data_5CA9
#
_model_server_result.job_id            rTfOrTjab0zT_GKfigDK3w 
_model_server_result.datetime_utc      '2024-11-26 02:02:34' 
_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          5ca9 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":703}' 
#
_entry.id    5CA9 
#
_exptl.entry_id    5CA9 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              443.201 
_entity.id                          4 
_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            5CA9 
_cell.length_a            76.272 
_cell.length_b            120.527 
_cell.length_c            190.198 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5CA9 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        24 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'I 21 21 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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    1,2 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 6_555 -x,-y+1/2,z -1 0 0 0 -1 0 0 0 1 0 60.2635 0 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      4 
_struct_asym.id                             D 
_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 LYS 188 A LYS 188 1_555 A N GLU 190 A GLU 190 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.21 ? 
covale ? covale2 A O GLN 662 A GLN 662 1_555 A N LYS 664 A LYS 664 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.234 ? 
metalc ? metalc1 A OG SER 72 A SER 72 1_555 B MG MG . A MG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.515 ? 
metalc ? metalc2 A OG1 THR 95 A THR 95 1_555 B MG MG . A MG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? 
metalc ? metalc3 B MG MG . A MG 701 1_555 D O1B GDP . A GDP 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? 
metalc ? metalc4 B MG MG . A MG 701 1_555 D O3B GDP . A GDP 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.627 ? 
#
_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 87 n n 
PB O2B GDP sing 88 n n 
PB O3B GDP sing 89 n n 
PB O3A GDP sing 90 n n 
O2B HOB2 GDP sing 91 n n 
O3B HOB3 GDP sing 92 n n 
O3A PA GDP sing 93 n n 
PA O1A GDP doub 94 n n 
PA O2A GDP sing 95 n n 
PA O5' GDP sing 96 n n 
O2A HOA2 GDP sing 97 n n 
O5' C5' GDP sing 98 n n 
C5' C4' GDP sing 99 n n 
C5' H5' GDP sing 100 n n 
C5' "H5''" GDP sing 101 n n 
C4' O4' GDP sing 102 n n 
C4' C3' GDP sing 103 n n 
C4' H4' GDP sing 104 n n 
O4' C1' GDP sing 105 n n 
C3' O3' GDP sing 106 n n 
C3' C2' GDP sing 107 n n 
C3' H3' GDP sing 108 n n 
O3' HO3' GDP sing 109 n n 
C2' O2' GDP sing 110 n n 
C2' C1' GDP sing 111 n n 
C2' H2' GDP sing 112 n n 
O2' HO2' GDP sing 113 n n 
C1' N9 GDP sing 114 n n 
C1' H1' GDP sing 115 n n 
N9 C8 GDP sing 116 n y 
N9 C4 GDP sing 117 n y 
C8 N7 GDP doub 118 n y 
C8 H8 GDP sing 119 n n 
N7 C5 GDP sing 120 n y 
C5 C6 GDP sing 121 n n 
C5 C4 GDP doub 122 n y 
C6 O6 GDP doub 123 n n 
C6 N1 GDP sing 124 n n 
N1 C2 GDP sing 125 n n 
N1 HN1 GDP sing 126 n n 
C2 N2 GDP sing 127 n n 
C2 N3 GDP doub 128 n n 
N2 HN21 GDP sing 129 n n 
N2 HN22 GDP sing 130 n n 
N3 C4 GDP sing 131 n n 
#
_atom_sites.entry_id                     5CA9 
_atom_sites.fract_transf_matrix[1][1]    0.013111 
_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]    0.008297 
_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]    0.005258 
_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 2 MG MG . 
C 3 ALF A 1 702 3 ALF ALF . 
D 4 GDP A 1 703 1000 GDP GDP . 
E 5 HOH A 1 801 70 HOH HOH . 
E 5 HOH A 2 802 121 HOH HOH . 
E 5 HOH A 3 803 28 HOH HOH . 
E 5 HOH A 4 804 5 HOH HOH . 
E 5 HOH A 5 805 112 HOH HOH . 
E 5 HOH A 6 806 1 HOH HOH . 
E 5 HOH A 7 807 79 HOH HOH . 
E 5 HOH A 8 808 24 HOH HOH . 
E 5 HOH A 9 809 35 HOH HOH . 
E 5 HOH A 10 810 110 HOH HOH . 
E 5 HOH A 11 811 47 HOH HOH . 
E 5 HOH A 12 812 69 HOH HOH . 
E 5 HOH A 13 813 62 HOH HOH . 
E 5 HOH A 14 814 36 HOH HOH . 
E 5 HOH A 15 815 42 HOH HOH . 
E 5 HOH A 16 816 66 HOH HOH . 
E 5 HOH A 17 817 109 HOH HOH . 
E 5 HOH A 18 818 23 HOH HOH . 
E 5 HOH A 19 819 30 HOH HOH . 
E 5 HOH A 20 820 72 HOH HOH . 
