data_4DCT
#
_model_server_result.job_id            EQN3bG3kwM4vssuc2eZQGQ 
_model_server_result.datetime_utc      '2024-11-29 14:39:53' 
_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          4dct 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":502}' 
#
_entry.id    4DCT 
#
_exptl.entry_id    4DCT 
_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    2 
_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            4DCT 
_cell.length_a            62.76 
_cell.length_b            65.26 
_cell.length_c            112.5 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4DCT 
_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,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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 B N N 
? 2 C N 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                     4DCT 
_atom_sites.fract_transf_matrix[1][1]    0.015934 
_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]    0.015323 
_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]    0.008889 
_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 1 501 500 GDP GDP . 
C 2 GDP A 1 502 800 GDP GDP . 
D 3 SO4 A 1 503 1 SO4 SO4 . 
E 4 HOH A 1 601 1 HOH HOH . 
E 4 HOH A 2 602 2 HOH HOH . 
E 4 HOH A 3 603 3 HOH HOH . 
E 4 HOH A 4 604 4 HOH HOH . 
E 4 HOH A 5 605 5 HOH HOH . 
E 4 HOH A 6 606 6 HOH HOH . 
E 4 HOH A 7 607 7 HOH HOH . 
E 4 HOH A 8 608 8 HOH HOH . 
E 4 HOH A 9 609 9 HOH HOH . 
E 4 HOH A 10 610 10 HOH HOH . 
E 4 HOH A 11 611 11 HOH HOH . 
E 4 HOH A 12 612 12 HOH HOH . 
E 4 HOH A 13 613 13 HOH HOH . 
E 4 HOH A 14 614 14 HOH HOH . 
E 4 HOH A 15 615 15 HOH HOH . 
E 4 HOH A 16 616 16 HOH HOH . 
E 4 HOH A 17 617 17 HOH HOH . 
E 4 HOH A 18 618 18 HOH HOH . 
E 4 HOH A 19 619 19 HOH HOH . 
E 4 HOH A 20 620 20 HOH HOH . 
E 4 HOH A 21 621 21 HOH HOH . 
E 4 HOH A 22 622 22 HOH HOH . 
E 4 HOH A 23 623 23 HOH HOH . 
E 4 HOH A 24 624 24 HOH HOH . 
E 4 HOH A 25 625 25 HOH HOH . 
E 4 HOH A 26 626 26 HOH HOH . 
E 4 HOH A 27 627 27 HOH HOH . 
E 4 HOH A 28 628 28 HOH HOH . 
E 4 HOH A 29 629 29 HOH HOH . 
E 4 HOH A 30 630 30 HOH HOH . 
E 4 HOH A 31 631 31 HOH HOH . 
E 4 HOH A 32 632 32 HOH HOH . 
E 4 HOH A 33 633 33 HOH HOH . 
E 4 HOH A 34 634 34 HOH HOH . 
E 4 HOH A 35 635 35 HOH HOH . 
E 4 HOH A 36 636 36 HOH HOH . 
E 4 HOH A 37 637 37 HOH HOH . 
E 4 HOH A 38 638 38 HOH HOH . 
E 4 HOH A 39 639 39 HOH HOH . 
E 4 HOH A 40 640 40 HOH HOH . 
E 4 HOH A 41 641 41 HOH HOH . 
E 4 HOH A 42 642 42 HOH HOH . 
E 4 HOH A 43 643 43 HOH HOH . 
E 4 HOH A 44 644 44 HOH HOH . 
E 4 HOH A 45 645 45 HOH HOH . 
E 4 HOH A 46 646 46 HOH HOH . 
E 4 HOH A 47 647 47 HOH HOH . 
E 4 HOH A 48 648 48 HOH HOH . 
E 4 HOH A 49 649 49 HOH HOH . 
E 4 HOH A 50 650 50 HOH HOH . 
E 4 HOH A 51 651 51 HOH HOH . 
E 4 HOH A 52 652 52 HOH HOH . 
E 4 HOH A 53 653 53 HOH HOH . 
E 4 HOH A 54 654 54 HOH HOH . 
E 4 HOH A 55 655 55 HOH HOH . 
E 4 HOH A 56 656 56 HOH HOH . 
E 4 HOH A 57 657 57 HOH HOH . 
E 4 HOH A 58 658 58 HOH HOH . 
E 4 HOH A 59 659 59 HOH HOH . 
E 4 HOH A 60 660 60 HOH HOH . 
E 4 HOH A 61 661 61 HOH HOH . 
E 4 HOH A 62 662 62 HOH HOH . 
E 4 HOH A 63 663 63 HOH HOH . 
E 4 HOH A 64 664 64 HOH HOH . 
E 4 HOH A 65 665 65 HOH HOH . 
E 4 HOH A 66 666 66 HOH HOH . 
E 4 HOH A 67 667 67 HOH HOH . 
E 4 HOH A 68 668 68 HOH HOH . 
E 4 HOH A 69 669 69 HOH HOH . 
E 4 HOH A 70 670 70 HOH HOH . 
