data_2DGN # _model_server_result.job_id vrdTsEYgB4JG8TUN1FMOAg _model_server_result.datetime_utc '2024-11-18 12:37:52' _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 2dgn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1451}' # _entry.id 2DGN # _exptl.entry_id 2DGN _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 90 _cell.entry_id 2DGN _cell.length_a 70.112 _cell.length_b 70.112 _cell.length_c 199.033 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2DGN _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # _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 _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' 8_775 -y+2,-x+2,-z+1/2 0 -1 0 -1 0 0 0 0 -1 140.224 140.224 99.5165 # _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 43 A ASP 43 1_555 B MG MG . A MG 1454 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.255 ? metalc ? metalc2 A O GLY 70 A GLY 70 1_555 B MG MG . A MG 1454 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.116 ? metalc ? metalc3 E O HOH . A HOH 513 1_555 B MG MG . A MG 1454 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.234 ? metalc ? metalc4 C O16 DOI . A DOI 1451 1_555 B MG MG . A MG 1454 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? metalc ? metalc5 D O2A GDP . A GDP 1452 1_555 B MG MG . A MG 1454 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? metalc ? metalc6 D O2B GDP . A GDP 1452 1_555 B MG MG . A MG 1454 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? # _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 2DGN _atom_sites.fract_transf_matrix[1][1] 0.014263 _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] 0.014263 _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] 0.005024 _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 1454 1454 MG MG . C 3 DOI A 1 1451 1451 DOI DOI . D 4 GDP A 1 1452 1452 GDP GDP . E 5 HOH A 1 501 501 HOH HOH . E 5 HOH A 2 502 502 HOH HOH . E 5 HOH A 3 503 503 HOH HOH . E 5 HOH A 4 504 504 HOH HOH . E 5 HOH A 5 505 505 HOH HOH . E 5 HOH A 6 506 506 HOH HOH . E 5 HOH A 7 507 507 HOH HOH . E 5 HOH A 8 508 508 HOH HOH . E 5 HOH A 9 509 509 HOH HOH . E 5 HOH A 10 510 510 HOH HOH . E 5 HOH A 11 511 511 HOH HOH . E 5 HOH A 12 512 512 HOH HOH . E 5 HOH A 13 513 513 HOH HOH . E 5 HOH A 14 514 514 HOH HOH . E 5 HOH A 15 515 515 HOH HOH . E 5 HOH A 16 516 516 HOH HOH . E 5 HOH A 17 517 517 HOH HOH . E 5 HOH A 18 518 518 HOH HOH . E 5 HOH A 19 519 519 HOH HOH . E 5 HOH A 20 520 520 HOH HOH . E 5 HOH A 21 521 521 HOH HOH . E 5 HOH A 22 522 522 HOH HOH . E 5 HOH A 23 523 523 HOH HOH . E 5 HOH A 24 524 524 HOH HOH . E 5 HOH A 25 525 525 HOH HOH . E 5 HOH A 26 526 526 