'2" A3P sing 16 n n C4' O4' A3P sing 17 n n C4' C3' A3P sing 18 n n C4' H4' A3P sing 19 n n O4' C1' A3P sing 20 n n C3' O3' A3P sing 21 n n C3' C2' A3P sing 22 n n C3' H3' A3P sing 23 n n C2' O2' A3P sing 24 n n C2' C1' A3P sing 25 n n C2' H2' A3P sing 26 n n O2' HO2' A3P sing 27 n n C1' N9 A3P sing 28 n n C1' H1' A3P sing 29 n n N9 C8 A3P sing 30 n y N9 C4 A3P sing 31 n y C8 N7 A3P doub 32 n y C8 H8 A3P sing 33 n n N7 C5 A3P sing 34 n y C5 C6 A3P sing 35 n y C5 C4 A3P doub 36 n y C6 N6 A3P sing 37 n n C6 N1 A3P doub 38 n y N6 HN61 A3P sing 39 n n N6 HN62 A3P sing 40 n n N1 C2 A3P sing 41 n y C2 N3 A3P doub 42 n y C2 H2 A3P sing 43 n n N3 C4 A3P sing 44 n y # _atom_sites.entry_id 1X8J _atom_sites.fract_transf_matrix[1][1] 0.01223 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004736 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014979 _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] 0.01269 _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 CA A 1 600 100 CA CA . D 3 A3P A 1 601 100 A3P A3P . E 3 A3P A 1 602 200 A3P A3P . F 4 AOI A 1 400 100 AOI AE2 . G 2 CA B 1 700 200 CA CA . H 4 AOI B 1 500 200 AOI AE2 . I 5 HOH A 1 603 2 HOH HOH . I 5 HOH A 2 604 3 HOH HOH . I 5 HOH A 3 605 4 HOH HOH . I 5 HOH A 4 606 7 HOH HOH . I 5 HOH A 5 607 10 HOH HOH . I 5 HOH A 6 608 11 HOH HOH . I 5 HOH A 7 609 15 HOH HOH . I 5 HOH A 8 610 16 HOH HOH . I 5 HOH A 9 611 17 HOH HOH . I 5 HOH A 10 612 18 HOH HOH . I 5 HOH A 11 613 20 HOH HOH . I 5 HOH A 12 614 21 HOH HOH . I 5 HOH A 13 615 25 HOH HOH . I 5 HOH A 14 616 27 HOH HOH . I 5 HOH A 15 617 28 HOH HOH . I 5 HOH A 16 618 29 HOH HOH . I 5 HOH A 17 619 31 HOH HOH . I 5 HOH A 18 620 32 HOH HOH . I 5 HOH A 19 621 33 HOH HOH . I 5 HOH A 20 622 34 HOH HOH . I 5 HOH A 21 623 36 HOH HOH . I 5 HOH A 22 624 37 HOH HOH . I 5 HOH A 23 625 41 HOH HOH . I 5 HOH A 24 626 45 HOH HOH . I 5 HOH A 25 627 48 HOH HOH . I 5 HOH A 26 628 49 HOH HOH . I 5 HOH A 27 629 50 HOH HOH . I 5 HOH A 28 630 55 HOH HOH . I 5 HOH A 29 631 57 HOH HOH . I 5 HOH A 30 632 58 HOH HOH . I 5 HOH A 31 633 59 HOH HOH . I 5 HOH A 32 634 62 HOH HOH . I 5 HOH A 33 635 63 HOH HOH . I 5 HOH A 34 636 64 HOH HOH . I 5 HOH A 35 637 65 HOH HOH . I 5 HOH A 36 638 66 HOH HOH . I 5 HOH A 37 639 68 HOH HOH . I 5 HOH A 38 640 69 HOH HOH . I 5 HOH A 39 641 70 HOH HOH . I 5 HOH A 40 642 71 HOH HOH . I 5 HOH A 41 643 72 HOH HOH . I 5 HOH A 42 644 73 HOH HOH . I 5 HOH A 43 645 76 HOH HOH . I 5 HOH A 44 646 