data_5M70
#
_model_server_result.job_id            LpvJTY3W1xZOvnk03kISLg 
_model_server_result.datetime_utc      '2024-10-11 06:22:28' 
_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          5m70 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":202}' 
#
_entry.id    5M70 
#
_exptl.entry_id    5M70 
_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    2 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          96.07 
_cell.angle_gamma         90 
_cell.entry_id            5M70 
_cell.length_a            72.554 
_cell.length_b            66.063 
_cell.length_c            76.759 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5M70 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,E,F,G,K,L 1 1 
C,D,H,I,J,M,N 2 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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 4 F N N 
? 4 I N 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 B OG1 THR 18 B THR 19 1_555 E MG MG . B MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.17 ? 
metalc ? metalc2 B OG1 THR 36 B THR 37 1_555 E MG MG . B MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? 
metalc ? metalc3 E MG MG . B MG 201 1_555 F O1B GDP . B GDP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.169 ? 
metalc ? metalc4 E MG MG . B MG 201 1_555 L O HOH . B HOH 309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? 
metalc ? metalc5 E MG MG . B MG 201 1_555 L O HOH . B HOH 317 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.166 ? 
metalc ? metalc6 D OG1 THR 18 G THR 19 1_555 H MG MG . G MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.166 ? 
metalc ? metalc7 D OG1 THR 36 G THR 37 1_555 H MG MG . G MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? 
metalc ? metalc8 H MG MG . G MG 201 1_555 I O2B GDP . G GDP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.176 ? 
metalc ? metalc9 H MG MG . G MG 201 1_555 N O HOH . G HOH 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.168 ? 
metalc ? metalc10 H MG MG . G MG 201 1_555 N O HOH . G HOH 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.165 ? 
#
_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                     5M70 
_atom_sites.fract_transf_matrix[1][1]    0.013783 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.001465 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.015137 
_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]    0.013101 
_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
E 3 MG B 1 201 681 MG MG . 
F 4 GDP B 1 202 680 GDP GDP . 
G 5 ALF B 1 203 1 ALF ALF . 
H 3 MG G 1 201 681 MG MG . 
I 4 GDP G 1 202 680 GDP GDP . 
J 5 ALF G 1 203 1 ALF ALF . 
K 6 HOH A 1 301 10 HOH HOH . 
K 6 HOH A 2 302 57 HOH HOH . 
K 6 HOH A 3 303 151 HOH HOH . 
K 6 HOH A 4 304 61 HOH HOH . 
K 6 HOH A 5 305 49 HOH HOH . 
K 6 HOH A 6 306 47 HOH HOH . 
K 6 HOH A 7 307 71 HOH HOH . 
K 6 HOH A 8 308 88 HOH HOH . 
K 6 HOH A 9 309 60 HOH HOH . 
K 6 HOH A 10 310 55 HOH HOH . 
K 6 HOH A 11 311 13 HOH HOH . 
K 6 HOH A 12 312 7 HOH HOH . 
K 6 HOH A 13 313 38 HOH HOH . 
K 6 HOH A 14 314 5 HOH HOH . 
K 6 HOH A 15 315 26 HOH HOH . 
K 6 HOH A 16 316 14 HOH HOH . 
K 6 HOH A 17 317 37 HOH HOH . 
K 6 HOH A 18 318 117 HOH HOH . 
K 6 HOH A 19 319 101 HOH HOH . 
K 6 HOH A 20 320 28 HOH HOH . 
K 6 HOH A 21 321 17 HOH HOH . 
K 6 HOH A 22 322 82 HOH HOH . 
K 6 HOH A 23 323 150 HOH HOH . 
K 6 HOH A 24 324 109 HOH HOH . 
K 6 HOH A 25 325 154 HOH HOH . 
K 6 HOH A 26 326 97 HOH HOH . 
K 6 HOH A 27 327 156 HOH HOH . 
K 6 HOH A 28 328 110 HOH HOH . 
L 6 HOH B 1 301 140 HOH HOH . 
L 6 HOH B 2 302 45 HOH HOH . 
L 6 HOH B 3 303 84 HOH HOH . 
L 6 HOH B 4 304 51 HOH HOH . 
L 6 HOH B 5 305 134 HOH HOH . 
L 6 HOH B 6 306 86 HOH HOH . 
L 6 HOH B 7 307 11 HOH HOH . 