HOH HOH . E 5 HOH A 27 527 527 HOH HOH . E 5 HOH A 28 528 528 HOH HOH . E 5 HOH A 29 529 529 HOH HOH . E 5 HOH A 30 530 530 HOH HOH . E 5 HOH A 31 531 531 HOH HOH . E 5 HOH A 32 532 532 HOH HOH . E 5 HOH A 33 533 533 HOH HOH . E 5 HOH A 34 534 534 HOH HOH . E 5 HOH A 35 535 535 HOH HOH . E 5 HOH A 36 536 536 HOH HOH . E 5 HOH A 37 537 537 HOH HOH . E 5 HOH A 38 538 538 HOH HOH . E 5 HOH A 39 539 539 HOH HOH . E 5 HOH A 40 540 540 HOH HOH . E 5 HOH A 41 541 541 HOH HOH . E 5 HOH A 42 542 542 HOH HOH . E 5 HOH A 43 543 543 HOH HOH . E 5 HOH A 44 544 544 HOH HOH . E 5 HOH A 45 545 545 HOH HOH . E 5 HOH A 46 546 546 HOH HOH . E 5 HOH A 47 547 547 HOH HOH . E 5 HOH A 48 548 548 HOH HOH . E 5 HOH A 49 549 549 HOH HOH . E 5 HOH A 50 550 550 HOH HOH . E 5 HOH A 51 551 551 HOH HOH . E 5 HOH A 52 552 552 HOH HOH . E 5 HOH A 53 553 553 HOH HOH . E 5 HOH A 54 554 554 HOH HOH . E 5 HOH A 55 555 555 HOH HOH . E 5 HOH A 56 556 556 HOH HOH . E 5 HOH A 57 557 557 HOH HOH . E 5 HOH A 58 558 558 HOH HOH . E 5 HOH A 59 559 559 HOH HOH . E 5 HOH A 60 560 560 HOH HOH . E 5 HOH A 61 561 561 HOH HOH . E 5 HOH A 62 562 562 HOH HOH . E 5 HOH A 63 563 563 HOH HOH . E 5 HOH A 64 564 564 HOH HOH . E 5 HOH A 65 565 565 HOH HOH . E 5 HOH A 66 566 566 HOH HOH . E 5 HOH A 67 567 567 HOH HOH . E 5 HOH A 68 568 568 HOH HOH . E 5 HOH A 69 569 569 HOH HOH . E 5 HOH A 70 570 570 HOH HOH . E 5 HOH A 71 571 571 HOH HOH . E 5 HOH A 72 572 572 HOH HOH . E 5 HOH A 73 573 573 HOH HOH . E 5 HOH A 74 574 574 HOH HOH . E 5 HOH A 75 575 575 HOH HOH . E 5 HOH A 76 576 576 HOH HOH . E 5 HOH A 77 577 577 HOH HOH . E 5 HOH A 78 578 578 HOH HOH . E 5 HOH A 79 579 579 HOH HOH . E 5 HOH A 80 580 580 HOH HOH . E 5 HOH A 81 581 581 HOH HOH . E 5 HOH A 82 582 582 HOH HOH . E 5 HOH A 83 583 583 HOH HOH . E 5 HOH A 84 584 584 HOH HOH . E 5 HOH A 85 585 585 HOH HOH . E 5 HOH A 86 586 586 HOH HOH . E 5 HOH A 87 587 587 HOH HOH . E 5 HOH A 88 588 588 HOH HOH . E 5 HOH A 89 589 589 HOH HOH . E 5 HOH A 90 590 590 HOH HOH . E 5 HOH A 91 591 591 HOH HOH . E 5 HOH A 92 592 592 HOH HOH . E 5 HOH A 93 593 593 HOH HOH . E 5 HOH A 94 594 594 HOH HOH . E 5 HOH A 95 595 595 HOH HOH . E 5 HOH A 96 597 597 HOH HOH . E 5 HOH A 97 598 598 HOH HOH . E 5 HOH A 98 599 599 HOH HOH . E 5 HOH A 99 600 600 HOH HOH . E 5 HOH A 100 601 601 HOH HOH . E 5 HOH A 101 602 602 HOH HOH . E 5 HOH A 102 603 603 HOH HOH . E 5 HOH A 103 604 604 HOH HOH . E 5 HOH A 104 605 605 HOH HOH . E 5 HOH A 105 606 606 HOH HOH . E 5 HOH A 106 607 607 HOH HOH . E 5 HOH A 107 608 608 HOH HOH . E 5 HOH A 108 609 609 HOH HOH . E 5 HOH A 109 610 610 HOH HOH . E 5 HOH A 110 611 611 HOH HOH . E 5 HOH A 111 612 