data_3CNO # _model_server_result.job_id KxaHOHCol1202bdu7O_VHQ _model_server_result.datetime_utc '2024-10-15 15:28:57' _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 3cno # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 3CNO # _exptl.entry_id 3CNO _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-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 90 _cell.angle_gamma 90 _cell.entry_id 3CNO _cell.length_a 34.222 _cell.length_b 76.66 _cell.length_c 104.895 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3CNO _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _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 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C10 H15 N5 O11 P2' _chem_comp.formula_weight 443.201 _chem_comp.id GDP _chem_comp.mon_nstd_flag n _chem_comp.name "GUANOSINE-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 PB O1B GDP doub 70 n n PB O2B GDP sing 71 n n PB O3B GDP sing 72 n n PB O3A GDP sing 73 n n O2B HOB2 GDP sing 74 n n O3B HOB3 GDP sing 75 n n O3A PA GDP sing 76 n n PA O1A GDP doub 77 n n PA O2A GDP sing 78 n n PA O5' GDP sing 79 n n O2A HOA2 GDP sing 80 n n O5' C5' GDP sing 81 n n C5' C4' GDP sing 82 n n C5' H5' GDP sing 83 n n C5' "H5''" GDP sing 84 n n C4' O4' GDP sing 85 n n C4' C3' GDP sing 86 n n C4' H4' GDP sing 87 n n O4' C1' GDP sing 88 n n C3' O3' GDP sing 89 n n C3' C2' GDP sing 90 n n C3' H3' GDP sing 91 n n O3' HO3' GDP sing 92 n n C2' O2' GDP sing 93 n n C2' C1' GDP sing 94 n n C2' H2' GDP sing 95 n n O2' HO2' GDP sing 96 n n C1' N9 GDP sing 97 n n C1' H1' GDP sing 98 n n N9 C8 GDP sing 99 n y N9 C4 GDP sing 100 n y C8 N7 GDP doub 101 n y C8 H8 GDP sing 102 n n N7 C5 GDP sing 103 n y C5 C6 GDP sing 104 n n C5 C4 GDP doub 105 n y C6 O6 GDP doub 106 n n C6 N1 GDP sing 107 n n N1 C2 GDP sing 108 n n N1 HN1 GDP sing 109 n n C2 N2 GDP sing 110 n n C2 N3 GDP doub 111 n n N2 HN21 GDP sing 112 n n N2 HN22 GDP sing 113 n n N3 C4 GDP sing 114 n n # _atom_sites.entry_id 3CNO _atom_sites.fract_transf_matrix[1][1] 0.029221 _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] 0.013045 _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] 0.009533 _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 GDP A 1 501 501 GDP GDP . C 3 HOH A 1 502 1 HOH HOH . C 3 HOH A 2 503 2 HOH HOH . C 3 HOH A 3 504 3 HOH HOH . C 3 HOH A 4 505 4 HOH HOH . C 3 HOH A 5 506 5 HOH HOH . C 3 HOH A 6 507 6 HOH HOH . C 3 HOH A 7 508 7 HOH HOH . C 3 HOH A 8 509 8 HOH HOH . C 3 HOH A 9 510 9 HOH HOH . C 3 HOH A 10 511 10 HOH HOH . C 3 HOH A 11 512 11 HOH HOH . C 3 HOH A 12 513 12 