data_1Z4P
#
_model_server_result.job_id            5NIO4zbKC_7lrMz660bt9g 
_model_server_result.datetime_utc      '2024-11-04 22:39:42' 
_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          1z4p 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":1}' 
#
_entry.id    1Z4P 
#
_exptl.entry_id    1Z4P 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              347.221 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" 
_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            1Z4P 
_cell.length_a            73.38 
_cell.length_b            73.38 
_cell.length_c            105.437 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1Z4P 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        96 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 43 21 2' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               author_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    1,2 
#
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' 8_665 -y+1,-x+1,-z+1/2 0 -1 0 -1 0 0 0 0 -1 73.38 73.38 52.7185 
#
_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
metalc ? metalc1 C OP3 DGP . X DGP 1 1_555 B MG MG . X MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? 
metalc ? metalc2 A OD1 ASN 10 X ASN 41 1_555 B MG MG . X MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.005 ? 
metalc ? metalc3 A O ASP 12 X ASP 43 1_555 B MG MG . X MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? 
metalc ? metalc4 A OD1 ASP 145 X ASP 176 1_555 B MG MG . X MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.173 ? 
metalc ? metalc5 B MG MG . X MG 1001 1_555 D O HOH . X HOH 1075 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? 
metalc ? metalc6 B MG MG . X MG 1001 1_555 D O HOH . X HOH 1110 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.158 ? 
#
_chem_comp.formula           'C10 H14 N5 O7 P' 
_chem_comp.formula_weight    347.221 
_chem_comp.id                DGP 
_chem_comp.mon_nstd_flag     n 
_chem_comp.name              "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" 
_chem_comp.type              non-polymer 
_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
P OP1 DGP doub 83 n n 
P OP2 DGP sing 84 n n 
P OP3 DGP sing 85 n n 
P O5' DGP sing 86 n n 
OP2 HOP2 DGP sing 87 n n 
OP3 HOP3 DGP sing 88 n n 
O5' C5' DGP sing 89 n n 
C5' C4' DGP sing 90 n n 
C5' H5' DGP sing 91 n n 
C5' "H5''" DGP sing 92 n n 
C4' O4' DGP sing 93 n n 
C4' C3' DGP sing 94 n n 
C4' H4' DGP sing 95 n n 
O4' C1' DGP sing 96 n n 
C3' O3' DGP sing 97 n n 
C3' C2' DGP sing 98 n n 
C3' H3' DGP sing 99 n n 
O3' HO3' DGP sing 100 n n 
C2' C1' DGP sing 101 n n 
C2' H2' DGP sing 102 n n 
C2' "H2''" DGP sing 103 n n 
C1' N9 DGP sing 104 n n 
C1' H1' DGP sing 105 n n 
N9 C8 DGP sing 106 n y 
N9 C4 DGP sing 107 n y 
C8 N7 DGP doub 108 n y 
C8 H8 DGP sing 109 n n 
N7 C5 DGP sing 110 n y 
C5 C6 DGP sing 111 n n 
C5 C4 DGP doub 112 n y 
C6 O6 DGP doub 113 n n 
C6 N1 DGP sing 114 n n 
N1 C2 DGP sing 115 n n 
N1 HN1 DGP sing 116 n n 
C2 N2 DGP sing 117 n n 
C2 N3 DGP doub 118 n n 
N2 HN21 DGP sing 119 n n 
N2 HN22 DGP sing 120 n n 
N3 C4 DGP sing 121 n n 
#
_atom_sites.entry_id                     1Z4P 
_atom_sites.fract_transf_matrix[1][1]    0.013628 
_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]    0.013628 
_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]    0.009484 
_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 X 1 1001 1 MG MG . 
C 3 DGP X 1 1 1 DGP DGP . 
D 4 HOH X 1 1002 3 HOH HOH . 
D 4 HOH X 2 1003 4 HOH HOH . 
D 4 HOH X 3 1004 5 HOH HOH . 
D 4 HOH X 4 1005 7 HOH HOH . 
D 4 HOH X 5 1006 8 HOH HOH . 
D 4 HOH X 6 1007 13 HOH HOH . 
D 4 HOH X 7 1008 14 HOH HOH . 
D 4 HOH X 8 1009 15 HOH HOH . 
D 4 HOH X 9 1010 16 HOH HOH . 
D 4 HOH X 10 1011 17 HOH HOH . 
D 4 HOH X 11 1012 18 HOH HOH . 
D 4 HOH X 12 1013 19 HOH HOH . 
D 4 HOH X 13 1014 20 HOH HOH . 
D 4 HOH X 14 1015 21 HOH HOH . 
D 4 HOH X 15 1016 22 HOH HOH . 
D 4 HOH X 16 1017 23 HOH HOH . 
D 4 HOH X 17 1018 24 HOH HOH . 
D 4 HOH X 18 1019 26 HOH HOH . 
D 4 HOH X 19 1020 27 HOH HOH . 
D 4 HOH X 20 1021 28 HOH HOH . 
D 4 HOH X 21 1022 29 HOH HOH . 
D 4 HOH X 22 1023 30 HOH HOH . 
