data_2VP3 # _model_server_result.job_id aIBa3RTIwvE-NwEpKDtTiw _model_server_result.datetime_utc '2024-11-09 02:26:28' _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 2vp3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 2VP3 # _exptl.entry_id 2VP3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 458.235 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE" _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 117.3 _cell.angle_gamma 90 _cell.entry_id 2VP3 _cell.length_a 84.6 _cell.length_b 67.3 _cell.length_c 79.6 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2VP3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 1 2 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 _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 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C11 H18 N5 O11 P2 1' _chem_comp.formula_weight 458.235 _chem_comp.id M7G _chem_comp.mon_nstd_flag . _chem_comp.name "7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE" _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 PA O1A M7G doub 218 n n PA O2A M7G sing 219 n n PA O3A M7G sing 220 n n PA O5' M7G sing 221 n n O2A HOA2 M7G sing 222 n n O3A PB M7G sing 223 n n O5' C5' M7G sing 224 n n PB O1B M7G doub 225 n n PB O2B M7G sing 226 n n PB O3B M7G sing 227 n n O2B HOB2 M7G sing 228 n n O3B HOB3 M7G sing 229 n n C5' C4' M7G sing 230 n n C5' "H5'1" M7G sing 231 n n C5' "H5'2" M7G sing 232 n n C4' O4' M7G sing 233 n n C4' C3' M7G sing 234 n n C4' H4' M7G sing 235 n n O4' C1' M7G sing 236 n n C3' O3' M7G sing 237 n n C3' C2' M7G sing 238 n n C3' H3' M7G sing 239 n n O3' HO3' M7G sing 240 n n C2' O2' M7G sing 241 n n C2' C1' M7G sing 242 n n C2' H2' M7G sing 243 n n O2' HO2' M7G sing 244 n n C1' N9 M7G sing 245 n n C1' H1' M7G sing 246 n n N9 C8 M7G sing 247 n y N9 C4 M7G sing 248 n y C8 N7 M7G doub 249 n y C8 H81 M7G sing 250 n n N7 CM7 M7G sing 251 n n N7 C5 M7G sing 252 n y CM7 HM71 M7G sing 253 n n CM7 HM72 M7G sing 254 n n CM7 HM73 M7G sing 255 n n C5 C6 M7G sing 256 n n C5 C4 M7G doub 257 n y C6 O6 M7G doub 258 n n C6 N1 M7G sing 259 n n N1 C2 M7G sing 260 n n N1 HN1 M7G sing 261 n n C2 N2 M7G sing 262 n n C2 N3 M7G doub 263 n n N2 HN21 M7G sing 264 n n N2 HN22 M7G sing 265 n n N3 C4 M7G sing 266 n n # _atom_sites.entry_id 2VP3 _atom_sites.fract_transf_matrix[1][1] 0.01182 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.006101 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014859 _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] 0.014137 _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 SAH A 1 400 400 SAH SAH . C 3 M7G A 1 401 401 M7G MDG . D 4 HOH A 1 501 501 HOH HOH . D 4 HOH A 2 502 502 HOH HOH . D 4 HOH A 3 504 504 HOH HOH . D 4 HOH A 4 505 505 HOH HOH . D 4 HOH A 5 506 506 HOH HOH . D 4 HOH A 6 507 507 HOH HOH . D 4 HOH A 7 508 508 HOH HOH . D 4 HOH A 8 509 509 HOH HOH . D 4 