data_1Q21
#
_model_server_result.job_id            85zhXUkCLUTSuPt800GY0w 
_model_server_result.datetime_utc      '2024-11-04 20:08:33' 
_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          1q21 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":180}' 
#
_entry.id    1Q21 
#
_exptl.entry_id    1Q21 
_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          90 
_cell.angle_gamma         120 
_cell.entry_id            1Q21 
_cell.length_a            83.2 
_cell.length_b            83.2 
_cell.length_c            105.1 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1Q21 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        179 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 65 2 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' 11_655 -x+y+1,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 83.2 0 52.55 
#
_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 A OG SER 17 A SER 17 1_555 B MG MG . A MG 173 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.376 ? 
metalc ? metalc2 B MG MG . A MG 173 1_555 C O3B GDP . A GDP 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.138 ? 
metalc ? metalc3 B MG MG . A MG 173 1_555 D O HOH . A HOH 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.235 ? 
metalc ? metalc4 B MG MG . A MG 173 1_555 D O HOH . A HOH 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.255 ? 
metalc ? metalc5 B MG MG . A MG 173 1_555 D O HOH . A HOH 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.367 ? 
metalc ? metalc6 B MG MG . A MG 173 1_555 D O HOH . A HOH 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.445 ? 
#
_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                     1Q21 
_atom_sites.fract_transf_matrix[1][1]    0.012019 
_atom_sites.fract_transf_matrix[1][2]    0.006939 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.013879 
_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]    0.009515 
_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 1 173 173 MG MG . 
C 3 GDP A 1 180 180 GDP GDP . 
D 4 HOH A 1 201 201 HOH HOH . 
D 4 HOH A 2 202 202 HOH HOH . 
D 4 HOH A 3 203 203 HOH HOH . 
D 4 HOH A 4 204 204 HOH HOH . 
D 4 HOH A 5 205 205 HOH HOH . 
D 4 HOH A 6 206 206 HOH HOH . 
D 4 HOH A 7 207 207 HOH HOH . 
D 4 HOH A 8 208 208 HOH HOH . 
D 4 HOH A 9 209 209 HOH HOH . 
D 4 HOH A 10 210 210 HOH HOH . 
D 4 HOH A 11 211 211 HOH HOH . 
D 4 HOH A 12 212 212 HOH HOH . 
D 4 HOH A 13 213 213 HOH HOH . 
D 4 HOH A 14 214 214 HOH HOH . 
D 4 HOH A 15 215 215 HOH HOH . 
D 4 HOH A 16 216 216 HOH HOH . 
D 4 HOH A 17 217 217 HOH HOH . 
D 4 HOH A 18 218 218 HOH HOH . 
D 4 HOH A 19 219 219 HOH HOH . 
D 4 HOH A 20 220 220 HOH HOH . 
D 4 HOH A 21 221 221 HOH HOH . 
D 4 HOH A 22 222 222 HOH HOH . 
D 4 HOH A 23 223 223 HOH HOH . 
D 4 HOH A 24 224 224 HOH HOH . 
D 4 HOH A 25 225 225 HOH HOH . 
D 4 HOH A 26 226 226 HOH HOH . 
D 4 HOH A 27 227 227 HOH HOH . 
D 4 HOH A 28 228 228 HOH HOH . 
D 4 HOH A 29 229 229 HOH HOH . 
D 4 HOH A 30 230 230 HOH HOH . 
D 4 HOH A 31 231 231 HOH HOH . 
D 4 HOH A 32 232 232 HOH HOH . 
D 4 HOH A 33 233 233 HOH HOH . 
D 4 HOH A 34 234 234 HOH HOH . 
D 4 HOH A 35 235 235 HOH HOH . 
D 4 HOH A 36 236 236 HOH HOH . 
D 4 HOH A 37 237 237 HOH HOH . 
D 4 HOH A 38 238 238 HOH HOH . 
