data_3CX7
#
_model_server_result.job_id            2mMapFK7H1dMlWAxvx8pdw 
_model_server_result.datetime_utc      '2024-12-08 04:16:33' 
_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          3cx7 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":875}' 
#
_entry.id    3CX7 
#
_exptl.entry_id    3CX7 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              443.201 
_entity.id                          5 
_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            3CX7 
_cell.length_a            57.952 
_cell.length_b            66.371 
_cell.length_c            151.19 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3CX7 
_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    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G 
_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                      5 
_struct_asym.id                             E 
_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 OG SER 23 A SER 62 1_555 C MG MG . A MG 378 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.311 ? 
metalc ? metalc2 A OG1 THR 164 A THR 203 1_555 C MG MG . A MG 378 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? 
metalc ? metalc3 C MG MG . A MG 378 1_555 E O2B GDP . A GDP 875 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.253 ? 
metalc ? metalc4 C MG MG . A MG 378 1_555 F O HOH . A HOH 937 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.161 ? 
metalc ? metalc5 C MG MG . A MG 378 1_555 F O HOH . A HOH 966 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.296 ? 
#
_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                     3CX7 
_atom_sites.fract_transf_matrix[1][1]    0.017256 
_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]    0.015067 
_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]    0.006614 
_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
C 3 MG A 1 378 275 MG MG . 
D 4 ALF A 1 775 775 ALF ALF . 
E 5 GDP A 1 875 875 GDP GDP . 
F 6 HOH A 1 876 1 HOH HOH . 
F 6 HOH A 2 877 2 HOH HOH . 
F 6 HOH A 3 878 4 HOH HOH . 
F 6 HOH A 4 879 5 HOH HOH . 
F 6 HOH A 5 880 6 HOH HOH . 
F 6 HOH A 6 881 7 HOH HOH . 
F 6 HOH A 7 882 8 HOH HOH . 
F 6 HOH A 8 883 9 HOH HOH . 
F 6 HOH A 9 884 11 HOH HOH . 
F 6 HOH A 10 885 12 HOH HOH . 
F 6 HOH A 11 886 13 HOH HOH . 
F 6 HOH A 12 887 16 HOH HOH . 
F 6 HOH A 13 888 17 HOH HOH . 
F 6 HOH A 14 889 18 HOH HOH . 
F 6 HOH A 15 890 19 HOH HOH . 
F 6 HOH A 16 891 20 HOH HOH . 
F 6 HOH A 17 892 21 HOH HOH . 
F 6 HOH A 18 893 22 HOH HOH . 
F 6 HOH A 19 894 23 HOH HOH . 
F 6 HOH A 20 895 24 HOH HOH . 
F 6 HOH A 21 896 25 HOH HOH . 
F 6 HOH A 22 897 27 HOH HOH . 
F 6 HOH A 23 898 28 HOH HOH . 
F 6 HOH A 24 899 29 HOH HOH . 
F 6 HOH A 25 900 30 HOH HOH . 
F 6 HOH A 26 901 31 HOH HOH . 
F 6 HOH A 27 902 32 HOH HOH . 
F 6 HOH A 28 903 33 HOH HOH . 
F 6 HOH A 29 904 34 HOH HOH . 
F 6 HOH A 30 905 35 HOH HOH . 
F 6 HOH A 31 906 37 HOH HOH . 
F 6 HOH A 32 907 38 HOH HOH . 
F 6 HOH A 33 908 39 HOH HOH . 
F 6 HOH A 34 909 40 HOH HOH . 
F 6 HOH A 35 910 41 HOH HOH . 
F 6 HOH A 36 911 42 HOH HOH . 
F 6 HOH A 37 912 43 HOH HOH . 
F 6 HOH A 38 913 44 HOH HOH . 
F 6 HOH A 39 914 45 HOH HOH . 
F 6 HOH A 40 915 46 HOH HOH . 
F 6 HOH A 41 916 48 HOH HOH . 
F 6 HOH A 42 917 49 HOH HOH . 
F 6 HOH A 43 918 50 HOH HOH . 
F 6 HOH A 44 919 52 HOH HOH . 