HOH A 9 510 510 HOH HOH . D 4 HOH A 10 511 511 HOH HOH . D 4 HOH A 11 512 512 HOH HOH . D 4 HOH A 12 513 513 HOH HOH . D 4 HOH A 13 517 517 HOH HOH . D 4 HOH A 14 518 518 HOH HOH . D 4 HOH A 15 519 519 HOH HOH . D 4 HOH A 16 520 520 HOH HOH . D 4 HOH A 17 521 521 HOH HOH . D 4 HOH A 18 522 522 HOH HOH . D 4 HOH A 19 523 523 HOH HOH . D 4 HOH A 20 524 524 HOH HOH . D 4 HOH A 21 525 525 HOH HOH . D 4 HOH A 22 526 526 HOH HOH . D 4 HOH A 23 527 527 HOH HOH . D 4 HOH A 24 528 528 HOH HOH . D 4 HOH A 25 529 529 HOH HOH . D 4 HOH A 26 530 530 HOH HOH . D 4 HOH A 27 531 531 HOH HOH . D 4 HOH A 28 532 532 HOH HOH . D 4 HOH A 29 533 533 HOH HOH . D 4 HOH A 30 534 534 HOH HOH . D 4 HOH A 31 535 535 HOH HOH . D 4 HOH A 32 536 536 HOH HOH . D 4 HOH A 33 537 537 HOH HOH . D 4 HOH A 34 538 538 HOH HOH . D 4 HOH A 35 539 539 HOH HOH . D 4 HOH A 36 540 540 HOH HOH . D 4 HOH A 37 541 541 HOH HOH . D 4 HOH A 38 542 542 HOH HOH . D 4 HOH A 39 543 543 HOH HOH . D 4 HOH A 40 544 544 HOH HOH . D 4 HOH A 41 545 545 HOH HOH . D 4 HOH A 42 546 546 HOH HOH . D 4 HOH A 43 547 547 HOH HOH . D 4 HOH A 44 548 548 HOH HOH . D 4 HOH A 45 549 549 HOH HOH . D 4 HOH A 46 550 550 HOH HOH . D 4 HOH A 47 551 551 HOH HOH . D 4 HOH A 48 552 552 HOH HOH . D 4 HOH A 49 553 553 HOH HOH . D 4 HOH A 50 554 554 HOH HOH . D 4 HOH A 51 555 555 HOH HOH . D 4 HOH A 52 556 556 HOH HOH . D 4 HOH A 53 557 557 HOH HOH . D 4 HOH A 54 558 558 HOH HOH . D 4 HOH A 55 559 559 HOH HOH . D 4 HOH A 56 560 560 HOH HOH . D 4 HOH A 57 561 561 HOH HOH . D 4 HOH A 58 562 562 HOH HOH . D 4 HOH A 59 563 563 HOH HOH . D 4 HOH A 60 564 564 HOH HOH . D 4 HOH A 61 565 565 HOH HOH . D 4 HOH A 62 566 566 HOH HOH . D 4 HOH A 63 568 568 HOH HOH . D 4 HOH A 64 569 569 HOH HOH . D 4 HOH A 65 570 570 HOH HOH . D 4 HOH A 66 571 571 HOH HOH . D 4 HOH A 67 572 572 HOH HOH . D 4 HOH A 68 574 574 HOH HOH . D 4 HOH A 69 575 575 HOH HOH . D 4 HOH A 70 576 576 HOH HOH . D 4 HOH A 71 577 577 HOH HOH . D 4 HOH A 72 578 578 HOH HOH . D 4 HOH A 73 579 579 HOH HOH . D 4 HOH A 74 580 580 HOH HOH . D 4 HOH A 75 581 581 HOH HOH . D 4 HOH A 76 582 582 HOH HOH . D 4 HOH A 77 583 583 HOH HOH . D 4 HOH A 78 584 584 HOH HOH . D 4 HOH A 79 585 585 HOH HOH . D 4 HOH A 80 586 586 HOH HOH . D 4 HOH A 81 587 587 HOH HOH . D 4 HOH A 82 588 588 HOH HOH . D 4 HOH A 83 589 589 HOH HOH . D 4 HOH A 84 590 590 HOH HOH . D 4 HOH A 85 591 591 HOH HOH . D 4 HOH A 86 592 592 HOH HOH . D 4 HOH A 87 593 593 HOH HOH . D 4 HOH A 88 595 595 HOH HOH . D 4 HOH A 89 596 596 HOH HOH . D 4 HOH A 90 597 597 HOH HOH . D 4 HOH A 91 598 598 HOH HOH . D 4 HOH A 92 599 599 HOH HOH . D 4 HOH A 93 600 600 HOH HOH . D 4 HOH A 94 601 601 HOH HOH . D 4 HOH A 95 602 602 HOH HOH . D 4 HOH A 96 603 603 HOH HOH . D 4 HOH A 97 604 604 HOH HOH . D 4 HOH A 98 605 605 HOH HOH . D 4 HOH A 99 606 606 HOH HOH . D 4 HOH A 100 607 607 HOH HOH . D 4 HOH A 101 