data_1VKJ # _model_server_result.job_id rGE2RB-rqHgpeNKJ4zHS9w _model_server_result.datetime_utc '2024-10-19 02:17:13' _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 1vkj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":602}' # _entry.id 1VKJ # _exptl.entry_id 1VKJ _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 3 _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 1VKJ _cell.length_a 300.136 _cell.length_b 300.136 _cell.length_c 84.196 _cell.Z_PDB 48 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1VKJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 98 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 41 2 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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,K _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 E N N ? 3 F N N ? 3 G 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 disulf ? disulf1 A SG CYS 234 A CYS 260 1_555 A SG CYS 243 A CYS 269 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf2 B SG CYS 234 B CYS 260 1_555 B SG CYS 243 B CYS 269 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf3 C SG CYS 234 C CYS 260 1_555 C SG CYS 243 C CYS 269 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? # _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 1VKJ _atom_sites.fract_transf_matrix[1][1] 0.003332 _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] 0.003332 _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] 0.011877 _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 D 2 SO4 A 1 601 601 SO4 SO4 . E 3 A3P A 1 602 301 A3P A3P . F 3 A3P A 1 603 302 A3P A3P . G 3 A3P A 1 604 303 A3P A3P . H 2 SO4 B 1 602 602 SO4 SO4 . I 4 HOH A 1 605 1 HOH HOH . I 4 HOH A 2 606 2 HOH HOH . I 4 HOH A 3 607 3 HOH HOH . I 4 HOH A 4 608 4 HOH HOH . I 4 HOH A 5 609 5 HOH HOH . I 4 HOH A 6 610 6 HOH HOH . I 4 HOH A 7 611 7 HOH HOH . I 4 HOH A 8 612 8 HOH HOH . I 4 HOH A 9 613 9 HOH HOH . I 4 HOH A 10 614 10 HOH HOH . I 4 HOH A 11 615 11 HOH HOH . I 4 HOH A 12 616 12 HOH HOH . I 4 HOH A 13 617 13 HOH HOH . I 4 HOH A 14 618 14 HOH HOH . I 4 HOH A 15 619 15 HOH HOH . I 4 HOH A 16 620 16 HOH HOH . I 4 HOH A 17 621 17 HOH HOH . I 4 HOH A 18 622 18 HOH HOH . I 4 HOH A 19 623 19 HOH HOH . I 4 HOH A 20 624 20 HOH HOH . I 4 HOH A 21 625 21 HOH HOH . I 4 HOH A 22 626 22 HOH HOH . I 4 HOH A 23 627 23 HOH HOH . I 4 HOH A 24 628 24 HOH HOH . I 4 HOH A 25 629 25 HOH HOH . I 4 HOH A 26 630 26 HOH HOH . I 4 HOH A 27 631 27 HOH HOH . I 4 HOH A 28 632 28 HOH HOH . I 4 HOH A 29 633 29 HOH HOH . I 4 HOH A 30 634 30 HOH HOH . I 4 HOH A 31 635 31 HOH HOH . I 4 HOH A 32 636 34 HOH HOH . I 4 HOH A 33 637 35 HOH HOH . I 4 HOH A 34 638 51 HOH HOH . I 4 HOH A 35 639 72 HOH HOH . I 4 HOH A 36 640 73 HOH HOH . I 4 HOH A 37 641 74 HOH HOH . I 4 HOH A 38 642 75 HOH HOH . I 4 HOH A 39 643 76 HOH HOH . I 4 HOH A 40 644 77 HOH HOH . I 4 HOH A 41 645 78 HOH HOH . I 4 HOH A 42 646 79 HOH HOH . I 4 HOH A 43 647 81 HOH HOH . I 4 HOH A 44 648 86 HOH HOH . I 4 HOH A 45 649 87 HOH HOH . I 4 HOH A 46 650 88 HOH HOH . I 4 HOH A 47 651 89 HOH HOH . I 4 HOH A 48 652 90 