E 5 HOH A 21 821 7 HOH HOH . 
E 5 HOH A 22 822 8 HOH HOH . 
E 5 HOH A 23 823 32 HOH HOH . 
E 5 HOH A 24 824 19 HOH HOH . 
E 5 HOH A 25 825 25 HOH HOH . 
E 5 HOH A 26 826 3 HOH HOH . 
E 5 HOH A 27 827 74 HOH HOH . 
E 5 HOH A 28 828 58 HOH HOH . 
E 5 HOH A 29 829 83 HOH HOH . 
E 5 HOH A 30 830 31 HOH HOH . 
E 5 HOH A 31 831 82 HOH HOH . 
E 5 HOH A 32 832 2 HOH HOH . 
E 5 HOH A 33 833 18 HOH HOH . 
E 5 HOH A 34 834 85 HOH HOH . 
E 5 HOH A 35 835 63 HOH HOH . 
E 5 HOH A 36 836 27 HOH HOH . 
E 5 HOH A 37 837 17 HOH HOH . 
E 5 HOH A 38 838 108 HOH HOH . 
E 5 HOH A 39 839 111 HOH HOH . 
E 5 HOH A 40 840 29 HOH HOH . 
E 5 HOH A 41 841 122 HOH HOH . 
E 5 HOH A 42 842 21 HOH HOH . 
E 5 HOH A 43 843 44 HOH HOH . 
E 5 HOH A 44 844 103 HOH HOH . 
E 5 HOH A 45 845 78 HOH HOH . 
E 5 HOH A 46 846 76 HOH HOH . 
E 5 HOH A 47 847 48 HOH HOH . 
E 5 HOH A 48 848 64 HOH HOH . 
E 5 HOH A 49 849 10 HOH HOH . 
E 5 HOH A 50 850 105 HOH HOH . 
E 5 HOH A 51 851 84 HOH HOH . 
E 5 HOH A 52 852 77 HOH HOH . 
E 5 HOH A 53 853 49 HOH HOH . 
E 5 HOH A 54 854 39 HOH HOH . 
E 5 HOH A 55 855 46 HOH HOH . 
E 5 HOH A 56 856 86 HOH HOH . 
E 5 HOH A 57 857 104 HOH HOH . 
E 5 HOH A 58 858 65 HOH HOH . 
E 5 HOH A 59 859 80 HOH HOH . 
E 5 HOH A 60 860 87 HOH HOH . 
E 5 HOH A 61 861 54 HOH HOH . 
E 5 HOH A 62 862 75 HOH HOH . 
E 5 HOH A 63 863 99 HOH HOH . 
E 5 HOH A 64 864 117 HOH HOH . 
E 5 HOH A 65 865 20 HOH HOH . 
E 5 HOH A 66 866 41 HOH HOH . 
E 5 HOH A 67 867 26 HOH HOH . 
E 5 HOH A 68 868 53 HOH HOH . 
E 5 HOH A 69 869 71 HOH HOH . 
E 5 HOH A 70 870 11 HOH HOH . 
E 5 HOH A 71 871 73 HOH HOH . 
E 5 HOH A 72 872 57 HOH HOH . 
E 5 HOH A 73 873 59 HOH HOH . 
E 5 HOH A 74 874 14 HOH HOH . 
E 5 HOH A 75 875 33 HOH HOH . 
E 5 HOH A 76 876 55 HOH HOH . 
E 5 HOH A 77 877 60 HOH HOH . 
E 5 HOH A 78 878 38 HOH HOH . 
E 5 HOH A 79 879 61 HOH HOH . 
E 5 HOH A 80 880 96 HOH HOH . 
E 5 HOH A 81 881 115 HOH HOH . 
E 5 HOH A 82 882 113 HOH HOH . 
E 5 HOH A 83 883 94 HOH HOH . 
E 5 HOH A 84 884 81 HOH HOH . 
E 5 HOH A 85 885 118 HOH HOH . 
E 5 HOH A 86 886 95 HOH HOH . 
E 5 HOH A 87 887 101 HOH HOH . 
E 5 HOH A 88 888 88 HOH HOH . 
E 5 HOH A 89 889 106 HOH HOH . 
E 5 HOH A 90 890 50 HOH HOH . 
E 5 HOH A 91 891 56 HOH HOH . 
E 5 HOH A 92 892 93 HOH HOH . 
E 5 HOH A 93 893 68 HOH HOH . 
E 5 HOH A 94 894 9 HOH HOH . 
E 5 HOH A 95 895 97 HOH HOH . 
E 5 HOH A 96 896 119 HOH HOH . 
E 5 HOH A 97 897 37 HOH HOH . 
E 5 HOH A 98 898 90 HOH HOH . 
E 5 HOH A 99 899 100 HOH HOH . 
E 5 HOH A 100 900 98 HOH HOH . 
E 5 HOH A 101 901 92 HOH HOH . 
