data_4PAM # _model_server_result.job_id 80Yv0_A_1yyDrRfN0BTnEQ _model_server_result.datetime_utc '2024-10-18 17:19:25' _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 4pam # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 4PAM # _exptl.entry_id 4PAM _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 4PAM _cell.length_a 121.126 _cell.length_b 121.126 _cell.length_c 68.186 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4PAM _symmetry.cell_setting . _symmetry.Int_Tables_number 79 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 4' # _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,D,E _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 83 n n PB O2B GDP sing 84 n n PB O3B GDP sing 85 n n PB O3A GDP sing 86 n n O2B HOB2 GDP sing 87 n n O3B HOB3 GDP sing 88 n n O3A PA GDP sing 89 n n PA O1A GDP doub 90 n n PA O2A GDP sing 91 n n PA O5' GDP sing 92 n n O2A HOA2 GDP sing 93 n n O5' C5' GDP sing 94 n n C5' C4' GDP sing 95 n n C5' H5' GDP sing 96 n n C5' "H5''" GDP sing 97 n n C4' O4' GDP sing 98 n n C4' C3' GDP sing 99 n n C4' H4' GDP sing 100 n n O4' C1' GDP sing 101 n n C3' O3' GDP sing 102 n n C3' C2' GDP sing 103 n n C3' H3' GDP sing 104 n n O3' HO3' GDP sing 105 n n C2' O2' GDP sing 106 n n C2' C1' GDP sing 107 n n C2' H2' GDP sing 108 n n O2' HO2' GDP sing 109 n n C1' N9 GDP sing 110 n n C1' H1' GDP sing 111 n n N9 C8 GDP sing 112 n y N9 C4 GDP sing 113 n y C8 N7 GDP doub 114 n y C8 H8 GDP sing 115 n n N7 C5 GDP sing 116 n y C5 C6 GDP sing 117 n n C5 C4 GDP doub 118 n y C6 O6 GDP doub 119 n n C6 N1 GDP sing 120 n n N1 C2 GDP sing 121 n n N1 HN1 GDP sing 122 n n C2 N2 GDP sing 123 n n C2 N3 GDP doub 124 n n N2 HN21 GDP sing 125 n n N2 HN22 GDP sing 126 n n N3 C4 GDP sing 127 n n # _atom_sites.entry_id 4PAM _atom_sites.fract_transf_matrix[1][1] 0.008256 _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] 0.008256 _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] 0.014666 _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 1 401 356 GDP GDP . C 3 SO3 A 1 402 357 SO3 SO3 . D 4 CL A 1 403 1 CL CL . E 5 HOH A 1 501 63 HOH HOH . E 5 HOH A 2 502 4 HOH HOH . E 5 HOH A 3 503 52 HOH HOH . E 5 HOH A 4 504 131 HOH HOH . E 5 HOH A 5 505 103 HOH HOH . E 5 HOH A 6 506 104 HOH HOH . E 5 HOH A 7 507 44 HOH HOH . E 5 HOH A 8 508 95 HOH HOH . E 5 HOH A 9 509 102 HOH HOH . E 5 HOH A 10 510 115 HOH HOH . E 5 HOH A 11 511 99 HOH HOH . E 5 HOH A 12 512 100 HOH HOH . E 5 HOH A 13 513 120 HOH HOH . E 5 HOH A 14 514 66 HOH HOH . E 5 HOH A 15 515 38 HOH HOH . E 5 HOH A 16 516 20 HOH HOH . E 5 HOH A 17 517 51 HOH HOH . E 5 HOH A 18 518 128 HOH HOH . E 5 HOH A 19 519 62 HOH HOH . E 5 HOH A 20 520 101 HOH HOH . E 5 HOH A 21 521 111 HOH HOH . E 5 HOH A 22 522 118 HOH HOH . E 5 HOH A 