D 4 HOH X 23 1024 33 HOH HOH . 
D 4 HOH X 24 1025 36 HOH HOH . 
D 4 HOH X 25 1026 37 HOH HOH . 
D 4 HOH X 26 1027 38 HOH HOH . 
D 4 HOH X 27 1028 39 HOH HOH . 
D 4 HOH X 28 1029 40 HOH HOH . 
D 4 HOH X 29 1030 42 HOH HOH . 
D 4 HOH X 30 1031 44 HOH HOH . 
D 4 HOH X 31 1032 45 HOH HOH . 
D 4 HOH X 32 1033 49 HOH HOH . 
D 4 HOH X 33 1034 50 HOH HOH . 
D 4 HOH X 34 1035 54 HOH HOH . 
D 4 HOH X 35 1036 55 HOH HOH . 
D 4 HOH X 36 1037 56 HOH HOH . 
D 4 HOH X 37 1038 58 HOH HOH . 
D 4 HOH X 38 1039 61 HOH HOH . 
D 4 HOH X 39 1040 63 HOH HOH . 
D 4 HOH X 40 1041 64 HOH HOH . 
D 4 HOH X 41 1042 65 HOH HOH . 
D 4 HOH X 42 1043 66 HOH HOH . 
D 4 HOH X 43 1044 67 HOH HOH . 
D 4 HOH X 44 1045 68 HOH HOH . 
D 4 HOH X 45 1046 70 HOH HOH . 
D 4 HOH X 46 1047 71 HOH HOH . 
D 4 HOH X 47 1048 72 HOH HOH . 
D 4 HOH X 48 1049 74 HOH HOH . 
D 4 HOH X 49 1050 78 HOH HOH . 
D 4 HOH X 50 1051 80 HOH HOH . 
D 4 HOH X 51 1052 82 HOH HOH . 
D 4 HOH X 52 1053 83 HOH HOH . 
D 4 HOH X 53 1054 84 HOH HOH . 
D 4 HOH X 54 1055 85 HOH HOH . 
D 4 HOH X 55 1056 86 HOH HOH . 
D 4 HOH X 56 1057 88 HOH HOH . 
D 4 HOH X 57 1058 89 HOH HOH . 
D 4 HOH X 58 1059 90 HOH HOH . 
D 4 HOH X 59 1060 91 HOH HOH . 
D 4 HOH X 60 1061 93 HOH HOH . 
D 4 HOH X 61 1062 94 HOH HOH . 
D 4 HOH X 62 1063 96 HOH HOH . 
D 4 HOH X 63 1064 97 HOH HOH . 
D 4 HOH X 64 1065 98 HOH HOH . 
D 4 HOH X 65 1066 99 HOH HOH . 
D 4 HOH X 66 1067 100 HOH HOH . 
D 4 HOH X 67 1068 101 HOH HOH . 
D 4 HOH X 68 1069 103 HOH HOH . 
D 4 HOH X 69 1070 105 HOH HOH . 
D 4 HOH X 70 1071 106 HOH HOH . 
D 4 HOH X 71 1072 107 HOH HOH . 
D 4 HOH X 72 1073 108 HOH HOH . 
D 4 HOH X 73 1074 109 HOH HOH . 
D 4 HOH X 74 1075 110 HOH HOH . 
D 4 HOH X 75 1076 111 HOH HOH . 
D 4 HOH X 76 1077 112 HOH HOH . 
D 4 HOH X 77 1078 113 HOH HOH . 
D 4 HOH X 78 1079 116 HOH HOH . 
D 4 HOH X 79 1080 117 HOH HOH . 
D 4 HOH X 80 1081 121 HOH HOH . 
D 4 HOH X 81 1082 123 HOH HOH . 
D 4 HOH X 82 1083 124 HOH HOH . 
D 4 HOH X 83 1084 126 HOH HOH . 
D 4 HOH X 84 1085 128 HOH HOH . 
D 4 HOH X 85 1086 129 HOH HOH . 
D 4 HOH X 86 1087 133 HOH HOH . 
D 4 HOH X 87 1088 134 HOH HOH . 
D 4 HOH X 88 1089 135 HOH HOH . 
D 4 HOH X 89 1090 136 HOH HOH . 
D 4 HOH X 90 1091 137 HOH HOH . 
D 4 HOH X 91 1092 138 HOH HOH . 
D 4 HOH X 92 1093 139 HOH HOH . 
D 4 HOH X 93 1094 140 HOH HOH . 
D 4 HOH X 94 1095 142 HOH HOH . 
D 4 HOH X 95 1096 143 HOH HOH . 
D 4 HOH X 96 1097 145 HOH HOH . 
D 4 HOH X 97 1098 146 HOH HOH . 
D 4 HOH X 98 1099 147 HOH HOH . 
D 4 HOH X 99 1100 148 HOH HOH . 
D 4 HOH X 100 1101 157 HOH HOH . 
D 4 HOH X 101 1102 158 HOH HOH . 
D 4 HOH X 102 1103 159 HOH HOH . 
D 4 HOH X 103 1104 160 HOH HOH . 
D 4 HOH X 104 1105 161 HOH HOH . 