E 5 HOH A 102 902 12 HOH HOH . 
E 5 HOH A 103 903 123 HOH HOH . 
E 5 HOH A 104 904 91 HOH HOH . 
E 5 HOH A 105 905 89 HOH HOH . 
E 5 HOH A 106 906 107 HOH HOH . 
E 5 HOH A 107 907 40 HOH HOH . 
E 5 HOH A 108 908 13 HOH HOH . 
E 5 HOH A 109 909 43 HOH HOH . 
E 5 HOH A 110 910 45 HOH HOH . 
E 5 HOH A 111 911 126 HOH HOH . 
E 5 HOH A 112 912 52 HOH HOH . 
E 5 HOH A 113 913 125 HOH HOH . 
E 5 HOH A 114 914 116 HOH HOH . 
E 5 HOH A 115 915 124 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 . . . D 4 -8.964 20.875 -31.449 1 34.54 ? PB GDP 703 A 1 
HETATM 2 O O1B GDP . . . D 4 -9.442 19.476 -31.639 1 38.26 ? O1B GDP 703 A 1 
HETATM 3 O O2B GDP . . . D 4 -7.445 21.022 -31.055 1 26.73 ? O2B GDP 703 A 1 
HETATM 4 O O3B GDP . . . D 4 -9.97 21.536 -30.506 1 31.17 ? O3B GDP 703 A 1 
HETATM 5 O O3A GDP . . . D 4 -9.146 21.469 -33.009 1 34.28 ? O3A GDP 703 A 1 
HETATM 6 P PA GDP . . . D 4 -10.192 21.118 -34.238 1 37.38 ? PA GDP 703 A 1 
HETATM 7 O O1A GDP . . . D 4 -9.643 20.044 -35.086 1 40.8 ? O1A GDP 703 A 1 
HETATM 8 O O2A GDP . . . D 4 -11.679 21.136 -33.999 1 33.66 ? O2A GDP 703 A 1 
HETATM 9 O O5' GDP . . . D 4 -9.866 22.25 -35.348 1 38.96 ? O5' GDP 703 A 1 
HETATM 10 C C5' GDP . . . D 4 -9.707 23.653 -34.992 1 36.66 ? C5' GDP 703 A 1 
HETATM 11 C C4' GDP . . . D 4 -9.812 24.532 -36.234 1 32.39 ? C4' GDP 703 A 1 
HETATM 12 O O4' GDP . . . D 4 -8.543 24.617 -36.887 1 28.24 ? O4' GDP 703 A 1 
HETATM 13 C C3' GDP . . . D 4 -10.706 23.9 -37.238 1 31.56 ? C3' GDP 703 A 1 
HETATM 14 O O3' GDP . . . D 4 -11.391 24.949 -37.836 1 32.45 ? O3' GDP 703 A 1 
HETATM 15 C C2' GDP . . . D 4 -9.794 23.389 -38.284 1 31.64 ? C2' GDP 703 A 1 
HETATM 16 O O2' GDP . . . D 4 -10.378 23.549 -39.585 1 42.61 ? O2' GDP 703 A 1 
HETATM 17 C C1' GDP . . . D 4 -8.648 24.295 -38.247 1 27.93 ? C1' GDP 703 A 1 
HETATM 18 N N9 GDP . . . D 4 -7.426 23.656 -38.544 1 25.98 ? N9 GDP 703 A 1 
HETATM 19 C C8 GDP . . . D 4 -7.216 22.341 -38.471 1 27.53 ? C8 GDP 703 A 1 
HETATM 20 N N7 GDP . . . D 4 -5.894 22.015 -38.704 1 25.47 ? N7 GDP 703 A 1 
HETATM 21 C C5 GDP . . . D 4 -5.306 23.152 -38.927 1 25.17 ? C5 GDP 703 A 1 
HETATM 22 C C6 GDP . . . D 4 -3.973 23.447 -39.199 1 26.3 ? C6 GDP 703 A 1 
HETATM 23 O O6 GDP . . . D 4 -3.225 22.493 -39.296 1 25.53 ? O6 GDP 703 A 1 
HETATM 24 N N1 GDP . . . D 4 -3.634 24.728 -39.345 1 28.75 ? N1 GDP 703 A 1 
HETATM 25 C C2 GDP . . . D 4 -4.569 25.717 -39.249 1 27.81 ? C2 GDP 703 A 1 
HETATM 26 N N2 GDP . . . D 4 -4.104 26.984 -39.467 1 29.31 ? N2 GDP 703 A 1 
HETATM 27 N N3 GDP . . . D 4 -5.866 25.51 -39.007 1 22.73 ? N3 GDP 703 A 1 
HETATM 28 C C4 GDP . . . D 4 -6.272 24.266 -38.808 1 25.44 ? C4 GDP 703 A 1 
#
_model_server_stats.io_time_ms              77 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           282 
_model_server_stats.encode_time_ms          28 
_model_server_stats.element_count           28 
#