data_5CA8
#
_model_server_result.job_id            JwTtMGbAlNPpIQtFl5NzPA 
_model_server_result.datetime_utc      '2025-02-27 13:11:52' 
_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          5ca8 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":702}' 
#
_entry.id    5CA8 
#
_exptl.entry_id    5CA8 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              443.201 
_entity.id                          3 
_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          108.12 
_cell.angle_gamma         90 
_cell.entry_id            5CA8 
_cell.length_a            228.12 
_cell.length_b            43.62 
_cell.length_c            97.56 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5CA8 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
_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 
_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                      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
covale ? covale1 A O SER 535 A SER 535 1_555 A N THR 537 A THR 537 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.341 ? 
metalc ? metalc1 A OG SER 72 A SER 72 1_555 B MG MG . A MG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.349 ? 
metalc ? metalc2 A OE2 GLU 125 A GLU 125 1_555 B MG MG . A MG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.831 ? 
metalc ? metalc3 B MG MG . A MG 701 1_555 C O3B GDP . A GDP 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.749 ? 
metalc ? metalc4 B MG MG . A MG 701 1_555 D O HOH . A HOH 829 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? 
#
_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                     5CA8 
_atom_sites.fract_transf_matrix[1][1]    0.004384 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.001434 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.022925 
_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]    0.010785 
_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 1 701 4 MG MG . 
C 3 GDP A 1 702 1000 GDP GDP . 
D 4 HOH A 1 801 52 HOH HOH . 
D 4 HOH A 2 802 39 HOH HOH . 
D 4 HOH A 3 803 108 HOH HOH . 
D 4 HOH A 4 804 144 HOH HOH . 
D 4 HOH A 5 805 97 HOH HOH . 
D 4 HOH A 6 806 107 HOH HOH . 
D 4 HOH A 7 807 115 HOH HOH . 
D 4 HOH A 8 808 27 HOH HOH . 
D 4 HOH A 9 809 79 HOH HOH . 
D 4 HOH A 10 810 6 HOH HOH . 
D 4 HOH A 11 811 33 HOH HOH . 
D 4 HOH A 12 812 112 HOH HOH . 
D 4 HOH A 13 813 66 HOH HOH . 
D 4 HOH A 14 814 1 HOH HOH . 
D 4 HOH A 15 815 42 HOH HOH . 
D 4 HOH A 16 816 90 HOH HOH . 
D 4 HOH A 17 817 113 HOH HOH . 
D 4 HOH A 18 818 67 HOH HOH . 
D 4 HOH A 19 819 40 HOH HOH . 
D 4 HOH A 20 820 61 HOH HOH . 
D 4 HOH A 21 821 20 HOH HOH . 
D 4 HOH A 22 822 119 HOH HOH . 
D 4 HOH A 23 823 54 HOH HOH . 
D 4 HOH A 24 824 3 HOH HOH . 
D 4 HOH A 25 825 17 HOH HOH . 
D 4 HOH A 26 826 128 HOH HOH . 
D 4 HOH A 27 827 68 HOH HOH . 
D 4 HOH A 28 828 74 HOH HOH . 
D 4 HOH A 29 829 139 HOH HOH . 
D 4 HOH A 30 830 100 HOH HOH . 
D 4 HOH A 31 831 44 HOH HOH . 
D 4 HOH A 32 832 2 HOH HOH . 
D 4 HOH A 33 833 114 HOH HOH . 
D 4 HOH A 34 834 41 HOH HOH . 
D 4 HOH A 35 835 71 HOH HOH . 
D 4 HOH A 36 836 130 HOH HOH . 
D 4 HOH A 37 837 98 HOH HOH . 
D 4 HOH A 38 838 55 HOH HOH . 
D 4 HOH A 39 839 117 HOH HOH . 
D 4 HOH A 40 840 29 HOH HOH . 
D 4 HOH A 41 841 36 HOH HOH . 
D 4 HOH A 42 842 14 HOH HOH . 
D 4 HOH A 43 843 92 HOH HOH . 
D 4 HOH A 44 844 77 HOH HOH . 
D 4 HOH A 45 845 23 HOH HOH . 
D 4 HOH A 46 846 105 HOH HOH . 
D 4 HOH A 47 847 103 HOH HOH . 
D 4 HOH A 48 848 48 HOH HOH . 
D 4 HOH A 49 849 38 HOH HOH . 
D 4 HOH A 50 850 2 HOH HOH . 
D 4 HOH A 51 851 34 HOH HOH . 
D 4 HOH A 52 852 16 HOH HOH . 