F 6 HOH A 45 920 53 HOH HOH . 
F 6 HOH A 46 921 54 HOH HOH . 
F 6 HOH A 47 922 55 HOH HOH . 
F 6 HOH A 48 923 56 HOH HOH . 
F 6 HOH A 49 924 58 HOH HOH . 
F 6 HOH A 50 925 59 HOH HOH . 
F 6 HOH A 51 926 60 HOH HOH . 
F 6 HOH A 52 927 61 HOH HOH . 
F 6 HOH A 53 928 62 HOH HOH . 
F 6 HOH A 54 929 63 HOH HOH . 
F 6 HOH A 55 930 64 HOH HOH . 
F 6 HOH A 56 931 65 HOH HOH . 
F 6 HOH A 57 932 67 HOH HOH . 
F 6 HOH A 58 933 68 HOH HOH . 
F 6 HOH A 59 934 69 HOH HOH . 
F 6 HOH A 60 935 71 HOH HOH . 
F 6 HOH A 61 936 72 HOH HOH . 
F 6 HOH A 62 937 73 HOH HOH . 
F 6 HOH A 63 938 75 HOH HOH . 
F 6 HOH A 64 939 76 HOH HOH . 
F 6 HOH A 65 940 77 HOH HOH . 
F 6 HOH A 66 941 78 HOH HOH . 
F 6 HOH A 67 942 79 HOH HOH . 
F 6 HOH A 68 943 80 HOH HOH . 
F 6 HOH A 69 944 81 HOH HOH . 
F 6 HOH A 70 945 83 HOH HOH . 
F 6 HOH A 71 946 84 HOH HOH . 
F 6 HOH A 72 947 85 HOH HOH . 
F 6 HOH A 73 948 86 HOH HOH . 
F 6 HOH A 74 949 87 HOH HOH . 
F 6 HOH A 75 950 90 HOH HOH . 
F 6 HOH A 76 951 91 HOH HOH . 
F 6 HOH A 77 952 92 HOH HOH . 
F 6 HOH A 78 953 93 HOH HOH . 
F 6 HOH A 79 954 94 HOH HOH . 
F 6 HOH A 80 955 95 HOH HOH . 
F 6 HOH A 81 956 96 HOH HOH . 
F 6 HOH A 82 957 97 HOH HOH . 
F 6 HOH A 83 958 98 HOH HOH . 
F 6 HOH A 84 959 99 HOH HOH . 
F 6 HOH A 85 960 101 HOH HOH . 
F 6 HOH A 86 961 104 HOH HOH . 
F 6 HOH A 87 962 106 HOH HOH . 
F 6 HOH A 88 963 109 HOH HOH . 
F 6 HOH A 89 964 110 HOH HOH . 
F 6 HOH A 90 965 111 HOH HOH . 
F 6 HOH A 91 966 112 HOH HOH . 
F 6 HOH A 92 967 113 HOH HOH . 
F 6 HOH A 93 968 114 HOH HOH . 
G 6 HOH B 1 3 3 HOH HOH . 
G 6 HOH B 2 10 10 HOH HOH . 
G 6 HOH B 3 14 14 HOH HOH . 
G 6 HOH B 4 15 15 HOH HOH . 
G 6 HOH B 5 26 26 HOH HOH . 
G 6 HOH B 6 36 36 HOH HOH . 
G 6 HOH B 7 47 47 HOH HOH . 
G 6 HOH B 8 51 51 HOH HOH . 
G 6 HOH B 9 57 57 HOH HOH . 
G 6 HOH B 10 66 66 HOH HOH . 
G 6 HOH B 11 70 70 HOH HOH . 
G 6 HOH B 12 74 74 HOH HOH . 
G 6 HOH B 13 82 82 HOH HOH . 
G 6 HOH B 14 88 88 HOH HOH . 
G 6 HOH B 15 89 89 HOH HOH . 
G 6 HOH B 16 100 100 HOH HOH . 
G 6 HOH B 17 102 102 HOH HOH . 
G 6 HOH B 18 103 103 HOH HOH . 
G 6 HOH B 19 105 105 HOH HOH . 