77 HOH HOH . I 5 HOH A 45 647 81 HOH HOH . I 5 HOH A 46 648 83 HOH HOH . I 5 HOH A 47 649 86 HOH HOH . I 5 HOH A 48 650 88 HOH HOH . I 5 HOH A 49 651 89 HOH HOH . I 5 HOH A 50 652 92 HOH HOH . I 5 HOH A 51 653 94 HOH HOH . I 5 HOH A 52 654 97 HOH HOH . I 5 HOH A 53 655 98 HOH HOH . I 5 HOH A 54 656 101 HOH HOH . I 5 HOH A 55 657 107 HOH HOH . I 5 HOH A 56 658 112 HOH HOH . I 5 HOH A 57 659 113 HOH HOH . I 5 HOH A 58 660 115 HOH HOH . I 5 HOH A 59 661 119 HOH HOH . I 5 HOH A 60 662 120 HOH HOH . I 5 HOH A 61 663 121 HOH HOH . I 5 HOH A 62 664 124 HOH HOH . I 5 HOH A 63 665 125 HOH HOH . I 5 HOH A 64 666 126 HOH HOH . I 5 HOH A 65 667 128 HOH HOH . I 5 HOH A 66 668 130 HOH HOH . I 5 HOH A 67 669 133 HOH HOH . J 5 HOH B 1 701 1 HOH HOH . J 5 HOH B 2 702 5 HOH HOH . J 5 HOH B 3 703 6 HOH HOH . J 5 HOH B 4 704 8 HOH HOH . J 5 HOH B 5 705 9 HOH HOH . J 5 HOH B 6 706 12 HOH HOH . J 5 HOH B 7 707 13 HOH HOH . J 5 HOH B 8 708 14 HOH HOH . J 5 HOH B 9 709 19 HOH HOH . J 5 HOH B 10 710 22 HOH HOH . J 5 HOH B 11 711 23 HOH HOH . J 5 HOH B 12 712 24 HOH HOH . J 5 HOH B 13 713 26 HOH HOH . J 5 HOH B 14 714 30 HOH HOH . J 5 HOH B 15 715 35 HOH HOH . J 5 HOH B 16 716 38 HOH HOH . J 5 HOH B 17 717 39 HOH HOH . J 5 HOH B 18 718 40 HOH HOH . J 5 HOH B 19 719 42 HOH HOH . J 5 HOH B 20 720 43 HOH HOH . J 5 HOH B 21 721 44 HOH HOH . J 5 HOH B 22 722 46 HOH HOH . J 5 HOH B 23 723 47 HOH HOH . J 5 HOH B 24 724 51 HOH HOH . J 5 HOH B 25 725 52 HOH HOH . J 5 HOH B 26 726 53 HOH HOH . J 5 HOH B 27 727 54 HOH HOH . J 5 HOH B 28 728 56 HOH HOH . J 5 HOH B 29 729 60 HOH HOH . J 5 HOH B 30 730 61 HOH HOH . J 5 HOH B 31 731 67 HOH HOH . J 5 HOH B 32 732 74 HOH HOH . J 5 HOH B 33 733 75 HOH HOH . J 5 HOH B 34 734 78 HOH HOH . J 5 HOH B 35 735 79 HOH HOH . J 5 HOH B 36 736 80 HOH HOH . J 5 HOH B 37 737 82 HOH HOH . J 5 HOH B 38 738 84 HOH HOH . J 5 HOH B 39 739 85 HOH HOH . J 5 HOH B 40 740 87 HOH HOH . J 5 HOH B 41 741 90 HOH HOH . J 5 HOH B 42 742 91 HOH HOH . J 5 HOH B 43 743 93 HOH HOH . J 5 HOH B 44 744 95 HOH HOH . J 5 HOH B 45 745 96 HOH HOH . J 5 HOH B 46 746 99 HOH HOH . J 5 HOH B 47 747 100 HOH HOH . J 5 HOH B 48 748 102 HOH HOH . J 5 HOH B 49 749 103 HOH HOH . J 5 HOH B 50 750 104 HOH HOH . J 5 HOH B 51 751 105 HOH HOH . J 5 HOH B 52 752 106 HOH HOH . J 5 HOH B 53 753 108 HOH HOH . J 5 HOH B 54 754 109 HOH HOH . J 5 HOH B 55 755 110 HOH HOH . J 5 HOH B 56 756 111 HOH HOH . J 5 HOH B 57 757 114 HOH HOH . J 5 HOH B 58 758 116 