D 4 HOH A 53 853 53 HOH HOH . 
D 4 HOH A 54 854 75 HOH HOH . 
D 4 HOH A 55 855 57 HOH HOH . 
D 4 HOH A 56 856 63 HOH HOH . 
D 4 HOH A 57 857 28 HOH HOH . 
D 4 HOH A 58 858 82 HOH HOH . 
D 4 HOH A 59 859 10 HOH HOH . 
D 4 HOH A 60 860 60 HOH HOH . 
D 4 HOH A 61 861 84 HOH HOH . 
D 4 HOH A 62 862 45 HOH HOH . 
D 4 HOH A 63 863 72 HOH HOH . 
D 4 HOH A 64 864 9 HOH HOH . 
D 4 HOH A 65 865 47 HOH HOH . 
D 4 HOH A 66 866 37 HOH HOH . 
D 4 HOH A 67 867 78 HOH HOH . 
D 4 HOH A 68 868 3 HOH HOH . 
D 4 HOH A 69 869 138 HOH HOH . 
D 4 HOH A 70 870 62 HOH HOH . 
D 4 HOH A 71 871 70 HOH HOH . 
D 4 HOH A 72 872 31 HOH HOH . 
D 4 HOH A 73 873 118 HOH HOH . 
D 4 HOH A 74 874 46 HOH HOH . 
D 4 HOH A 75 875 49 HOH HOH . 
D 4 HOH A 76 876 106 HOH HOH . 
D 4 HOH A 77 877 51 HOH HOH . 
D 4 HOH A 78 878 73 HOH HOH . 
D 4 HOH A 79 879 59 HOH HOH . 
D 4 HOH A 80 880 135 HOH HOH . 
D 4 HOH A 81 881 116 HOH HOH . 
D 4 HOH A 82 882 87 HOH HOH . 
D 4 HOH A 83 883 22 HOH HOH . 
D 4 HOH A 84 884 56 HOH HOH . 
D 4 HOH A 85 885 91 HOH HOH . 
D 4 HOH A 86 886 121 HOH HOH . 
D 4 HOH A 87 887 76 HOH HOH . 
D 4 HOH A 88 888 80 HOH HOH . 
D 4 HOH A 89 889 131 HOH HOH . 
D 4 HOH A 90 890 143 HOH HOH . 
D 4 HOH A 91 891 24 HOH HOH . 
D 4 HOH A 92 892 89 HOH HOH . 
D 4 HOH A 93 893 104 HOH HOH . 
D 4 HOH A 94 894 4 HOH HOH . 
D 4 HOH A 95 895 58 HOH HOH . 
D 4 HOH A 96 896 19 HOH HOH . 
D 4 HOH A 97 897 26 HOH HOH . 
D 4 HOH A 98 898 5 HOH HOH . 
D 4 HOH A 99 899 85 HOH HOH . 
D 4 HOH A 100 900 129 HOH HOH . 
D 4 HOH A 101 901 21 HOH HOH . 
D 4 HOH A 102 902 111 HOH HOH . 
D 4 HOH A 103 903 145 HOH HOH . 
D 4 HOH A 104 904 93 HOH HOH . 
D 4 HOH A 105 905 94 HOH HOH . 
D 4 HOH A 106 906 132 HOH HOH . 
D 4 HOH A 107 907 35 HOH HOH . 
D 4 HOH A 108 908 140 HOH HOH . 
D 4 HOH A 109 909 146 HOH HOH . 
D 4 HOH A 110 910 88 HOH HOH . 
D 4 HOH A 111 911 86 HOH HOH . 
D 4 HOH A 112 912 109 HOH HOH . 
D 4 HOH A 113 913 65 HOH HOH . 
D 4 HOH A 114 914 125 HOH HOH . 
D 4 HOH A 115 915 142 HOH HOH . 
D 4 HOH A 116 916 124 HOH HOH . 
D 4 HOH A 117 917 96 HOH HOH . 
D 4 HOH A 118 918 99 HOH HOH . 
D 4 HOH A 119 919 81 HOH HOH . 
D 4 HOH A 120 920 136 HOH HOH . 
D 4 HOH A 121 921 69 HOH HOH . 
D 4 HOH A 122 922 137 HOH HOH . 
D 4 HOH A 123 923 120 HOH HOH . 
D 4 HOH A 124 924 141 HOH HOH . 
D 4 HOH A 125 925 123 HOH HOH . 
D 4 HOH A 126 926 95 HOH HOH . 
D 4 HOH A 127 927 8 HOH HOH . 