HOH HOH . I 4 HOH A 49 653 119 HOH HOH . I 4 HOH A 50 654 120 HOH HOH . I 4 HOH A 51 655 121 HOH HOH . I 4 HOH A 52 656 122 HOH HOH . I 4 HOH A 53 657 123 HOH HOH . I 4 HOH A 54 658 124 HOH HOH . I 4 HOH A 55 659 125 HOH HOH . I 4 HOH A 56 660 126 HOH HOH . I 4 HOH A 57 661 127 HOH HOH . I 4 HOH A 58 662 128 HOH HOH . I 4 HOH A 59 663 129 HOH HOH . I 4 HOH A 60 664 130 HOH HOH . I 4 HOH A 61 665 131 HOH HOH . I 4 HOH A 62 666 132 HOH HOH . I 4 HOH A 63 667 133 HOH HOH . I 4 HOH A 64 668 134 HOH HOH . I 4 HOH A 65 669 135 HOH HOH . I 4 HOH A 66 670 136 HOH HOH . I 4 HOH A 67 671 137 HOH HOH . I 4 HOH A 68 672 138 HOH HOH . I 4 HOH A 69 673 139 HOH HOH . I 4 HOH A 70 674 149 HOH HOH . I 4 HOH A 71 675 160 HOH HOH . I 4 HOH A 72 676 162 HOH HOH . I 4 HOH A 73 677 163 HOH HOH . I 4 HOH A 74 678 164 HOH HOH . I 4 HOH A 75 679 165 HOH HOH . I 4 HOH A 76 680 166 HOH HOH . I 4 HOH A 77 681 168 HOH HOH . I 4 HOH A 78 682 176 HOH HOH . I 4 HOH A 79 683 178 HOH HOH . J 4 HOH B 1 603 32 HOH HOH . J 4 HOH B 2 604 33 HOH HOH . J 4 HOH B 3 605 36 HOH HOH . J 4 HOH B 4 606 37 HOH HOH . J 4 HOH B 5 607 38 HOH HOH . J 4 HOH B 6 608 39 HOH HOH . J 4 HOH B 7 609 40 HOH HOH . J 4 HOH B 8 610 41 HOH HOH . J 4 HOH B 9 611 42 HOH HOH . J 4 HOH B 10 612 43 HOH HOH . J 4 HOH B 11 613 44 HOH HOH . J 4 HOH B 12 614 45 HOH HOH . J 4 HOH B 13 615 46 HOH HOH . J 4 HOH B 14 616 47 HOH HOH . J 4 HOH B 15 617 48 HOH HOH . J 4 HOH B 16 618 49 HOH HOH . J 4 HOH B 17 619 50 HOH HOH . J 4 HOH B 18 620 52 HOH HOH . J 4 HOH B 19 621 53 HOH HOH . J 4 HOH B 20 622 54 HOH HOH . J 4 HOH B 21 623 55 HOH HOH . J 4 HOH B 22 624 56 HOH HOH . J 4 HOH B 23 625 57 HOH HOH . J 4 HOH B 24 626 58 HOH HOH . J 4 HOH B 25 627 59 HOH HOH . J 4 HOH B 26 628 60 HOH HOH . J 4 HOH B 27 629 61 HOH HOH . J 4 HOH B 28 630 62 HOH HOH . J 4 HOH B 29 631 63 HOH HOH . J 4 HOH B 30 632 64 HOH HOH . J 4 HOH B 31 633 65 HOH HOH . J 4 HOH B 32 634 66 HOH HOH . J 4 HOH B 33 635 67 HOH HOH . J 4 HOH B 34 636 69 HOH HOH . J 4 HOH B 35 637 70 HOH HOH . J 4 HOH B 36 638 71 HOH HOH . J 4 HOH B 37 639 80 HOH HOH . J 4 HOH B 38 640 82 HOH HOH . J 4 HOH B 39 641 83 HOH HOH . J 4 HOH B 40 642 84 HOH HOH . J 4 HOH B 41 643 85 HOH HOH . J 4 HOH B 42 644 91 HOH HOH . J 4 HOH B 43 645 92 HOH HOH . J 4 HOH B 44 646 93 HOH HOH . J 4 HOH B 45 647 94 HOH HOH . J 4 HOH B 46 648 95 HOH HOH . J 4 HOH B 47 649 96 HOH HOH . J 4 HOH B 48 650 97 HOH HOH . J 4 HOH B 49 651 98 HOH HOH . J 4 HOH B 50 652 99 HOH HOH . J 4 HOH B 51 653 100 HOH HOH . J 4 HOH B 52 654 101 HOH HOH . J 4 HOH B 53 655 102 HOH HOH . J 4 HOH B 54 656 103 HOH HOH . J 4 HOH B 55 657 104 HOH HOH . J 4 HOH B 56 658 105 HOH HOH . J 4 HOH B 57 659 106 HOH HOH . J 4 HOH B 58 660 107 HOH HOH . J 4 HOH B 59 661 108 HOH HOH . J 4 HOH B 60 662 109 HOH HOH . J 4 HOH B 61 663 110 HOH HOH . J 4 HOH B 62 664 111 HOH HOH . J 4 HOH B 63 665 112 HOH HOH . J 4 HOH B 64 666 113 HOH HOH . J 4 HOH B 65 667 114 HOH HOH . J 4 HOH B 66 668 115 HOH HOH . J 4 HOH B 67 669 116 HOH HOH . J 4 HOH B 68 670 117 HOH HOH . J 4 HOH B 69 671 118 HOH HOH . J 4 HOH B 70 672 140 HOH HOH . J 4 HOH B 