23 523 124 HOH HOH . E 5 HOH A 24 524 19 HOH HOH . E 5 HOH A 25 525 41 HOH HOH . E 5 HOH A 26 526 76 HOH HOH . E 5 HOH A 27 527 133 HOH HOH . E 5 HOH A 28 528 42 HOH HOH . E 5 HOH A 29 529 119 HOH HOH . E 5 HOH A 30 530 18 HOH HOH . E 5 HOH A 31 531 116 HOH HOH . E 5 HOH A 32 532 96 HOH HOH . E 5 HOH A 33 533 53 HOH HOH . E 5 HOH A 34 534 121 HOH HOH . E 5 HOH A 35 535 117 HOH HOH . E 5 HOH A 36 536 114 HOH HOH . E 5 HOH A 37 537 1 HOH HOH . E 5 HOH A 38 538 2 HOH HOH . E 5 HOH A 39 539 3 HOH HOH . E 5 HOH A 40 540 5 HOH HOH . E 5 HOH A 41 541 6 HOH HOH . E 5 HOH A 42 542 7 HOH HOH . E 5 HOH A 43 543 8 HOH HOH . E 5 HOH A 44 544 9 HOH HOH . E 5 HOH A 45 545 10 HOH HOH . E 5 HOH A 46 546 11 HOH HOH . E 5 HOH A 47 547 12 HOH HOH . E 5 HOH A 48 548 13 HOH HOH . E 5 HOH A 49 549 14 HOH HOH . E 5 HOH A 50 550 15 HOH HOH . E 5 HOH A 51 551 16 HOH HOH . E 5 HOH A 52 552 17 HOH HOH . E 5 HOH A 53 553 21 HOH HOH . E 5 HOH A 54 554 22 HOH HOH . E 5 HOH A 55 555 23 HOH HOH . E 5 HOH A 56 556 25 HOH HOH . E 5 HOH A 57 557 28 HOH HOH . E 5 HOH A 58 558 29 HOH HOH . E 5 HOH A 59 559 30 HOH HOH . E 5 HOH A 60 560 31 HOH HOH . E 5 HOH A 61 561 32 HOH HOH . E 5 HOH A 62 562 33 HOH HOH . E 5 HOH A 63 563 34 HOH HOH . E 5 HOH A 64 564 35 HOH HOH . E 5 HOH A 65 565 36 HOH HOH . E 5 HOH A 66 566 37 HOH HOH . E 5 HOH A 67 567 45 HOH HOH . E 5 HOH A 68 568 46 HOH HOH . E 5 HOH A 69 569 47 HOH HOH . E 5 HOH A 70 570 49 HOH HOH . E 5 HOH A 71 571 56 HOH HOH . E 5 HOH A 72 572 57 HOH HOH . E 5 HOH A 73 573 58 HOH HOH . E 5 HOH A 74 574 60 HOH HOH . E 5 HOH A 75 575 61 HOH HOH . E 5 HOH A 76 576 67 HOH HOH . E 5 HOH A 77 577 68 HOH HOH . E 5 HOH A 78 578 69 HOH HOH . E 5 HOH A 79 579 70 HOH HOH . E 5 HOH A 80 580 71 HOH HOH . E 5 HOH A 81 581 72 HOH HOH . E 5 HOH A 82 582 73 HOH HOH . E 5 HOH A 83 583 74 HOH HOH . E 5 HOH A 84 584 75 HOH HOH . E 5 HOH A 85 585 77 HOH HOH . E 5 HOH A 86 586 78 HOH HOH . E 5 HOH A 87 587 79 HOH HOH . E 5 HOH A 88 588 80 HOH HOH . E 5 HOH A 89 589 81 HOH HOH . E 5 HOH A 90 590 82 HOH HOH . E 5 HOH A 91 591 83 HOH HOH . E 5 HOH A 92 592 84 HOH HOH . E 5 HOH A 93 593 85 HOH HOH . E 5 HOH A 94 594 86 HOH HOH . E 5 HOH A 95 595 87 HOH HOH . E 5 HOH A 96 596 88 HOH HOH . E 5 HOH A 97 597 89 HOH HOH . E 5 HOH A 98 598 90 HOH HOH . E 5 HOH A 99 599 91 HOH HOH . E 5 HOH A 100 600 92 HOH HOH . E 5 HOH A 101 601 94 HOH HOH . E 5 HOH A 102 602 97 HOH HOH . E 5 HOH A 103 603 98 HOH HOH . E 5 HOH A 104 604 105 HOH HOH . E 5 HOH A 105 605 106 HOH HOH . E 5 HOH A 106 606 107 HOH HOH . E 5 HOH A 107 607 108 HOH HOH . E 5 HOH A 108 608 109 HOH HOH . E 5 HOH A 109 609 110 HOH HOH . E 5 HOH A 110 610 112 HOH HOH . E 5 HOH A 111 611 113 HOH HOH . E 5 HOH A 112 612 122 HOH HOH . E 5 HOH A 113 613 123 HOH HOH . E 5 