D 4 HOH A 128 928 126 HOH HOH . 
D 4 HOH A 129 929 133 HOH HOH . 
D 4 HOH A 130 930 7 HOH HOH . 
D 4 HOH A 131 931 110 HOH HOH . 
D 4 HOH A 132 932 101 HOH HOH . 
D 4 HOH A 133 933 102 HOH HOH . 
D 4 HOH A 134 934 83 HOH HOH . 
D 4 HOH A 135 935 134 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 3 93.154 -8.49 31.329 1 47.14 ? PB GDP 702 A 1 
HETATM 2 O O1B GDP . . . C 3 94.173 -7.907 30.379 1 46.79 ? O1B GDP 702 A 1 
HETATM 3 O O2B GDP . . . C 3 92.666 -7.409 32.262 1 46.92 ? O2B GDP 702 A 1 
HETATM 4 O O3B GDP . . . C 3 91.996 -9.055 30.544 1 48.21 ? O3B GDP 702 A 1 
HETATM 5 O O3A GDP . . . C 3 93.831 -9.662 32.197 1 44.36 ? O3A GDP 702 A 1 
HETATM 6 P PA GDP . . . C 3 94.121 -11.094 31.529 1 45.56 ? PA GDP 702 A 1 
HETATM 7 O O1A GDP . . . C 3 94.676 -10.933 30.135 1 45.89 ? O1A GDP 702 A 1 
HETATM 8 O O2A GDP . . . C 3 92.859 -11.924 31.513 1 46.12 ? O2A GDP 702 A 1 
HETATM 9 O O5' GDP . . . C 3 95.219 -11.729 32.519 1 48.48 ? O5' GDP 702 A 1 
HETATM 10 C C5' GDP . . . C 3 96.599 -11.409 32.344 1 48.65 ? C5' GDP 702 A 1 
HETATM 11 C C4' GDP . . . C 3 97.453 -12.455 33.044 1 48.95 ? C4' GDP 702 A 1 
HETATM 12 O O4' GDP . . . C 3 97.01 -12.609 34.393 1 49.15 ? O4' GDP 702 A 1 
HETATM 13 C C3' GDP . . . C 3 97.299 -13.801 32.36 1 49.68 ? C3' GDP 702 A 1 
HETATM 14 O O3' GDP . . . C 3 98.589 -14.354 32.086 1 49.37 ? O3' GDP 702 A 1 
HETATM 15 C C2' GDP . . . C 3 96.564 -14.674 33.355 1 50.1 ? C2' GDP 702 A 1 
HETATM 16 O O2' GDP . . . C 3 97.093 -16.002 33.348 1 50.07 ? O2' GDP 702 A 1 
HETATM 17 C C1' GDP . . . C 3 96.788 -13.988 34.693 1 50.13 ? C1' GDP 702 A 1 
HETATM 18 N N9 GDP . . . C 3 95.599 -14.117 35.569 1 51.6 ? N9 GDP 702 A 1 
HETATM 19 C C8 GDP . . . C 3 94.312 -13.992 35.194 1 52.56 ? C8 GDP 702 A 1 
HETATM 20 N N7 GDP . . . C 3 93.478 -14.157 36.253 1 52.51 ? N7 GDP 702 A 1 
HETATM 21 C C5 GDP . . . C 3 94.242 -14.379 37.339 1 52.14 ? C5 GDP 702 A 1 
HETATM 22 C C6 GDP . . . C 3 94.008 -14.629 38.781 1 52.18 ? C6 GDP 702 A 1 
HETATM 23 O O6 GDP . . . C 3 92.85 -14.676 39.248 1 52.9 ? O6 GDP 702 A 1 
HETATM 24 N N1 GDP . . . C 3 95.078 -14.814 39.566 1 51.54 ? N1 GDP 702 A 1 
HETATM 25 C C2 GDP . . . C 3 96.339 -14.773 39.093 1 51.49 ? C2 GDP 702 A 1 
HETATM 26 N N2 GDP . . . C 3 97.365 -14.964 39.957 1 51.14 ? N2 GDP 702 A 1 
HETATM 27 N N3 GDP . . . C 3 96.626 -14.546 37.786 1 51.68 ? N3 GDP 702 A 1 
HETATM 28 C C4 GDP . . . C 3 95.638 -14.347 36.882 1 51.82 ? C4 GDP 702 A 1 
#
_model_server_stats.io_time_ms              14 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           235 
_model_server_stats.encode_time_ms          15 
_model_server_stats.element_count           28 
#