71 673 141 HOH HOH . J 4 HOH B 72 674 142 HOH HOH . J 4 HOH B 73 675 143 HOH HOH . J 4 HOH B 74 676 144 HOH HOH . J 4 HOH B 75 677 145 HOH HOH . J 4 HOH B 76 678 146 HOH HOH . J 4 HOH B 77 679 147 HOH HOH . J 4 HOH B 78 680 148 HOH HOH . J 4 HOH B 79 681 150 HOH HOH . J 4 HOH B 80 682 151 HOH HOH . J 4 HOH B 81 683 152 HOH HOH . J 4 HOH B 82 684 153 HOH HOH . J 4 HOH B 83 685 154 HOH HOH . J 4 HOH B 84 686 155 HOH HOH . J 4 HOH B 85 687 156 HOH HOH . J 4 HOH B 86 688 157 HOH HOH . J 4 HOH B 87 689 158 HOH HOH . J 4 HOH B 88 690 159 HOH HOH . J 4 HOH B 89 691 161 HOH HOH . J 4 HOH B 90 692 167 HOH HOH . J 4 HOH B 91 693 169 HOH HOH . J 4 HOH B 92 694 170 HOH HOH . J 4 HOH B 93 695 171 HOH HOH . J 4 HOH B 94 696 172 HOH HOH . J 4 HOH B 95 697 173 HOH HOH . J 4 HOH B 96 698 174 HOH HOH . J 4 HOH B 97 699 175 HOH HOH . J 4 HOH B 98 700 177 HOH HOH . K 4 HOH C 1 312 68 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 18.985 85.514 28.673 1 35.94 ? P1 A3P 602 A 1 HETATM 2 O O1P A3P . . . E 3 19 86.06 30.097 1 38.13 ? O1P A3P 602 A 1 HETATM 3 O O2P A3P . . . E 3 19.697 84.174 28.608 1 36.47 ? O2P A3P 602 A 1 HETATM 4 O O3P A3P . . . E 3 17.624 85.417 28.021 1 33.13 ? O3P A3P 602 A 1 HETATM 5 P P2 A3P . . . E 3 20.818 88.669 22.597 1 31.65 ? P2 A3P 602 A 1 HETATM 6 O O4P A3P . . . E 3 22.135 89.137 21.997 1 31.46 ? O4P A3P 602 A 1 HETATM 7 O O5P A3P . . . E 3 19.736 89.724 22.447 1 27.72 ? O5P A3P 602 A 1 HETATM 8 O O6P A3P . . . E 3 20.35 87.301 22.114 1 27.37 ? O6P A3P 602 A 1 HETATM 9 O O5' A3P . . . E 3 21.126 88.533 24.2 1 30.09 ? O5' A3P 602 A 1 HETATM 10 C C5' A3P . . . E 3 20.068 88.138 25.092 1 32.17 ? C5' A3P 602 A 1 HETATM 11 C C4' A3P . . . E 3 20.457 88.402 26.514 1 32.98 ? C4' A3P 602 A 1 HETATM 12 O O4' A3P . . . E 3 20.464 89.818 26.763 1 33.3 ? O4' A3P 602 A 1 HETATM 13 C C3' A3P . . . E 3 19.521 87.85 27.576 1 31.89 ? C3' A3P 602 A 1 HETATM 14 O O3' A3P . . . E 3 19.93 86.522 27.841 1 31.92 ? O3' A3P 602 A 1 HETATM 15 C C2' A3P . . . E 3 19.773 88.774 28.772 1 32.55 ? C2' A3P 602 A 1 HETATM 16 O O2' A3P . . . E 3 20.644 88.173 29.686 1 34.78 ? O2' A3P 602 A 1 HETATM 17 C C1' A3P . . . E 3 20.472 89.997 28.151 1 32.44 ? C1' A3P 602 A 1 HETATM 18 N N9 A3P . . . E 3 19.877 91.301 28.457 1 31.01 ? N9 A3P 602 A 1 HETATM 19 C C8 A3P . . . E 3 20.572 92.47 28.647 1 32.74 ? C8 A3P 602 A 1 HETATM 20 N N7 A3P . . . E 3 19.814 93.501 28.946 1 30.64 ? N7 A3P 602 A 1 HETATM 21 C C5 A3P . . . E 3 18.537 92.975 28.951 1 29.14 ? C5 A3P 602 A 1 HETATM 22 C C6 A3P . . . E 3 17.299 93.553 29.231 1 29.88 ? C6 A3P 602 A 1 HETATM 23 N N6 A3P . . . E 3 17.169 94.813 29.647 1 29.62 ? N6 A3P 602 A 1 HETATM 24 N N1 A3P . . . E 3 16.191 92.781 29.099 1 27.92 ? N1 A3P 602 A 1 HETATM 25 C C2 A3P . . . E 3 16.356 91.496 28.764 1 28.61 ? C2 A3P 602 A 1 HETATM 26 N N3 A3P . . . E 3 17.491 90.814 28.545 1 29.53 ? N3 A3P 602 A 1 HETATM 27 C C4 A3P . . . E 3 18.555 91.626 28.636 1 29.38 ? C4 A3P 602 A 1 # _model_server_stats.io_time_ms 117 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 342 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 27 #