data_7EVE # _model_server_result.job_id Zgvwz7l2iBHKbRMdjNppqw _model_server_result.datetime_utc '2024-10-19 09:18:57' _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 7eve # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 7EVE # _exptl.entry_id 7EVE _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 7EVE _cell.length_a 40.13 _cell.length_b 88.421 _cell.length_c 95.47 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7EVE _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall 'P 2ac 2ab' _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_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 # 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 O ASN 247 B ASN 247 1_555 C NA NA . B NA 502 1_655 ? ? ? ? ? ? ? ? ? ? ? ? 2.362 ? metalc ? metalc2 A OE1 GLU 252 B GLU 252 1_555 C NA NA . B NA 502 1_655 ? ? ? ? ? ? ? ? ? ? ? ? 2.817 ? metalc ? metalc3 A OE2 GLU 252 B GLU 252 1_555 C NA NA . B NA 502 1_655 ? ? ? ? ? ? ? ? ? ? ? ? 2.427 ? metalc ? metalc4 B O1B GDP . B GDP 501 1_555 D NA NA . B NA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.636 ? metalc ? metalc5 C NA NA . B NA 502 1_555 E O HOH . B HOH 626 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.264 ? metalc ? metalc6 C NA NA . B NA 502 1_555 E O HOH . B HOH 647 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.413 ? metalc ? metalc7 C NA NA . B NA 502 1_555 E O HOH . B HOH 690 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.793 ? metalc ? metalc8 C NA NA . B NA 502 1_555 E O HOH . B HOH 701 1_455 ? ? ? ? ? ? ? ? ? ? ? ? 3.186 ? metalc ? metalc9 D NA NA . B NA 503 1_555 E O HOH . B HOH 626 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.343 ? metalc ? metalc10 D NA NA . B NA 503 1_555 E O HOH . B HOH 628 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.676 ? metalc ? metalc11 D NA NA . B NA 503 1_555 E O HOH . B HOH 647 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.998 ? metalc ? metalc12 D NA NA . B NA 503 1_555 E O HOH . B HOH 673 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.336 ? metalc ? metalc13 D NA NA . B NA 503 1_555 E O HOH . B HOH 701 1_455 ? ? ? ? ? ? ? ? ? ? ? ? 2.401 ? # _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 7EVE _atom_sites.fract_transf_matrix[1][1] 0.024919 _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] 0.01131 _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] 0.010474 _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 B 1 501 501 GDP GDP . C 3 NA B 1 502 2 NA NA . D 3 NA B 1 503 3 NA NA . E 4 HOH B 1 601 147 HOH HOH . E 4 HOH B 2 602 112 HOH HOH . E 4 HOH B 3 603 136 HOH HOH . E 4 HOH B 4 604 71 HOH HOH . E 4 HOH B 5 605 25 HOH HOH . E 4 HOH B 6 606 21 HOH HOH . E 4 HOH B 7 607 146 HOH HOH . E 4 HOH B 8 608 54 HOH HOH . E 4 HOH B 9 609 85 HOH HOH . E 4 HOH B 10 610 100 HOH HOH . E 4 HOH B 11 611 110 HOH HOH . E 4 HOH B 12 612 7 HOH HOH . E 4 HOH B 13 613 65 HOH HOH . E 4 HOH B 14 614 55 HOH HOH . E 4 HOH B 15 615 89 HOH HOH . E 4 HOH B 16 616 48 HOH HOH . E 4 HOH B 17 617 56 HOH HOH . E 4 HOH B 18 618 43 HOH HOH . E 4 HOH B 19 619 50 HOH HOH . E 4 HOH B 20 620 9 HOH HOH . E 