HOH A 114 614 125 HOH HOH . E 5 HOH A 115 615 126 HOH HOH . E 5 HOH A 116 616 127 HOH HOH . E 5 HOH A 117 617 129 HOH HOH . E 5 HOH A 118 618 130 HOH HOH . E 5 HOH A 119 619 132 HOH HOH . E 5 HOH A 120 620 134 HOH HOH . E 5 HOH A 121 621 135 HOH HOH . E 5 HOH A 122 622 136 HOH HOH . E 5 HOH A 123 623 137 HOH HOH . E 5 HOH A 124 624 138 HOH HOH . E 5 HOH A 125 625 139 HOH HOH . E 5 HOH A 126 626 140 HOH HOH . E 5 HOH A 127 627 141 HOH HOH . E 5 HOH A 128 628 142 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 22.263 38.474 0.425 1 23.55 ? PB GDP 401 A 1 HETATM 2 O O1B GDP . . . B 2 23.329 39.367 -0.133 1 19.01 ? O1B GDP 401 A 1 HETATM 3 O O2B GDP . . . B 2 21.894 38.866 1.847 1 23.3 ? O2B GDP 401 A 1 HETATM 4 O O3B GDP . . . B 2 22.736 37.043 0.387 1 19.84 ? O3B GDP 401 A 1 HETATM 5 O O3A GDP . . . B 2 20.938 38.679 -0.479 1 22.75 ? O3A GDP 401 A 1 HETATM 6 P PA GDP . . . B 2 19.971 37.512 -1.03 1 21.7 ? PA GDP 401 A 1 HETATM 7 O O1A GDP . . . B 2 20.605 36.769 -2.183 1 19.82 ? O1A GDP 401 A 1 HETATM 8 O O2A GDP . . . B 2 19.498 36.579 0.076 1 20.46 ? O2A GDP 401 A 1 HETATM 9 O O5' GDP . . . B 2 18.762 38.413 -1.618 1 20.22 ? O5' GDP 401 A 1 HETATM 10 C C5' GDP . . . B 2 17.795 38.966 -0.723 1 23.35 ? C5' GDP 401 A 1 HETATM 11 C C4' GDP . . . B 2 16.394 38.834 -1.32 1 21.91 ? C4' GDP 401 A 1 HETATM 12 O O4' GDP . . . B 2 16.317 39.57 -2.554 1 21.66 ? O4' GDP 401 A 1 HETATM 13 C C3' GDP . . . B 2 16.058 37.393 -1.663 1 21.91 ? C3' GDP 401 A 1 HETATM 14 O O3' GDP . . . B 2 14.682 37.177 -1.32 1 20.46 ? O3' GDP 401 A 1 HETATM 15 C C2' GDP . . . B 2 16.195 37.295 -3.175 1 22.7 ? C2' GDP 401 A 1 HETATM 16 O O2' GDP . . . B 2 15.289 36.345 -3.764 1 19.91 ? O2' GDP 401 A 1 HETATM 17 C C1' GDP . . . B 2 15.876 38.715 -3.615 1 22.37 ? C1' GDP 401 A 1 HETATM 18 N N9 GDP . . . B 2 16.639 39.163 -4.805 1 22.73 ? N9 GDP 401 A 1 HETATM 19 C C8 GDP . . . B 2 17.975 39.13 -4.995 1 19.55 ? C8 GDP 401 A 1 HETATM 20 N N7 GDP . . . B 2 18.304 39.675 -6.197 1 22.34 ? N7 GDP 401 A 1 HETATM 21 C C5 GDP . . . B 2 17.156 40.081 -6.769 1 20.47 ? C5 GDP 401 A 1 HETATM 22 C C6 GDP . . . B 2 16.775 40.73 -8.03 1 18.26 ? C6 GDP 401 A 1 HETATM 23 O O6 GDP . . . B 2 17.65 41.06 -8.857 1 21.77 ? O6 GDP 401 A 1 HETATM 24 N N1 GDP . . . B 2 15.477 40.971 -8.244 1 20.86 ? N1 GDP 401 A 1 HETATM 25 C C2 GDP . . . B 2 14.516 40.655 -7.365 1 21.67 ? C2 GDP 401 A 1 HETATM 26 N N2 GDP . . . B 2 13.226 40.946 -7.684 1 20.87 ? N2 GDP 401 A 1 HETATM 27 N N3 GDP . . . B 2 14.787 40.056 -6.176 1 20.06 ? N3 GDP 401 A 1 HETATM 28 C C4 GDP . . . B 2 16.068 39.753 -5.845 1 20.89 ? C4 GDP 401 A 1 # _model_server_stats.io_time_ms 49 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 281 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 28 #