609 609 HOH HOH . D 4 HOH A 102 610 610 HOH HOH . D 4 HOH A 103 611 611 HOH HOH . D 4 HOH A 104 612 612 HOH HOH . D 4 HOH A 105 613 613 HOH HOH . D 4 HOH A 106 614 614 HOH HOH . D 4 HOH A 107 615 615 HOH HOH . D 4 HOH A 108 616 616 HOH HOH . D 4 HOH A 109 618 618 HOH HOH . D 4 HOH A 110 619 619 HOH HOH . D 4 HOH A 111 620 620 HOH HOH . D 4 HOH A 112 621 621 HOH HOH . D 4 HOH A 113 622 622 HOH HOH . D 4 HOH A 114 623 623 HOH HOH . D 4 HOH A 115 624 624 HOH HOH . D 4 HOH A 116 625 625 HOH HOH . D 4 HOH A 117 626 626 HOH HOH . D 4 HOH A 118 627 627 HOH HOH . D 4 HOH A 119 628 628 HOH HOH . D 4 HOH A 120 629 629 HOH HOH . D 4 HOH A 121 630 630 HOH HOH . D 4 HOH A 122 631 631 HOH HOH . D 4 HOH A 123 632 632 HOH HOH . D 4 HOH A 124 633 633 HOH HOH . D 4 HOH A 125 634 634 HOH HOH . D 4 HOH A 126 635 635 HOH HOH . D 4 HOH A 127 636 636 HOH HOH . D 4 HOH A 128 637 637 HOH HOH . D 4 HOH A 129 638 638 HOH HOH . D 4 HOH A 130 639 639 HOH HOH . D 4 HOH A 131 640 640 HOH HOH . D 4 HOH A 132 641 641 HOH HOH . D 4 HOH A 133 642 642 HOH HOH . D 4 HOH A 134 643 643 HOH HOH . D 4 HOH A 135 644 644 HOH HOH . D 4 HOH A 136 645 645 HOH HOH . D 4 HOH A 137 646 646 HOH HOH . D 4 HOH A 138 647 647 HOH HOH . D 4 HOH A 139 648 648 HOH HOH . D 4 HOH A 140 649 649 HOH HOH . D 4 HOH A 141 650 650 HOH HOH . D 4 HOH A 142 651 651 HOH HOH . D 4 HOH A 143 652 652 HOH HOH . D 4 HOH A 144 653 653 HOH HOH . D 4 HOH A 145 654 654 HOH HOH . D 4 HOH A 146 655 655 HOH HOH . D 4 HOH A 147 656 656 HOH HOH . D 4 HOH A 148 657 657 HOH HOH . D 4 HOH A 149 658 658 HOH HOH . D 4 HOH A 150 659 659 HOH HOH . D 4 HOH A 151 660 660 HOH HOH . D 4 HOH A 152 661 661 HOH HOH . D 4 HOH A 153 662 662 HOH HOH . D 4 HOH A 154 663 663 HOH HOH . D 4 HOH A 155 664 664 HOH HOH . D 4 HOH A 156 665 665 HOH HOH . D 4 HOH A 157 666 666 HOH HOH . D 4 HOH A 158 667 667 HOH HOH . D 4 HOH A 159 668 668 HOH HOH . D 4 HOH A 160 669 669 HOH HOH . D 4 HOH A 161 670 670 HOH HOH . D 4 HOH A 162 671 671 HOH HOH . D 4 HOH A 163 672 672 HOH HOH . D 4 HOH A 164 673 673 HOH HOH . D 4 HOH A 165 674 674 HOH HOH . D 4 HOH A 166 675 675 HOH HOH . D 4 HOH A 167 676 676 HOH HOH . D 4 HOH A 168 677 677 HOH HOH . D 4 HOH A 169 678 678 HOH HOH . D 4 HOH A 170 679 679 HOH HOH . D 4 HOH A 171 680 680 HOH HOH . D 4 HOH A 172 801 801 HOH HOH . D 4 HOH A 173 802 802 HOH HOH . D 4 HOH A 174 803 803 HOH HOH . D 4 HOH A 175 804 804 HOH HOH . D 4 HOH A 176 805 805 HOH HOH . D 4 HOH A 177 806 806 HOH HOH . D 4 HOH A 178 807 807 HOH HOH . D 4 HOH A 179 808 808 HOH HOH . D 4 HOH A 180 809 809 HOH HOH . D 4 HOH A 181 810 810 HOH HOH . D 4 HOH A 182 811 811 HOH HOH . D 4 HOH A 183 812 812 HOH HOH . D 4 HOH A 184 813 813 HOH HOH . D 4 HOH A 185 814 814 HOH HOH . D 4 HOH A 186 815 815 HOH HOH . D 4 HOH A 187 816 816 HOH HOH . D 4 HOH A 188 817 817 HOH HOH . D 4 HOH A 189 818 818 HOH HOH . D 4 HOH A 190 819 819 HOH HOH . D 4 HOH A 191 820 820 HOH HOH . D 4 HOH A 192 821 821 HOH HOH . D 4 HOH A 193 822 822 HOH HOH . D 4 HOH A 194 823 823 HOH HOH . D 4 HOH A 195 824 824 HOH HOH . D 4 HOH A 196 825 825 HOH HOH . D 4 HOH A 197 826 826 HOH HOH . D 4 HOH A 198 827 827 HOH HOH . D 4 HOH A 199 828 828 HOH HOH . D 4 HOH A 200 829 829 HOH HOH . D 4 HOH A 201 830 830 HOH HOH . D 4 HOH A 202 831 831 HOH HOH . D 4 HOH A 203 832 832 HOH HOH . D 4 HOH A 204 833 833 HOH HOH . D 4 HOH A 205 901 901 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 PA M7G . . . C 3 12.513 11.708 23.654 1 82.19 ? PA M7G 401 A 1 HETATM 2 O O1A M7G . . . C 3 13.258 12.442 22.588 1 88.55 ? O1A M7G 401 A 1 HETATM 3 O O2A M7G . . . C 3 11.915 12.516 24.747 1 84.52 ? O2A M7G 401 A 1 HETATM 4 O O3A M7G . . . C 3 11.427 10.704 23.016 1 88.95 ? O3A M7G 401 A 1 HETATM 5 O O5' M7G . . . C 3 13.563 10.703 24.346 1 80.71 ? O5' M7G 401 A 1 HETATM 6 P PB M7G . . . C 3 10.139 11.137 22.177 1 91.19 ? PB M7G 401 A 1 HETATM 7 O O1B M7G . . . C 3 9.091 11.703 23.25 1 92.48 ? O1B M7G 401 A 1 HETATM 8 O O2B M7G . . . C 3 9.553 9.9 21.586 1 91.96 ? O2B M7G 401 A 1 HETATM 9 O O3B M7G . . . C 3 10.514 12.238 21.272 1 91.64 ? O3B M7G 401 A 1 HETATM 10 C C5' M7G . . . C 3 13.856 9.404 23.804 1 72.57 ? C5' M7G 401 A 1 HETATM 11 C C4' M7G . . . C 3 15.207 9.315 23.094 1 65.6 ? C4' M7G 401 A 1 HETATM 12 O O4' M7G . . . C 3 15.299 10.302 22.067 1 60.46 ? O4' M7G 401 A 1 HETATM 13 C C3' M7G . . . C 3 16.349 9.637 24.038 1 64.82 ? C3' M7G 401 A 1 HETATM 14 O O3' M7G . . . C 3 16.717 8.48 24.811 1 69.08 ? O3' M7G 401 A 1 HETATM 15 C C2' M7G . . . C 3 17.468 10.021 23.088 1 63.66 ? C2' M7G 401 A 1 HETATM 16 O O2' M7G . . . C 3 18.219 8.888 22.635 1 66.18 ? O2' M7G 401 A 1 HETATM 17 C C1' M7G . . . C 3 16.702 10.567 21.879 1 58.78 ? C1' M7G 401 A 1 HETATM 18 N N9 M7G . . . C 3 16.826 12.025 21.717 1 52.17 ? N9 M7G 401 A 1 HETATM 19 C C8 M7G . . . C 3 16.136 12.992 22.389 1 42.95 ? C8 M7G 401 A 1 HETATM 20 N N7 M7G . . . C 3 16.363 14.19 21.974 1 44.59 ? N7 M7G 401 A 1 HETATM 21 C CM7 M7G . . . C 3 15.72 15.376 22.497 1 33.45 ? CM7 M7G 401 A 1 HETATM 22 C C5 M7G . . . C 3 17.28 14.022 20.954 1 46.15 ? C5 M7G 401 A 1 HETATM 23 C C6 M7G . . . C 3 17.891 14.991 20.136 1 44.95 ? C6 M7G 401 A 1 HETATM 24 O O6 M7G . . . C 3 17.721 16.202 20.161 1 36.66 ? O6 M7G 401 A 1 HETATM 25 N N1 M7G . . . C 3 18.76 14.424 19.232 1 47.35 ? N1 M7G 401 A 1 HETATM 26 C C2 M7G . . . C 3 19.028 13.075 19.104 1 47.67 ? C2 M7G 401 A 1 HETATM 27 N N2 M7G . . . C 3 19.896 12.712 18.158 1 49.14 ? N2 M7G 401 A 1 HETATM 28 N N3 M7G . . . C 3 18.441 12.155 19.882 1 47.26 ? N3 M7G 401 A 1 HETATM 29 C C4 M7G . . . C 3 17.581 12.697 20.783 1 49.1 ? C4 M7G 401 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 5 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 251 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 29 #