612 HOH HOH . E 5 HOH A 112 613 613 HOH HOH . E 5 HOH A 113 614 614 HOH HOH . E 5 HOH A 114 615 615 HOH HOH . E 5 HOH A 115 616 616 HOH HOH . E 5 HOH A 116 617 617 HOH HOH . E 5 HOH A 117 618 618 HOH HOH . E 5 HOH A 118 619 619 HOH HOH . E 5 HOH A 119 620 620 HOH HOH . E 5 HOH A 120 621 621 HOH HOH . E 5 HOH A 121 622 622 HOH HOH . E 5 HOH A 122 623 623 HOH HOH . E 5 HOH A 123 624 624 HOH HOH . E 5 HOH A 124 625 625 HOH HOH . E 5 HOH A 125 626 626 HOH HOH . E 5 HOH A 126 627 627 HOH HOH . E 5 HOH A 127 628 628 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 60.758 66.545 39.999 1 32.51 ? PA DOI 1451 A 1 HETATM 2 O O1A DOI . . . C 3 59.347 65.979 40.069 1 33.58 ? O1A DOI 1451 A 1 HETATM 3 O O2A DOI . . . C 3 60.891 67.868 40.733 1 34.15 ? O2A DOI 1451 A 1 HETATM 4 O O3A DOI . . . C 3 61.789 65.519 40.432 1 32.29 ? O3A DOI 1451 A 1 HETATM 5 O O5' DOI . . . C 3 61.029 66.863 38.419 1 32.93 ? O5' DOI 1451 A 1 HETATM 6 P P6 DOI . . . C 3 63.328 57.471 38.197 1 38.23 ? P6 DOI 1451 A 1 HETATM 7 O O16 DOI . . . C 3 61.956 56.968 37.744 1 29.06 ? O16 DOI 1451 A 1 HETATM 8 O O26 DOI . . . C 3 63.668 57.007 39.61 1 30.65 ? O26 DOI 1451 A 1 HETATM 9 O O36 DOI . . . C 3 64.439 57.18 37.188 1 27.46 ? O36 DOI 1451 A 1 HETATM 10 C C5' DOI . . . C 3 62.258 67.473 37.965 1 29.56 ? C5' DOI 1451 A 1 HETATM 11 C C4' DOI . . . C 3 62.809 66.716 36.776 1 25.48 ? C4' DOI 1451 A 1 HETATM 12 O O4' DOI . . . C 3 63.191 65.386 37.186 1 28.67 ? O4' DOI 1451 A 1 HETATM 13 C C1' DOI . . . C 3 62.755 64.45 36.23 1 24.77 ? C1' DOI 1451 A 1 HETATM 14 N N9 DOI . . . C 3 62.379 63.238 36.95 1 24.29 ? N9 DOI 1451 A 1 HETATM 15 C C4 DOI . . . C 3 62.552 61.964 36.469 1 24.71 ? C4 DOI 1451 A 1 HETATM 16 N N3 DOI . . . C 3 62.656 61.585 35.183 1 24.8 ? N3 DOI 1451 A 1 HETATM 17 C C2 DOI . . . C 3 62.834 60.266 35.096 1 19.46 ? C2 DOI 1451 A 1 HETATM 18 N N1 DOI . . . C 3 62.917 59.358 36.074 1 21.38 ? N1 DOI 1451 A 1 HETATM 19 C C6 DOI . . . C 3 62.816 59.773 37.357 1 22.79 ? C6 DOI 1451 A 1 HETATM 20 O O6 DOI . . . C 3 63.218 59.084 38.294 1 25.56 ? O6 DOI 1451 A 1 HETATM 21 C C5 DOI . . . C 3 62.609 61.144 37.584 1 23.51 ? C5 DOI 1451 A 1 HETATM 22 N N7 DOI . . . C 3 62.454 61.885 38.747 1 22.39 ? N7 DOI 1451 A 1 HETATM 23 C C8 DOI . . . C 3 62.32 63.115 38.319 1 22.51 ? C8 DOI 1451 A 1 HETATM 24 C C2' DOI . . . C 3 61.561 65.074 35.513 1 23.85 ? C2' DOI 1451 A 1 HETATM 25 C C3' DOI . . . C 3 61.874 66.565 35.577 1 27.34 ? C3' DOI 1451 A 1 HETATM 26 O O3' DOI . . . C 3 62.482 67.033 34.378 1 21.45 ? O3' DOI 1451 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 286 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 26 #