L 6 HOH B 8 308 27 HOH HOH . 
L 6 HOH B 9 309 107 HOH HOH . 
L 6 HOH B 10 310 75 HOH HOH . 
L 6 HOH B 11 311 63 HOH HOH . 
L 6 HOH B 12 312 58 HOH HOH . 
L 6 HOH B 13 313 62 HOH HOH . 
L 6 HOH B 14 314 146 HOH HOH . 
L 6 HOH B 15 315 65 HOH HOH . 
L 6 HOH B 16 316 16 HOH HOH . 
L 6 HOH B 17 317 1 HOH HOH . 
L 6 HOH B 18 318 74 HOH HOH . 
L 6 HOH B 19 319 8 HOH HOH . 
L 6 HOH B 20 320 121 HOH HOH . 
L 6 HOH B 21 321 59 HOH HOH . 
L 6 HOH B 22 322 159 HOH HOH . 
L 6 HOH B 23 323 54 HOH HOH . 
L 6 HOH B 24 324 89 HOH HOH . 
L 6 HOH B 25 325 133 HOH HOH . 
L 6 HOH B 26 326 3 HOH HOH . 
L 6 HOH B 27 327 145 HOH HOH . 
L 6 HOH B 28 328 124 HOH HOH . 
L 6 HOH B 29 329 72 HOH HOH . 
L 6 HOH B 30 330 102 HOH HOH . 
L 6 HOH B 31 331 111 HOH HOH . 
L 6 HOH B 32 332 160 HOH HOH . 
M 6 HOH F 1 301 41 HOH HOH . 
M 6 HOH F 2 302 23 HOH HOH . 
M 6 HOH F 3 303 19 HOH HOH . 
M 6 HOH F 4 304 36 HOH HOH . 
M 6 HOH F 5 305 85 HOH HOH . 
M 6 HOH F 6 306 148 HOH HOH . 
M 6 HOH F 7 307 4 HOH HOH . 
M 6 HOH F 8 308 30 HOH HOH . 
M 6 HOH F 9 309 127 HOH HOH . 
M 6 HOH F 10 310 50 HOH HOH . 
M 6 HOH F 11 311 144 HOH HOH . 
M 6 HOH F 12 312 80 HOH HOH . 
M 6 HOH F 13 313 40 HOH HOH . 
M 6 HOH F 14 314 22 HOH HOH . 
M 6 HOH F 15 315 6 HOH HOH . 
M 6 HOH F 16 316 79 HOH HOH . 
M 6 HOH F 17 317 87 HOH HOH . 
M 6 HOH F 18 318 155 HOH HOH . 
M 6 HOH F 19 319 52 HOH HOH . 
M 6 HOH F 20 320 56 HOH HOH . 
M 6 HOH F 21 321 138 HOH HOH . 
M 6 HOH F 22 322 93 HOH HOH . 
M 6 HOH F 23 323 48 HOH HOH . 
M 6 HOH F 24 324 70 HOH HOH . 
N 6 HOH G 1 301 34 HOH HOH . 
N 6 HOH G 2 302 46 HOH HOH . 
N 6 HOH G 3 303 83 HOH HOH . 
N 6 HOH G 4 304 131 HOH HOH . 
N 6 HOH G 5 305 2 HOH HOH . 
N 6 HOH G 6 306 108 HOH HOH . 
N 6 HOH G 7 307 66 HOH HOH . 
N 6 HOH G 8 308 18 HOH HOH . 
N 6 HOH G 9 309 12 HOH HOH . 
N 6 HOH G 10 310 53 HOH HOH . 
N 6 HOH G 11 311 31 HOH HOH . 
N 6 HOH G 12 312 92 HOH HOH . 
N 6 HOH G 13 313 33 HOH HOH . 
N 6 HOH G 14 314 149 HOH HOH . 
N 6 HOH G 15 315 76 HOH HOH . 
N 6 HOH G 16 316 68 HOH HOH . 
N 6 HOH G 17 317 32 HOH HOH . 
N 6 HOH G 18 318 158 HOH HOH . 
N 6 HOH G 19 319 143 HOH HOH . 
N 6 HOH G 20 320 91 HOH HOH . 
N 6 HOH G 21 321 69 HOH HOH . 
N 6 HOH G 22 322 9 HOH HOH . 
N 6 HOH G 23 323 98 HOH HOH . 