E 4 HOH A 71 671 71 HOH HOH . 
E 4 HOH A 72 672 72 HOH HOH . 
E 4 HOH A 73 673 73 HOH HOH . 
E 4 HOH A 74 674 74 HOH HOH . 
E 4 HOH A 75 675 75 HOH HOH . 
E 4 HOH A 76 676 76 HOH HOH . 
E 4 HOH A 77 677 77 HOH HOH . 
E 4 HOH A 78 678 78 HOH HOH . 
E 4 HOH A 79 679 79 HOH HOH . 
E 4 HOH A 80 680 80 HOH HOH . 
E 4 HOH A 81 681 81 HOH HOH . 
E 4 HOH A 82 682 82 HOH HOH . 
E 4 HOH A 83 683 83 HOH HOH . 
E 4 HOH A 84 684 84 HOH HOH . 
E 4 HOH A 85 685 85 HOH HOH . 
E 4 HOH A 86 686 86 HOH HOH . 
E 4 HOH A 87 687 87 HOH HOH . 
E 4 HOH A 88 688 88 HOH HOH . 
E 4 HOH A 89 689 89 HOH HOH . 
E 4 HOH A 90 690 90 HOH HOH . 
E 4 HOH A 91 691 91 HOH HOH . 
E 4 HOH A 92 692 92 HOH HOH . 
E 4 HOH A 93 693 93 HOH HOH . 
E 4 HOH A 94 694 94 HOH HOH . 
E 4 HOH A 95 695 95 HOH HOH . 
E 4 HOH A 96 696 96 HOH HOH . 
E 4 HOH A 97 697 97 HOH HOH . 
E 4 HOH A 98 698 98 HOH HOH . 
E 4 HOH A 99 699 99 HOH HOH . 
E 4 HOH A 100 700 100 HOH HOH . 
E 4 HOH A 101 701 101 HOH HOH . 
E 4 HOH A 102 702 102 HOH HOH . 
E 4 HOH A 103 703 103 HOH HOH . 
E 4 HOH A 104 704 104 HOH HOH . 
E 4 HOH A 105 705 105 HOH HOH . 
E 4 HOH A 106 706 106 HOH HOH . 
E 4 HOH A 107 707 107 HOH HOH . 
E 4 HOH A 108 708 108 HOH HOH . 
E 4 HOH A 109 709 109 HOH HOH . 
E 4 HOH A 110 710 110 HOH HOH . 
E 4 HOH A 111 711 111 HOH HOH . 
E 4 HOH A 112 712 112 HOH HOH . 
E 4 HOH A 113 713 113 HOH HOH . 
E 4 HOH A 114 714 114 HOH HOH . 
E 4 HOH A 115 715 115 HOH HOH . 
E 4 HOH A 116 716 116 HOH HOH . 
E 4 HOH A 117 717 117 HOH HOH . 
E 4 HOH A 118 718 118 HOH HOH . 
E 4 HOH A 119 719 119 HOH HOH . 
E 4 HOH A 120 720 120 HOH HOH . 
E 4 HOH A 121 721 121 HOH HOH . 
E 4 HOH A 122 722 122 HOH HOH . 
E 4 HOH A 123 723 123 HOH HOH . 
E 4 HOH A 124 724 124 HOH HOH . 
E 4 HOH A 125 725 125 HOH HOH . 
E 4 HOH A 126 726 126 HOH HOH . 
E 4 HOH A 127 727 127 HOH HOH . 
E 4 HOH A 128 728 128 HOH HOH . 
E 4 HOH A 129 729 129 HOH HOH . 
E 4 HOH A 130 730 130 HOH HOH . 
E 4 HOH A 131 731 131 HOH HOH . 
E 4 HOH A 132 732 132 HOH HOH . 
E 4 HOH A 133 733 133 HOH HOH . 
E 4 HOH A 134 734 134 HOH HOH . 
E 4 HOH A 135 735 135 HOH HOH . 
E 4 HOH A 136 736 136 HOH HOH . 
E 4 HOH A 137 737 137 HOH HOH . 
E 4 HOH A 138 738 138 HOH HOH . 
E 4 HOH A 139 739 139 HOH HOH . 
E 4 HOH A 140 740 140 HOH HOH . 
E 4 HOH A 141 741 141 HOH HOH . 
E 4 HOH A 142 742 142 HOH HOH . 
E 4 HOH A 143 743 143 HOH HOH . 
E 4 HOH A 144 744 144 HOH HOH . 
E 4 HOH A 145 745 145 HOH HOH . 
E 4 HOH A 146 746 146 HOH HOH . 
E 4 HOH A 147 747 147 HOH HOH . 
E 4 HOH A 148 748 148 HOH HOH . 
E 4 HOH A 149 749 149 HOH HOH . 
E 4 HOH A 150 750 150 HOH HOH . 
E 4 HOH A 151 751 151 HOH HOH . 
E 4 HOH A 152 752 152 HOH HOH . 
E 4 HOH A 153 753 153 HOH HOH . 