D 4 HOH A 39 239 239 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 25.775 20.955 13.12 1 25.78 ? PB GDP 180 A 1 
HETATM 2 O O1B GDP . . . C 3 26.489 19.999 14.083 1 21.83 ? O1B GDP 180 A 1 
HETATM 3 O O2B GDP . . . C 3 26.427 22.259 12.984 1 24.74 ? O2B GDP 180 A 1 
HETATM 4 O O3B GDP . . . C 3 24.231 21.182 13.545 1 24.21 ? O3B GDP 180 A 1 
HETATM 5 O O3A GDP . . . C 3 25.677 20.368 11.639 1 23.19 ? O3A GDP 180 A 1 
HETATM 6 P PA GDP . . . C 3 24.373 19.869 10.711 1 30.44 ? PA GDP 180 A 1 
HETATM 7 O O1A GDP . . . C 3 23.832 21.136 10.034 1 31.46 ? O1A GDP 180 A 1 
HETATM 8 O O2A GDP . . . C 3 23.395 18.966 11.507 1 29.52 ? O2A GDP 180 A 1 
HETATM 9 O O5' GDP . . . C 3 25.109 19.087 9.672 1 26.47 ? O5' GDP 180 A 1 
HETATM 10 C C5' GDP . . . C 3 26.305 19.532 9.084 1 25.96 ? C5' GDP 180 A 1 
HETATM 11 C C4' GDP . . . C 3 26.495 18.952 7.764 1 26.82 ? C4' GDP 180 A 1 
HETATM 12 O O4' GDP . . . C 3 26.824 17.511 7.88 1 28.05 ? O4' GDP 180 A 1 
HETATM 13 C C3' GDP . . . C 3 25.286 18.955 6.85 1 26.17 ? C3' GDP 180 A 1 
HETATM 14 O O3' GDP . . . C 3 25.688 18.997 5.508 1 29.2 ? O3' GDP 180 A 1 
HETATM 15 C C2' GDP . . . C 3 24.598 17.673 7.227 1 27.37 ? C2' GDP 180 A 1 
HETATM 16 O O2' GDP . . . C 3 23.755 17.249 6.14 1 28.43 ? O2' GDP 180 A 1 
HETATM 17 C C1' GDP . . . C 3 25.848 16.758 7.212 1 24.88 ? C1' GDP 180 A 1 
HETATM 18 N N9 GDP . . . C 3 25.616 15.551 8.011 1 21.36 ? N9 GDP 180 A 1 
HETATM 19 C C8 GDP . . . C 3 25.144 15.468 9.303 1 18.98 ? C8 GDP 180 A 1 
HETATM 20 N N7 GDP . . . C 3 25.13 14.237 9.767 1 20.21 ? N7 GDP 180 A 1 
HETATM 21 C C5 GDP . . . C 3 25.626 13.462 8.726 1 22.27 ? C5 GDP 180 A 1 
HETATM 22 C C6 GDP . . . C 3 25.822 12.161 8.659 1 21.86 ? C6 GDP 180 A 1 
HETATM 23 O O6 GDP . . . C 3 25.549 11.301 9.548 1 27.39 ? O6 GDP 180 A 1 
HETATM 24 N N1 GDP . . . C 3 26.305 11.728 7.436 1 18.77 ? N1 GDP 180 A 1 
HETATM 25 C C2 GDP . . . C 3 26.689 12.545 6.425 1 22.67 ? C2 GDP 180 A 1 
HETATM 26 N N2 GDP . . . C 3 27.254 11.922 5.328 1 19.29 ? N2 GDP 180 A 1 
HETATM 27 N N3 GDP . . . C 3 26.554 13.899 6.469 1 20.23 ? N3 GDP 180 A 1 
HETATM 28 C C4 GDP . . . C 3 25.944 14.272 7.621 1 21.04 ? C4 GDP 180 A 1 
#
_model_server_stats.io_time_ms              6 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           286 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           28 
#