HOH HOH . C 3 HOH A 13 514 13 HOH HOH . C 3 HOH A 14 515 14 HOH HOH . C 3 HOH A 15 516 15 HOH HOH . C 3 HOH A 16 517 16 HOH HOH . C 3 HOH A 17 518 17 HOH HOH . C 3 HOH A 18 519 18 HOH HOH . C 3 HOH A 19 520 19 HOH HOH . C 3 HOH A 20 521 20 HOH HOH . C 3 HOH A 21 522 21 HOH HOH . C 3 HOH A 22 523 22 HOH HOH . C 3 HOH A 23 524 23 HOH HOH . C 3 HOH A 24 525 24 HOH HOH . C 3 HOH A 25 526 25 HOH HOH . C 3 HOH A 26 527 26 HOH HOH . C 3 HOH A 27 528 27 HOH HOH . C 3 HOH A 28 529 29 HOH HOH . C 3 HOH A 29 530 30 HOH HOH . C 3 HOH A 30 531 31 HOH HOH . C 3 HOH A 31 532 32 HOH HOH . C 3 HOH A 32 533 33 HOH HOH . C 3 HOH A 33 534 34 HOH HOH . C 3 HOH A 34 535 35 HOH HOH . C 3 HOH A 35 536 36 HOH HOH . C 3 HOH A 36 537 38 HOH HOH . C 3 HOH A 37 538 39 HOH HOH . C 3 HOH A 38 539 41 HOH HOH . C 3 HOH A 39 540 42 HOH HOH . C 3 HOH A 40 541 43 HOH HOH . C 3 HOH A 41 542 44 HOH HOH . C 3 HOH A 42 543 46 HOH HOH . C 3 HOH A 43 544 47 HOH HOH . C 3 HOH A 44 545 49 HOH HOH . C 3 HOH A 45 546 52 HOH HOH . C 3 HOH A 46 547 53 HOH HOH . C 3 HOH A 47 548 54 HOH HOH . C 3 HOH A 48 549 55 HOH HOH . C 3 HOH A 49 550 56 HOH HOH . C 3 HOH A 50 551 57 HOH HOH . C 3 HOH A 51 552 58 HOH HOH . C 3 HOH A 52 553 59 HOH HOH . C 3 HOH A 53 554 60 HOH HOH . C 3 HOH A 54 555 61 HOH HOH . C 3 HOH A 55 556 62 HOH HOH . C 3 HOH A 56 557 63 HOH HOH . C 3 HOH A 57 558 64 HOH HOH . C 3 HOH A 58 559 65 HOH HOH . C 3 HOH A 59 560 66 HOH HOH . C 3 HOH A 60 561 67 HOH HOH . C 3 HOH A 61 562 68 HOH HOH . C 3 HOH A 62 563 69 HOH HOH . C 3 HOH A 63 564 70 HOH HOH . C 3 HOH A 64 565 71 HOH HOH . C 3 HOH A 65 566 72 HOH HOH . C 3 HOH A 66 567 73 HOH HOH . C 3 HOH A 67 568 74 HOH HOH . C 3 HOH A 68 569 75 HOH HOH . C 3 HOH A 69 570 76 HOH HOH . C 3 HOH A 70 571 77 HOH HOH . C 3 HOH A 71 572 78 HOH HOH . C 3 HOH A 72 573 79 HOH HOH . C 3 HOH A 73 574 80 HOH HOH . C 3 HOH A 74 575 81 HOH HOH . C 3 HOH A 75 576 82 HOH HOH . C 3 HOH A 76 577 83 HOH HOH . C 3 HOH A 77 578 84 HOH HOH . C 3 HOH A 78 579 85 HOH HOH . C 3 HOH A 79 580 86 HOH HOH . C 3 HOH A 80 581 87 HOH HOH . C 3 HOH A 81 582 89 HOH HOH . C 3 HOH A 82 583 90 HOH HOH . C 3 HOH A 83 584 91 HOH HOH . C 3 HOH A 84 585 92 HOH HOH . C 3 HOH A 85 586 94 HOH HOH . C 3 HOH A 86 587 95 HOH HOH . C 3 HOH A 87 588 96 HOH HOH . C 3 HOH A 88 589 97 HOH HOH . C 3 HOH A 89 590 98 HOH HOH . C 3 HOH A 90 591 99 HOH HOH . C 3 HOH A 91 592 100 HOH HOH . C 3 HOH A 92 593 101 HOH HOH . C 3 HOH A 93 594 102 HOH HOH . C 3 HOH A 94 595 104 HOH HOH . C 3 HOH A 95 596 105 HOH HOH . C 3 HOH A 96 597 106 HOH HOH . C 3 HOH A 97 598 107 HOH HOH . C 3 HOH A 98 599 109 HOH HOH . C 3 HOH A 99 600 110 HOH HOH . C 3 HOH A 100 601 111 HOH HOH . C 3 HOH A 101 602 112 HOH HOH . C 3 HOH A 102 603 113 HOH HOH . C 3 HOH A 103 604 114 HOH HOH . C 3 HOH A 104 605 115 HOH HOH . C 3 HOH A 105 606 116 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 PB GDP . . . B 2 4.878 -5.228 26.05 1 30.63 ? PB GDP 501 A 1 HETATM 2 O O1B GDP . . . B 2 4.216 -5.252 27.402 1 31.04 ? O1B GDP 501 A 1 HETATM 3 O O2B GDP . . . B 2 6.236 -4.576 26.233 1 30.87 ? O2B GDP 501 A 1 HETATM 4 O O3B GDP . . . B 2 4.147 -4.373 25.04 1 28.49 ? O3B GDP 501 A 1 HETATM 5 O O3A GDP . . . B 2 5.079 -6.708 25.469 1 30.16 ? O3A GDP 501 A 1 HETATM 6 P PA GDP . . . B 2 4.445 -8.1 25.946 1 30.06 ? PA GDP 501 A 1 HETATM 7 O O1A GDP . . . B 2 4.872 -8.549 27.322 1 30.82 ? O1A GDP 501 A 1 HETATM 8 O O2A GDP . . . B 2 2.947 -8.099 25.772 1 32.18 ? O2A GDP 501 A 1 HETATM 9 O O5' GDP . . . B 2 5.116 -9.086 24.884 1 30.45 ? O5' GDP 501 A 1 HETATM 10 C C5' GDP . . . B 2 4.989 -8.807 23.493 1 29.99 ? C5' GDP 501 A 1 HETATM 11 C C4' GDP . . . B 2 5.18 -10.096 22.713 1 30.29 ? C4' GDP 501 A 1 HETATM 12 O O4' GDP . . . B 2 6.488 -10.617 22.932 1 29.17 ? O4' GDP 501 A 1 HETATM 13 C C3' GDP . . . B 2 4.209 -11.174 23.147 1 30.92 ? C3' GDP 501 A 1 HETATM 14 O O3' GDP . . . B 2 3.816 -11.894 21.971 1 34.51 ? O3' GDP 501 A 1 HETATM 15 C C2' GDP . . . B 2 5.022 -12.073 24.046 1 31.28 ? C2' GDP 501 A 1 HETATM 16 O O2' GDP . . . B 2 4.462 -13.389 24.036 1 31.69 ? O2' GDP 501 A 1 HETATM 17 C C1' GDP . . . B 2 6.419 -11.947 23.443 1 28.6 ? C1' GDP 501 A 1 HETATM 18 N N9 GDP . . . B 2 7.557 -12.04 24.388 1 28.49 ? N9 GDP 501 A 1 HETATM 19 C C8 GDP . . . B 2 7.743 -11.352 25.53 1 27.46 ? C8 GDP 501 A 1 HETATM 20 N N7 GDP . . . B 2 8.924 -11.682 26.111 1 26.83 ? N7 GDP 501 A 1 HETATM 21 C C5 GDP . . . B 2 9.52 -12.597 25.325 1 27.71 ? C5 GDP 501 A 1 HETATM 22 C C6 GDP . . . B 2 10.781 -13.376 25.342 1 28.49 ? C6 GDP 501 A 1 HETATM 23 O O6 GDP . . . B 2 11.604 -13.25 26.272 1 27.96 ? O6 GDP 501 A 1 HETATM 24 N N1 GDP . . . B 2 11.015 -14.218 24.321 1 28.52 ? N1 GDP 501 A 1 HETATM 25 C C2 GDP . . . B 2 10.142 -14.388 23.306 1 27.72 ? C2 GDP 501 A 1 HETATM 26 N N2 GDP . . . B 2 10.454 -15.255 22.319 1 27.19 ? N2 GDP 501 A 1 HETATM 27 N N3 GDP . . . B 2 8.97 -13.716 23.232 1 27.23 ? N3 GDP 501 A 1 HETATM 28 C C4 GDP . . . B 2 8.617 -12.828 24.19 1 28.15 ? C4 GDP 501 A 1 # _model_server_stats.io_time_ms 123 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 270 _model_server_stats.encode_time_ms 20 _model_server_stats.element_count 28 #