N 6 HOH G 24 324 64 HOH HOH . 
N 6 HOH G 25 325 136 HOH HOH . 
N 6 HOH G 26 326 161 HOH HOH . 
N 6 HOH G 27 327 43 HOH HOH . 
N 6 HOH G 28 328 29 HOH HOH . 
N 6 HOH G 29 329 78 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 . . . F 4 13.167 -2.279 26.015 1 31.82 ? PB GDP 202 B 1 
HETATM 2 O O1B GDP . . . F 4 13.482 -1.201 25.02 1 30.39 ? O1B GDP 202 B 1 
HETATM 3 O O2B GDP . . . F 4 12.429 -3.436 25.4 1 32.96 ? O2B GDP 202 B 1 
HETATM 4 O O3B GDP . . . F 4 12.542 -1.828 27.316 1 33.1 ? O3B GDP 202 B 1 
HETATM 5 O O3A GDP . . . F 4 14.596 -2.883 26.461 1 32.37 ? O3A GDP 202 B 1 
HETATM 6 P PA GDP . . . F 4 15.961 -2.75 25.613 1 32.04 ? PA GDP 202 B 1 
HETATM 7 O O1A GDP . . . F 4 15.731 -2.966 24.144 1 33.03 ? O1A GDP 202 B 1 
HETATM 8 O O2A GDP . . . F 4 16.615 -1.465 26.042 1 33.67 ? O2A GDP 202 B 1 
HETATM 9 O O5' GDP . . . F 4 16.815 -3.97 26.21 1 33.56 ? O5' GDP 202 B 1 
HETATM 10 C C5' GDP . . . F 4 16.817 -4.181 27.623 1 35.07 ? C5' GDP 202 B 1 
HETATM 11 C C4' GDP . . . F 4 18.025 -4.993 28.044 1 35 ? C4' GDP 202 B 1 
HETATM 12 O O4' GDP . . . F 4 18.041 -6.189 27.272 1 35.52 ? O4' GDP 202 B 1 
HETATM 13 C C3' GDP . . . F 4 19.322 -4.257 27.778 1 35.46 ? C3' GDP 202 B 1 
HETATM 14 O O3' GDP . . . F 4 20.23 -4.478 28.857 1 35.32 ? O3' GDP 202 B 1 
HETATM 15 C C2' GDP . . . F 4 19.826 -4.865 26.492 1 36.71 ? C2' GDP 202 B 1 
HETATM 16 O O2' GDP . . . F 4 21.254 -4.898 26.419 1 39.52 ? O2' GDP 202 B 1 
HETATM 17 C C1' GDP . . . F 4 19.239 -6.267 26.507 1 36.4 ? C1' GDP 202 B 1 
HETATM 18 N N9 GDP . . . F 4 18.93 -6.8 25.158 1 36 ? N9 GDP 202 B 1 
HETATM 19 C C8 GDP . . . F 4 18.156 -6.233 24.213 1 36.62 ? C8 GDP 202 B 1 
HETATM 20 N N7 GDP . . . F 4 18.095 -7.02 23.109 1 36.74 ? N7 GDP 202 B 1 
HETATM 21 C C5 GDP . . . F 4 18.826 -8.119 23.332 1 36.19 ? C5 GDP 202 B 1 
HETATM 22 C C6 GDP . . . F 4 19.184 -9.349 22.579 1 36.35 ? C6 GDP 202 B 1 
HETATM 23 O O6 GDP . . . F 4 18.764 -9.564 21.414 1 34.85 ? O6 GDP 202 B 1 
HETATM 24 N N1 GDP . . . F 4 19.976 -10.236 23.199 1 36.67 ? N1 GDP 202 B 1 
HETATM 25 C C2 GDP . . . F 4 20.449 -10.047 24.456 1 36.84 ? C2 GDP 202 B 1 
HETATM 26 N N2 GDP . . . F 4 21.246 -10.982 25.025 1 37.57 ? N2 GDP 202 B 1 
HETATM 27 N N3 GDP . . . F 4 20.162 -8.945 25.191 1 36.63 ? N3 GDP 202 B 1 
HETATM 28 C C4 GDP . . . F 4 19.373 -7.966 24.692 1 36.61 ? C4 GDP 202 B 1 
#
_model_server_stats.io_time_ms              14 
_model_server_stats.parse_time_ms           22 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           323 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           28 
#