G 6 HOH B 20 107 107 HOH HOH . 
G 6 HOH B 21 108 108 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 . . . E 5 11.218 8.395 15.818 1 23.11 ? PB GDP 875 A 1 
HETATM 2 O O1B GDP . . . E 5 12.566 8.511 15.289 1 18.31 ? O1B GDP 875 A 1 
HETATM 3 O O2B GDP . . . E 5 10.344 7.552 15.007 1 22.14 ? O2B GDP 875 A 1 
HETATM 4 O O3B GDP . . . E 5 11.161 7.902 17.316 1 26.42 ? O3B GDP 875 A 1 
HETATM 5 O O3A GDP . . . E 5 10.501 9.778 15.953 1 23.14 ? O3A GDP 875 A 1 
HETATM 6 P PA GDP . . . E 5 9.177 10.419 15.41 1 27.73 ? PA GDP 875 A 1 
HETATM 7 O O1A GDP . . . E 5 9.142 10.565 13.941 1 25.32 ? O1A GDP 875 A 1 
HETATM 8 O O2A GDP . . . E 5 8.009 9.761 16.198 1 29.44 ? O2A GDP 875 A 1 
HETATM 9 O O5' GDP . . . E 5 9.414 11.886 15.913 1 25.96 ? O5' GDP 875 A 1 
HETATM 10 C C5' GDP . . . E 5 9.341 12.365 17.273 1 23.78 ? C5' GDP 875 A 1 
HETATM 11 C C4' GDP . . . E 5 8.634 13.698 17.374 1 19.28 ? C4' GDP 875 A 1 
HETATM 12 O O4' GDP . . . E 5 9.413 14.682 16.58 1 26.55 ? O4' GDP 875 A 1 
HETATM 13 C C3' GDP . . . E 5 7.289 13.725 16.735 1 25.55 ? C3' GDP 875 A 1 
HETATM 14 O O3' GDP . . . E 5 6.273 14.436 17.477 1 28.33 ? O3' GDP 875 A 1 
HETATM 15 C C2' GDP . . . E 5 7.55 14.371 15.355 1 24.28 ? C2' GDP 875 A 1 
HETATM 16 O O2' GDP . . . E 5 6.496 15.118 14.863 1 25.68 ? O2' GDP 875 A 1 
HETATM 17 C C1' GDP . . . E 5 8.54 15.414 15.685 1 24.1 ? C1' GDP 875 A 1 
HETATM 18 N N9 GDP . . . E 5 9.401 15.66 14.535 1 26.91 ? N9 GDP 875 A 1 
HETATM 19 C C8 GDP . . . E 5 10.035 14.737 13.738 1 27.16 ? C8 GDP 875 A 1 
HETATM 20 N N7 GDP . . . E 5 10.855 15.341 12.811 1 26.64 ? N7 GDP 875 A 1 
HETATM 21 C C5 GDP . . . E 5 10.712 16.697 13.033 1 26.89 ? C5 GDP 875 A 1 
HETATM 22 C C6 GDP . . . E 5 11.237 17.958 12.422 1 25.69 ? C6 GDP 875 A 1 
HETATM 23 O O6 GDP . . . E 5 12.095 17.915 11.503 1 26.49 ? O6 GDP 875 A 1 
HETATM 24 N N1 GDP . . . E 5 10.847 19.134 12.985 1 24.68 ? N1 GDP 875 A 1 
HETATM 25 C C2 GDP . . . E 5 9.986 19.237 14.036 1 22.64 ? C2 GDP 875 A 1 
HETATM 26 N N2 GDP . . . E 5 9.599 20.458 14.437 1 25.9 ? N2 GDP 875 A 1 
HETATM 27 N N3 GDP . . . E 5 9.416 18.174 14.626 1 22.14 ? N3 GDP 875 A 1 
HETATM 28 C C4 GDP . . . E 5 9.753 16.9 14.167 1 27.04 ? C4 GDP 875 A 1 
#
_model_server_stats.io_time_ms              54 
_model_server_stats.parse_time_ms           23 
_model_server_stats.create_model_time_ms    24 
_model_server_stats.query_time_ms           326 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           28 
#