E 4 HOH A 154 754 154 HOH HOH . 
E 4 HOH A 155 755 155 HOH HOH . 
E 4 HOH A 156 756 156 HOH HOH . 
E 4 HOH A 157 757 157 HOH HOH . 
E 4 HOH A 158 758 158 HOH HOH . 
E 4 HOH A 159 759 159 HOH HOH . 
E 4 HOH A 160 760 160 HOH HOH . 
E 4 HOH A 161 761 161 HOH HOH . 
E 4 HOH A 162 762 162 HOH HOH . 
E 4 HOH A 163 763 163 HOH HOH . 
E 4 HOH A 164 764 164 HOH HOH . 
E 4 HOH A 165 765 165 HOH HOH . 
E 4 HOH A 166 766 166 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 . . . C 2 32.169 -16.147 -5.701 0.5 72.23 ? PB GDP 502 A 1 
HETATM 2 O O1B GDP . . . C 2 32.615 -17.357 -4.911 0.5 72.64 ? O1B GDP 502 A 1 
HETATM 3 O O2B GDP . . . C 2 32.002 -16.408 -7.179 0.5 71.82 ? O2B GDP 502 A 1 
HETATM 4 O O3B GDP . . . C 2 31.023 -15.385 -5.083 0.5 70.88 ? O3B GDP 502 A 1 
HETATM 5 O O3A GDP . . . C 2 33.418 -15.125 -5.618 0.5 71.98 ? O3A GDP 502 A 1 
HETATM 6 P PA GDP . . . C 2 34.798 -15.541 -4.889 0.5 73.5 ? PA GDP 502 A 1 
HETATM 7 O O1A GDP . . . C 2 34.946 -14.707 -3.64 0.5 70.87 ? O1A GDP 502 A 1 
HETATM 8 O O2A GDP . . . C 2 34.847 -17.048 -4.79 0.5 74.06 ? O2A GDP 502 A 1 
HETATM 9 O O5' GDP . . . C 2 35.934 -15.077 -5.935 0.5 69.68 ? O5' GDP 502 A 1 
HETATM 10 C C5' GDP . . . C 2 36.778 -16.038 -6.566 0.5 65.31 ? C5' GDP 502 A 1 
HETATM 11 C C4' GDP . . . C 2 38.223 -15.55 -6.545 0.5 65.35 ? C4' GDP 502 A 1 
HETATM 12 O O4' GDP . . . C 2 38.631 -15.114 -7.849 0.5 64.36 ? O4' GDP 502 A 1 
HETATM 13 C C3' GDP . . . C 2 38.416 -14.375 -5.593 0.5 64.37 ? C3' GDP 502 A 1 
HETATM 14 O O3' GDP . . . C 2 39.083 -14.78 -4.388 0.5 62.02 ? O3' GDP 502 A 1 
HETATM 15 C C2' GDP . . . C 2 39.249 -13.363 -6.362 0.5 63.17 ? C2' GDP 502 A 1 
HETATM 16 O O2' GDP . . . C 2 40.516 -13.133 -5.738 0.5 61.04 ? O2' GDP 502 A 1 
HETATM 17 C C1' GDP . . . C 2 39.461 -13.954 -7.747 0.5 64.1 ? C1' GDP 502 A 1 
HETATM 18 N N9 GDP . . . C 2 39.078 -12.906 -8.722 0.5 64.6 ? N9 GDP 502 A 1 
HETATM 19 C C8 GDP . . . C 2 37.87 -12.321 -8.812 0.5 63.84 ? C8 GDP 502 A 1 
HETATM 20 N N7 GDP . . . C 2 37.853 -11.387 -9.795 0.5 63.94 ? N7 GDP 502 A 1 
HETATM 21 C C5 GDP . . . C 2 39.08 -11.361 -10.347 0.5 64.65 ? C5 GDP 502 A 1 
HETATM 22 C C6 GDP . . . C 2 39.75 -10.606 -11.434 0.5 63.75 ? C6 GDP 502 A 1 
HETATM 23 O O6 GDP . . . C 2 39.127 -9.744 -12.083 0.5 60.99 ? O6 GDP 502 A 1 
HETATM 24 N N1 GDP . . . C 2 41.036 -10.875 -11.696 0.5 64.04 ? N1 GDP 502 A 1 
HETATM 25 C C2 GDP . . . C 2 41.731 -11.802 -11.008 0.5 64.2 ? C2 GDP 502 A 1 
HETATM 26 N N2 GDP . . . C 2 43.03 -12.015 -11.334 0.5 63.32 ? N2 GDP 502 A 1 
HETATM 27 N N3 GDP . . . C 2 41.183 -12.532 -9.999 0.5 64.67 ? N3 GDP 502 A 1 
HETATM 28 C C4 GDP . . . C 2 39.887 -12.36 -9.633 0.5 64.93 ? C4 GDP 502 A 1 
#
_model_server_stats.io_time_ms              111 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           632 
_model_server_stats.encode_time_ms          10 
_model_server_stats.element_count           28 
#