HOH HOH . J 5 HOH B 59 759 117 HOH HOH . J 5 HOH B 60 760 118 HOH HOH . J 5 HOH B 61 761 122 HOH HOH . J 5 HOH B 62 762 123 HOH HOH . J 5 HOH B 63 763 127 HOH HOH . J 5 HOH B 64 764 129 HOH HOH . J 5 HOH B 65 765 131 HOH HOH . J 5 HOH B 66 766 132 HOH HOH . J 5 HOH B 67 767 134 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 P1 A3P . . . E 3 51.453 -8.155 7.775 1 33.84 ? P1 A3P 602 A 1 HETATM 2 O O1P A3P . . . E 3 50.629 -7.474 6.746 1 33.47 ? O1P A3P 602 A 1 HETATM 3 O O2P A3P . . . E 3 50.604 -8.901 8.7 1 32.38 ? O2P A3P 602 A 1 HETATM 4 O O3P A3P . . . E 3 52.44 -9.047 7.138 1 25.43 ? O3P A3P 602 A 1 HETATM 5 P P2 A3P . . . E 3 53.312 -1.156 9.961 1 31.56 ? P2 A3P 602 A 1 HETATM 6 O O4P A3P . . . E 3 52.346 -0.546 8.982 1 36 ? O4P A3P 602 A 1 HETATM 7 O O5P A3P . . . E 3 54.649 -0.59 9.804 1 28.01 ? O5P A3P 602 A 1 HETATM 8 O O6P A3P . . . E 3 52.816 -0.985 11.332 1 27.72 ? O6P A3P 602 A 1 HETATM 9 O O5' A3P . . . E 3 53.413 -2.692 9.635 1 36.08 ? O5' A3P 602 A 1 HETATM 10 C C5' A3P . . . E 3 52.288 -3.548 9.67 1 34.4 ? C5' A3P 602 A 1 HETATM 11 C C4' A3P . . . E 3 52.76 -5.002 9.691 1 36.25 ? C4' A3P 602 A 1 HETATM 12 O O4' A3P . . . E 3 53.195 -5.333 11.057 1 34.3 ? O4' A3P 602 A 1 HETATM 13 C C3' A3P . . . E 3 51.657 -5.989 9.362 1 35.77 ? C3' A3P 602 A 1 HETATM 14 O O3' A3P . . . E 3 52.261 -7.073 8.596 1 34.17 ? O3' A3P 602 A 1 HETATM 15 C C2' A3P . . . E 3 51.124 -6.321 10.763 1 34.16 ? C2' A3P 602 A 1 HETATM 16 O O2' A3P . . . E 3 50.238 -7.429 10.915 1 33.84 ? O2' A3P 602 A 1 HETATM 17 C C1' A3P . . . E 3 52.425 -6.42 11.547 1 32.63 ? C1' A3P 602 A 1 HETATM 18 N N9 A3P . . . E 3 52.219 -6.287 12.997 1 31.21 ? N9 A3P 602 A 1 HETATM 19 C C8 A3P . . . E 3 51.503 -5.335 13.708 1 30.84 ? C8 A3P 602 A 1 HETATM 20 N N7 A3P . . . E 3 51.506 -5.5 15.01 1 32.27 ? N7 A3P 602 A 1 HETATM 21 C C5 A3P . . . E 3 52.28 -6.645 15.186 1 33.9 ? C5 A3P 602 A 1 HETATM 22 C C6 A3P . . . E 3 52.701 -7.409 16.348 1 31.83 ? C6 A3P 602 A 1 HETATM 23 N N6 A3P . . . E 3 52.366 -7.098 17.607 1 28.9 ? N6 A3P 602 A 1 HETATM 24 N N1 A3P . . . E 3 53.498 -8.529 16.142 1 34.29 ? N1 A3P 602 A 1 HETATM 25 C C2 A3P . . . E 3 53.869 -8.898 14.881 1 30.44 ? C2 A3P 602 A 1 HETATM 26 N N3 A3P . . . E 3 53.535 -8.267 13.72 1 35.14 ? N3 A3P 602 A 1 HETATM 27 C C4 A3P . . . E 3 52.738 -7.146 13.939 1 31.48 ? C4 A3P 602 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 278 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #