data_2GCQ # _model_server_result.job_id r24GEPRck4tSWTCuDfEdNA _model_server_result.datetime_utc '2024-11-18 08:27:11' _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 2gcq # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":451}' # _entry.id 2GCQ # _exptl.entry_id 2GCQ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 412.186 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 9-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-6-(PHOSPHONOOXY)-9H-PURINE _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 90 _cell.angle_gamma 120 _cell.entry_id 2GCQ _cell.length_a 80.585 _cell.length_b 80.585 _cell.length_c 158.46 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2GCQ _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details PISA,PQS _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 _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' 4_557 y,x,-z+2 -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 316.92 # _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 # 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 OD1 ASP 13 A ASP 13 1_555 B MG MG . A MG 435 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.148 ? metalc ? metalc2 A O GLY 40 A GLY 40 1_555 B MG MG . A MG 435 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? metalc ? metalc3 D O2A GDP . A GDP 432 1_555 B MG MG . A MG 435 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.954 ? metalc ? metalc4 D O2B GDP . A GDP 432 1_555 B MG MG . A MG 435 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.173 ? metalc ? metalc5 B MG MG . A MG 435 1_555 E O HDA . A HDA 437 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.232 ? metalc ? metalc6 B MG MG . A MG 435 1_555 C O16 DOI . A DOI 451 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.191 ? # _chem_comp.formula 'C10 H14 N4 O10 P2' _chem_comp.formula_weight 412.186 _chem_comp.id DOI _chem_comp.mon_nstd_flag . _chem_comp.name 9-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-6-(PHOSPHONOOXY)-9H-PURINE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "2'-DEOXY-IMP" # 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 DOI doub 83 n n PA O2A DOI sing 84 n n PA O3A DOI sing 85 n n PA O5' DOI sing 86 n n O2A H2A DOI sing 87 n n O3A H3A DOI sing 88 n n O5' C5' DOI sing 89 n n P6 O16 DOI doub 90 n n P6 O26 DOI sing 91 n n P6 O36 DOI sing 92 n n P6 O6 DOI sing 93 n n O26 H26 DOI sing 94 n n O36 H36 DOI sing 95 n n C5' C4' DOI sing 96 n n C5' "H5'1" DOI sing 97 n n C5' "H5'2" DOI sing 98 n n C4' O4' DOI sing 99 n n C4' C3' DOI sing 100 n n C4' H4' DOI sing 101 n n O4' C1' DOI sing 102 n n C1' N9 DOI sing 103 n n C1' C2' DOI sing 104 n n C1' H1' DOI sing 105 n n N9 C4 DOI sing 106 n y N9 C8 DOI sing 107 n y C4 N3 DOI doub 108 n y C4 C5 DOI sing 109 n y N3 C2 DOI sing 110 n y C2 N1 DOI doub 111 n y C2 H2 DOI sing 112 n n N1 C6 DOI sing 113 n y C6 O6 DOI sing 114 n n C6 C5 DOI doub 115 n y C5 N7 DOI sing 116 n y N7 C8 DOI doub 117 n y C8 H8 DOI sing 118 n n C2' C3' DOI sing 119 n n C2' "H2'1" DOI sing 120 n n C2' "H2'2" DOI sing 121 n n C3' O3' DOI sing 122 n n C3' H3' DOI sing 123 n n O3' HO3' DOI sing 124 n n # _atom_sites.entry_id 2GCQ _atom_sites.fract_transf_matrix[1][1] 0.012409 _atom_sites.fract_transf_matrix[1][2] 0.007164 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014329 _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] 0.006311 _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 MG A 1 435 435 MG MG . C 3 DOI A 1 451 451 DOI DOI . D 4 GDP A 1 432 432 GDP GDP . E 5 HDA A 1 437 437 HDA HDA . F 6 HOH A 1 501 501 HOH HOH . F 6 HOH A 2 502 502 HOH HOH . F 6 HOH A 3 503 503 HOH HOH . F 6 HOH A 4 504 504 HOH HOH . F 6 HOH A 5 505 505 HOH HOH . F 6 HOH A 6 506 506 HOH HOH . F 6 HOH A 7 507 507 HOH HOH . F 6 HOH A 8 508 508 HOH HOH . F 6 HOH A 9 509 509 HOH HOH . F 6 HOH A 10 510 510 HOH HOH . F 6 HOH A 11 511 511 HOH HOH . F 6 HOH A 12 512 512 HOH HOH . F 6 HOH A 13 513 513 HOH HOH . F 6 HOH A 14 514 514 HOH HOH . F 6 HOH A 15 515 515 HOH HOH . F 6 HOH A 16 516 516 HOH HOH . F 6 HOH A 17 517 517 HOH HOH . F 6 HOH A 18 518 518 HOH HOH . F 6 HOH A 19 519 519 HOH HOH . F 6 HOH A 20 520 520 HOH HOH . F 6 HOH A 21 521 521 HOH HOH . F 6 HOH A 22 522 522 HOH HOH . F 6 HOH A 23 523 523 HOH HOH . F 6 HOH A 24 524 524 HOH HOH . F 6 HOH A 25 525 525 HOH HOH . F 6 HOH A 26 526 526 HOH HOH . F 6 HOH A 27 527 527 HOH HOH . F 6 HOH A 28 528 528 HOH HOH . F 6 HOH A 29 529 529 HOH HOH . F 6 HOH A 30 530 530 HOH HOH . F 6 HOH A 31 531 531 HOH HOH . F 6 HOH A 32 532 532 HOH HOH . F 6 HOH A 33 533 533 HOH HOH . F 6 HOH A 34 534 534 HOH HOH . F 6 HOH A 35 535 535 HOH HOH . F 6 HOH A 36 536 536 HOH HOH . F 6 HOH A 37 537 537 HOH HOH . F 6 HOH A 38 538 538 HOH HOH . F 6 HOH A 39 539 539 HOH HOH . F 6 HOH A 40 540 540 HOH HOH . F 6 HOH A 41 541 541 HOH HOH . F 6 HOH A 42 542 542 HOH HOH . F 6 HOH A 43 543 543 HOH HOH . F 6 HOH A 44 544 544 HOH HOH . F 6 HOH A 45 545 545 HOH HOH . F 6 HOH A 46 546 546 HOH HOH . F 6 HOH A 47 547 547 HOH HOH . F 6 HOH A 48 548 548 HOH HOH . F 6 HOH A 49 549 549 HOH HOH . F 6 HOH A 50 550 550 HOH HOH . F 6 HOH A 51 551 551 HOH HOH . F 6 HOH A 52 552 552 HOH HOH . F 6 HOH A 53 553 553 HOH HOH . F 6 HOH A 54 554 554 HOH HOH . F 6 HOH A 55 555 555 HOH HOH . F 6 HOH A 56 556 556 HOH HOH . F 6 HOH A 57 557 557 HOH HOH . F 6 HOH A 58 558 558 HOH HOH . F 6 HOH A 59 559 559 HOH HOH . F 6 HOH A 60 560 560 HOH HOH . F 6 HOH A 61 561 561 HOH HOH . F 6 HOH A 62 562 562 HOH HOH . F 6 HOH A 63 563 563 HOH HOH . F 6 HOH A 64 564 564 HOH HOH . F 6 HOH A 65 565 565 HOH HOH . F 6 HOH A 66 566 566 HOH HOH . F 6 HOH A 67 567 567 HOH HOH . F 6 HOH A 68 568 568 HOH HOH . F 6 HOH A 69 569 569 HOH HOH . F 6 HOH A 70 570 570 HOH HOH . F 6 HOH A 71 571 571 HOH HOH . F 6 HOH A 72 572 572 HOH HOH . F 6 HOH A 73 573 573 HOH HOH . F 6 HOH A 74 574 574 HOH HOH . F 6 HOH A 75 575 575 HOH HOH . F 6 HOH A 76 576 576 HOH HOH . F 6 HOH A 77 577 577 HOH HOH . F 6 HOH A 78 578 578 HOH HOH . F 6 HOH A 79 579 579 HOH HOH . F 6 HOH A 80 580 580 HOH HOH . F 6 HOH A 81 581 581 HOH HOH . F 6 HOH A 82 582 582 HOH HOH . F 6 HOH A 83 583 583 HOH HOH . F 6 HOH A 84 584 584 HOH HOH . F 6 HOH A 85 585 585 HOH HOH . F 6 HOH A 86 586 586 HOH HOH . F 6 HOH A 87 587 587 HOH HOH . F 6 HOH A 88 588 588 HOH HOH . F 6 HOH A 89 589 589 HOH HOH . F 6 HOH A 90 590 590 HOH HOH . F 6 HOH A 91 591 591 HOH HOH . F 6 HOH A 92 592 592 HOH HOH . F 6 HOH A 93 593 593 HOH HOH . F 6 HOH A 94 594 594 HOH HOH . F 6 HOH A 95 595 595 HOH HOH . F 6 HOH A 96 596 596 HOH HOH . F 6 HOH A 97 597 597 HOH HOH . F 6 HOH A 98 598 598 HOH HOH . F 6 HOH A 99 599 599 HOH HOH . F 6 HOH A 100 600 600 HOH HOH . F 6 HOH A 101 601 601 HOH HOH . F 6 HOH A 102 602 602 HOH HOH . F 6 HOH A 103 603 603 HOH HOH . F 6 HOH A 104 604 604 HOH HOH . F 6 HOH A 105 605 605 HOH HOH . F 6 HOH A 106 606 606 HOH HOH . F 6 HOH A 107 607 607 HOH HOH . F 6 HOH A 108 608 608 HOH HOH . F 6 HOH A 109 609 609 HOH HOH . F 6 HOH A 110 610 610 HOH HOH . F 6 HOH A 111 611 611 HOH HOH . F 6 HOH A 112 612 612 HOH HOH . F 6 HOH A 113 613 613 HOH HOH . F 6 HOH A 114 614 614 HOH HOH . F 6 HOH A 115 615 615 HOH HOH . F 6 HOH A 116 616 616 HOH HOH . F 6 HOH A 117 617 617 HOH HOH . F 6 HOH A 118 618 618 HOH HOH . F 6 HOH A 119 619 619 HOH HOH . F 6 HOH A 120 620 620 HOH HOH . F 6 HOH A 121 621 621 HOH HOH . F 6 HOH A 122 622 622 HOH HOH . F 6 HOH A 123 623 623 HOH HOH . F 6 HOH A 124 624 624 HOH HOH . F 6 HOH A 125 625 625 HOH HOH . F 6 HOH A 126 626 626 HOH HOH . F 6 HOH A 127 627 627 HOH HOH . F 6 HOH A 128 628 628 HOH HOH . F 6 HOH A 129 629 629 HOH HOH . F 6 HOH A 130 630 630 HOH HOH . F 6 HOH A 131 631 631 HOH HOH . F 6 HOH A 132 632 632 HOH HOH . F 6 HOH A 133 633 633 HOH HOH . F 6 HOH A 134 634 634 HOH HOH . F 6 HOH A 135 635 635 HOH HOH . F 6 HOH A 136 636 636 HOH HOH . F 6 HOH A 137 637 637 HOH HOH . F 6 HOH A 138 638 638 HOH HOH . F 6 HOH A 139 639 639 HOH HOH . F 6 HOH A 140 640 640 HOH HOH . F 6 HOH A 141 641 641 HOH HOH . F 6 HOH A 142 642 642 HOH HOH . F 6 HOH A 143 643 643 HOH HOH . F 6 HOH A 144 644 644 HOH HOH . F 6 HOH A 145 645 645 HOH HOH . F 6 HOH A 146 646 646 HOH HOH . F 6 HOH A 147 647 647 HOH HOH . F 6 HOH A 148 648 648 HOH HOH . F 6 HOH A 149 649 649 HOH HOH . F 6 HOH A 150 650 650 HOH HOH . F 6 HOH A 151 651 651 HOH HOH . F 6 HOH A 152 652 652 HOH HOH . F 6 HOH A 153 653 653 HOH HOH . F 6 HOH A 154 654 654 HOH HOH . F 6 HOH A 155 655 655 HOH HOH . F 6 HOH A 156 656 656 HOH HOH . F 6 HOH A 157 657 657 HOH HOH . F 6 HOH A 158 658 658 HOH HOH . F 6 HOH A 159 659 659 HOH HOH . F 6 HOH A 160 660 660 HOH HOH . F 6 HOH A 161 661 661 HOH HOH . F 6 HOH A 162 662 662 HOH HOH . F 6 HOH A 163 663 663 HOH HOH . F 6 HOH A 164 664 664 HOH HOH . F 6 HOH A 165 665 665 HOH HOH . F 6 HOH A 166 666 666 HOH HOH . F 6 HOH A 167 667 667 HOH HOH . F 6 HOH A 168 668 668 HOH HOH . F 6 HOH A 169 669 669 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 DOI . . . C 3 16.048 53.875 161.19 1 32.34 ? PA DOI 451 A 1 HETATM 2 O O1A DOI . . . C 3 15.753 54.743 162.399 1 33.97 ? O1A DOI 451 A 1 HETATM 3 O O2A DOI . . . C 3 17.46 54.062 160.659 1 31.87 ? O2A DOI 451 A 1 HETATM 4 O O3A DOI . . . C 3 15.692 52.417 161.429 1 32.3 ? O3A DOI 451 A 1 HETATM 5 O O5' DOI . . . C 3 15.05 54.428 160.029 1 31.32 ? O5' DOI 451 A 1 HETATM 6 P P6 DOI . . . C 3 8.511 48.877 164.275 1 42.89 ? P6 DOI 451 A 1 HETATM 7 O O16 DOI . . . C 3 7.761 49.713 165.309 1 41.14 ? O16 DOI 451 A 1 HETATM 8 O O26 DOI . . . C 3 9.358 47.766 164.883 1 40.37 ? O26 DOI 451 A 1 HETATM 9 O O36 DOI . . . C 3 7.603 48.355 163.175 1 41.67 ? O36 DOI 451 A 1 HETATM 10 C C5' DOI . . . C 3 15.064 53.88 158.695 1 32.65 ? C5' DOI 451 A 1 HETATM 11 C C4' DOI . . . C 3 13.649 53.746 158.188 1 33.47 ? C4' DOI 451 A 1 HETATM 12 O O4' DOI . . . C 3 12.942 52.767 158.984 1 34.1 ? O4' DOI 451 A 1 HETATM 13 C C1' DOI . . . C 3 11.678 53.275 159.348 1 33.89 ? C1' DOI 451 A 1 HETATM 14 N N9 DOI . . . C 3 11.342 52.732 160.662 1 33.65 ? N9 DOI 451 A 1 HETATM 15 C C4 DOI . . . C 3 10.152 52.13 160.994 1 34.43 ? C4 DOI 451 A 1 HETATM 16 N N3 DOI . . . C 3 8.985 52.209 160.33 1 33.82 ? N3 DOI 451 A 1 HETATM 17 C C2 DOI . . . C 3 8.047 51.485 160.945 1 37.01 ? C2 DOI 451 A 1 HETATM 18 N N1 DOI . . . C 3 8.141 50.745 162.063 1 34.91 ? N1 DOI 451 A 1 HETATM 19 C C6 DOI . . . C 3 9.33 50.685 162.698 1 36.06 ? C6 DOI 451 A 1 HETATM 20 O O6 DOI . . . C 3 9.601 49.884 163.596 1 38.12 ? O6 DOI 451 A 1 HETATM 21 C C5 DOI . . . C 3 10.4 51.418 162.152 1 34.61 ? C5 DOI 451 A 1 HETATM 22 N N7 DOI . . . C 3 11.719 51.582 162.554 1 34.43 ? N7 DOI 451 A 1 HETATM 23 C C8 DOI . . . C 3 12.231 52.366 161.64 1 32.79 ? C8 DOI 451 A 1 HETATM 24 C C2' DOI . . . C 3 11.819 54.795 159.362 1 34.47 ? C2' DOI 451 A 1 HETATM 25 C C3' DOI . . . C 3 12.828 55.032 158.239 1 35.97 ? C3' DOI 451 A 1 HETATM 26 O O3' DOI . . . C 3 12.217 55.288 156.979 1 37.6 ? O3' DOI 451 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 314 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 26 #