4 HOH B 21 621 102 HOH HOH . E 4 HOH B 22 622 10 HOH HOH . E 4 HOH B 23 623 145 HOH HOH . E 4 HOH B 24 624 113 HOH HOH . E 4 HOH B 25 625 68 HOH HOH . E 4 HOH B 26 626 22 HOH HOH . E 4 HOH B 27 627 6 HOH HOH . E 4 HOH B 28 628 4 HOH HOH . E 4 HOH B 29 629 138 HOH HOH . E 4 HOH B 30 630 11 HOH HOH . E 4 HOH B 31 631 5 HOH HOH . E 4 HOH B 32 632 107 HOH HOH . E 4 HOH B 33 633 84 HOH HOH . E 4 HOH B 34 634 24 HOH HOH . E 4 HOH B 35 635 35 HOH HOH . E 4 HOH B 36 636 2 HOH HOH . E 4 HOH B 37 637 12 HOH HOH . E 4 HOH B 38 638 44 HOH HOH . E 4 HOH B 39 639 78 HOH HOH . E 4 HOH B 40 640 104 HOH HOH . E 4 HOH B 41 641 32 HOH HOH . E 4 HOH B 42 642 96 HOH HOH . E 4 HOH B 43 643 34 HOH HOH . E 4 HOH B 44 644 16 HOH HOH . E 4 HOH B 45 645 77 HOH HOH . E 4 HOH B 46 646 17 HOH HOH . E 4 HOH B 47 647 40 HOH HOH . E 4 HOH B 48 648 47 HOH HOH . E 4 HOH B 49 649 26 HOH HOH . E 4 HOH B 50 650 61 HOH HOH . E 4 HOH B 51 651 57 HOH HOH . E 4 HOH B 52 652 28 HOH HOH . E 4 HOH B 53 653 69 HOH HOH . E 4 HOH B 54 654 8 HOH HOH . E 4 HOH B 55 655 15 HOH HOH . E 4 HOH B 56 656 87 HOH HOH . E 4 HOH B 57 657 70 HOH HOH . E 4 HOH B 58 658 31 HOH HOH . E 4 HOH B 59 659 79 HOH HOH . E 4 HOH B 60 660 75 HOH HOH . E 4 HOH B 61 661 3 HOH HOH . E 4 HOH B 62 662 59 HOH HOH . E 4 HOH B 63 663 97 HOH HOH . E 4 HOH B 64 664 111 HOH HOH . E 4 HOH B 65 665 116 HOH HOH . E 4 HOH B 66 666 52 HOH HOH . E 4 HOH B 67 667 73 HOH HOH . E 4 HOH B 68 668 140 HOH HOH . E 4 HOH B 69 669 63 HOH HOH . E 4 HOH B 70 670 67 HOH HOH . E 4 HOH B 71 671 76 HOH HOH . E 4 HOH B 72 672 14 HOH HOH . E 4 HOH B 73 673 1 HOH HOH . E 4 HOH B 74 674 144 HOH HOH . E 4 HOH B 75 675 86 HOH HOH . E 4 HOH B 76 676 19 HOH HOH . E 4 HOH B 77 677 41 HOH HOH . E 4 HOH B 78 678 83 HOH HOH . E 4 HOH B 79 679 119 HOH HOH . E 4 HOH B 80 680 36 HOH HOH . E 4 HOH B 81 681 74 HOH HOH . E 4 HOH B 82 682 46 HOH HOH . E 4 HOH B 83 683 23 HOH HOH . E 4 HOH B 84 684 72 HOH HOH . E 4 HOH B 85 685 45 HOH HOH . E 4 HOH B 86 686 30 HOH HOH . E 4 HOH B 87 687 81 HOH HOH . E 4 HOH B 88 688 90 HOH HOH . E 4 HOH B 89 689 93 HOH HOH . E 4 HOH B 90 690 20 HOH HOH . E 4 HOH B 91 691 49 HOH HOH . E 4 HOH B 92 692 64 HOH HOH . E 4 HOH B 93 693 115 HOH HOH . E 4 HOH B 94 694 121 HOH HOH . E 4 HOH B 95 695 118 HOH HOH . E 4 HOH B 96 696 129 HOH HOH . E 4 HOH B 97 697 29 HOH HOH . E 4 HOH B 98 698 51 HOH HOH . E 4 HOH B 99 699 101 HOH HOH . E 4 HOH B 100 700 38 HOH HOH . E 4 HOH B 101 701 37 HOH HOH . E 4 HOH B 102 702 42 HOH HOH . E 4 HOH B 103 703 33 HOH HOH . E 4 HOH B 104 704 53 HOH HOH . E 4 HOH B 105 705 27 HOH HOH . E 4 HOH B 106 706 92 HOH HOH . E 4 HOH B 107 707 91 HOH HOH . E 4 HOH B 108 708 108 HOH HOH . E 4 HOH B 109 709 94 HOH HOH . E 4 HOH B 110 710 80 HOH HOH . E 4 HOH B 111 711 105 HOH HOH . E 4 HOH B 112 712 126 HOH HOH . E 4 HOH B 113 713 143 HOH HOH . E 4 HOH B 114 714 18 HOH HOH . E 4 HOH B 115 715 13 HOH HOH . E 4 HOH B 116 716 109 HOH HOH . E 4 HOH B 117 717 58 HOH HOH . E 4 HOH B 118 718 132 HOH HOH . E 4 HOH B 119 719 62 HOH HOH . E 4 HOH B 120 720 98 HOH HOH . E 4 HOH B 121 721 60 HOH HOH . E 4 HOH B 122 722 125 HOH HOH . E 4 HOH B 