D 4 HOH X 105 1106 162 HOH HOH . 
D 4 HOH X 106 1107 163 HOH HOH . 
D 4 HOH X 107 1108 174 HOH HOH . 
D 4 HOH X 108 1109 175 HOH HOH . 
D 4 HOH X 109 1110 176 HOH HOH . 
D 4 HOH X 110 1111 177 HOH HOH . 
D 4 HOH X 111 1112 178 HOH HOH . 
D 4 HOH X 112 1113 179 HOH HOH . 
D 4 HOH X 113 1114 180 HOH HOH . 
D 4 HOH X 114 1115 181 HOH HOH . 
D 4 HOH X 115 1116 182 HOH HOH . 
D 4 HOH X 116 1117 183 HOH HOH . 
D 4 HOH X 117 1118 184 HOH HOH . 
D 4 HOH X 118 1119 185 HOH HOH . 
D 4 HOH X 119 1120 186 HOH HOH . 
D 4 HOH X 120 1121 187 HOH HOH . 
D 4 HOH X 121 1122 188 HOH HOH . 
D 4 HOH X 122 1123 189 HOH HOH . 
D 4 HOH X 123 1124 190 HOH HOH . 
D 4 HOH X 124 1125 191 HOH HOH . 
D 4 HOH X 125 1126 192 HOH HOH . 
D 4 HOH X 126 1127 193 HOH HOH . 
D 4 HOH X 127 1128 194 HOH HOH . 
D 4 HOH X 128 1129 195 HOH HOH . 
D 4 HOH X 129 1130 196 HOH HOH . 
D 4 HOH X 130 1131 197 HOH HOH . 
D 4 HOH X 131 1132 198 HOH HOH . 
D 4 HOH X 132 1133 199 HOH HOH . 
D 4 HOH X 133 1134 200 HOH HOH . 
D 4 HOH X 134 1135 201 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 P DGP . . . C 3 16.654 39.808 28.685 1 21.98 ? P DGP 1 X 1 
HETATM 2 O OP1 DGP . . . C 3 17.769 40.818 29.037 1 19.27 ? OP1 DGP 1 X 1 
HETATM 3 O OP2 DGP . . . C 3 17.154 38.53 28.063 1 16.08 ? OP2 DGP 1 X 1 
HETATM 4 O OP3 DGP . . . C 3 15.843 39.544 30.053 1 19.23 ? OP3 DGP 1 X 1 
HETATM 5 O O5' DGP . . . C 3 15.704 40.696 27.762 1 27.2 ? O5' DGP 1 X 1 
HETATM 6 C C5' DGP . . . C 3 14.631 40.107 27.128 1 25.23 ? C5' DGP 1 X 1 
HETATM 7 C C4' DGP . . . C 3 13.557 41.17 26.957 1 23.73 ? C4' DGP 1 X 1 
HETATM 8 O O4' DGP . . . C 3 12.619 40.585 26.096 1 21.59 ? O4' DGP 1 X 1 
HETATM 9 C C3' DGP . . . C 3 12.833 41.543 28.26 1 23.67 ? C3' DGP 1 X 1 
HETATM 10 O O3' DGP . . . C 3 12.586 42.956 28.271 1 22.49 ? O3' DGP 1 X 1 
HETATM 11 C C2' DGP . . . C 3 11.492 40.88 28.063 1 26.2 ? C2' DGP 1 X 1 
HETATM 12 C C1' DGP . . . C 3 11.334 40.969 26.563 1 24.55 ? C1' DGP 1 X 1 
HETATM 13 N N9 DGP . . . C 3 10.288 39.964 26.045 1 26.58 ? N9 DGP 1 X 1 
HETATM 14 C C8 DGP . . . C 3 9.611 39.031 26.713 1 24.62 ? C8 DGP 1 X 1 
HETATM 15 N N7 DGP . . . C 3 8.753 38.407 25.879 1 27.71 ? N7 DGP 1 X 1 
HETATM 16 C C5 DGP . . . C 3 8.867 38.94 24.651 1 27.18 ? C5 DGP 1 X 1 
HETATM 17 C C6 DGP . . . C 3 8.272 38.709 23.394 1 29.64 ? C6 DGP 1 X 1 
HETATM 18 O O6 DGP . . . C 3 7.397 37.862 23.127 1 28.52 ? O6 DGP 1 X 1 
HETATM 19 N N1 DGP . . . C 3 8.708 39.486 22.328 1 27.96 ? N1 DGP 1 X 1 
HETATM 20 C C2 DGP . . . C 3 9.656 40.466 22.45 1 27.96 ? C2 DGP 1 X 1 
HETATM 21 N N2 DGP . . . C 3 10.018 41.153 21.371 1 32.4 ? N2 DGP 1 X 1 
HETATM 22 N N3 DGP . . . C 3 10.253 40.694 23.684 1 27.43 ? N3 DGP 1 X 1 
HETATM 23 C C4 DGP . . . C 3 9.857 39.928 24.777 1 26.49 ? C4 DGP 1 X 1 
#
_model_server_stats.io_time_ms              51 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           243 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           23 
#