123 723 139 HOH HOH . E 4 HOH B 124 724 120 HOH HOH . E 4 HOH B 125 725 142 HOH HOH . E 4 HOH B 126 726 131 HOH HOH . E 4 HOH B 127 727 134 HOH HOH . E 4 HOH B 128 728 127 HOH HOH . E 4 HOH B 129 729 106 HOH HOH . E 4 HOH B 130 730 114 HOH HOH . E 4 HOH B 131 731 82 HOH HOH . E 4 HOH B 132 732 103 HOH HOH . E 4 HOH B 133 733 133 HOH HOH . E 4 HOH B 134 734 135 HOH HOH . E 4 HOH B 135 735 88 HOH HOH . E 4 HOH B 136 736 148 HOH HOH . E 4 HOH B 137 737 124 HOH HOH . E 4 HOH B 138 738 141 HOH HOH . E 4 HOH B 139 739 95 HOH HOH . E 4 HOH B 140 740 99 HOH HOH . E 4 HOH B 141 741 122 HOH HOH . E 4 HOH B 142 742 123 HOH HOH . E 4 HOH B 143 743 66 HOH HOH . E 4 HOH B 144 744 39 HOH HOH . E 4 HOH B 145 745 130 HOH HOH . E 4 HOH B 146 746 128 HOH HOH . E 4 HOH B 147 747 117 HOH HOH . E 4 HOH B 148 748 137 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 -19.503 -1.701 14.16 1 18.15 ? PB GDP 501 B 1 HETATM 2 O O1B GDP . . . B 2 -19.706 -3.195 14.24 1 12.59 ? O1B GDP 501 B 1 HETATM 3 O O2B GDP . . . B 2 -18.041 -1.356 14.331 1 19.26 ? O2B GDP 501 B 1 HETATM 4 O O3B GDP . . . B 2 -20.303 -1.047 15.261 1 22.76 ? O3B GDP 501 B 1 HETATM 5 O O3A GDP . . . B 2 -20.051 -1.154 12.75 1 18.41 ? O3A GDP 501 B 1 HETATM 6 P PA GDP . . . B 2 -19.263 -1.374 11.363 1 28.74 ? PA GDP 501 B 1 HETATM 7 O O1A GDP . . . B 2 -20.134 -2.115 10.374 1 25.87 ? O1A GDP 501 B 1 HETATM 8 O O2A GDP . . . B 2 -17.962 -2.111 11.577 1 19.75 ? O2A GDP 501 B 1 HETATM 9 O O5' GDP . . . B 2 -19 0.129 10.852 1 26.32 ? O5' GDP 501 B 1 HETATM 10 C C5' GDP . . . B 2 -19.618 0.591 9.654 1 20.49 ? C5' GDP 501 B 1 HETATM 11 C C4' GDP . . . B 2 -18.589 1.298 8.787 1 19.15 ? C4' GDP 501 B 1 HETATM 12 O O4' GDP . . . B 2 -17.497 0.402 8.59 1 18.33 ? O4' GDP 501 B 1 HETATM 13 C C3' GDP . . . B 2 -19.165 1.586 7.416 1 19.78 ? C3' GDP 501 B 1 HETATM 14 O O3' GDP . . . B 2 -18.582 2.783 6.893 1 15.85 ? O3' GDP 501 B 1 HETATM 15 C C2' GDP . . . B 2 -18.723 0.41 6.576 1 18.48 ? C2' GDP 501 B 1 HETATM 16 O O2' GDP . . . B 2 -18.55 0.789 5.207 1 15.5 ? O2' GDP 501 B 1 HETATM 17 C C1' GDP . . . B 2 -17.409 0.005 7.22 1 18.77 ? C1' GDP 501 B 1 HETATM 18 N N9 GDP . . . B 2 -17.219 -1.461 7.15 1 15.6 ? N9 GDP 501 B 1 HETATM 19 C C8 GDP . . . B 2 -17.985 -2.384 7.756 1 12.03 ? C8 GDP 501 B 1 HETATM 20 N N7 GDP . . . B 2 -17.537 -3.638 7.494 1 11.56 ? N7 GDP 501 B 1 HETATM 21 C C5 GDP . . . B 2 -16.447 -3.519 6.713 1 14.69 ? C5 GDP 501 B 1 HETATM 22 C C6 GDP . . . B 2 -15.483 -4.445 6.075 1 12.88 ? C6 GDP 501 B 1 HETATM 23 O O6 GDP . . . B 2 -15.593 -5.682 6.217 1 10.58 ? O6 GDP 501 B 1 HETATM 24 N N1 GDP . . . B 2 -14.494 -3.915 5.344 1 13.15 ? N1 GDP 501 B 1 HETATM 25 C C2 GDP . . . B 2 -14.354 -2.586 5.175 1 18.86 ? C2 GDP 501 B 1 HETATM 26 N N2 GDP . . . B 2 -13.324 -2.133 4.418 1 17.53 ? N2 GDP 501 B 1 HETATM 27 N N3 GDP . . . B 2 -15.199 -1.681 5.729 1 15.18 ? N3 GDP 501 B 1 HETATM 28 C C4 GDP . . . B 2 -16.241 -2.081 6.492 1 17.07 ? C4 GDP 501 B 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 29 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 291 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 28 #