data_3T1O
#
_model_server_result.job_id            yLGQRuv5GABDXPp9-FCdhg 
_model_server_result.datetime_utc      '2024-11-22 23:18:58' 
_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          3t1o 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"I","auth_seq_id":274}' 
#
_entry.id    3T1O 
#
_exptl.entry_id    3T1O 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              443.201 
_entity.id                          2 
_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         108.37 
_cell.angle_beta          100.1 
_cell.angle_gamma         92.92 
_cell.entry_id            3T1O 
_cell.length_a            45.3 
_cell.length_b            47.85 
_cell.length_c            53.08 
_cell.Z_PDB               2 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3T1O 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 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 monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 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,C,D,E,F,G,H,L 1 1 
B,I,J,K,M 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
? 2 C N N 
? 2 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 A O GLU 45 A GLU 43 1_555 H MG MG . A MG 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.798 ? 
metalc ? metalc2 A OD1 ASP 60 A ASP 58 1_555 H MG MG . A MG 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.596 ? 
metalc ? metalc3 A O VAL 81 A VAL 79 1_555 E MG MG . A MG 197 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.55 ? 
metalc ? metalc4 A O GLY 83 A GLY 81 1_555 E MG MG . A MG 197 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.714 ? 
metalc ? metalc5 A O ASP 106 A ASP 104 1_555 F MG MG . A MG 198 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.629 ? 
metalc ? metalc6 A O ALA 108 A ALA 106 1_555 F MG MG . A MG 198 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.818 ? 
metalc ? metalc7 A O ARG 123 A ARG 121 1_555 G MG MG . A MG 199 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.763 ? 
metalc ? metalc8 A O LEU 131 A LEU 129 1_555 G MG MG . A MG 199 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.592 ? 
metalc ? metalc9 E MG MG . A MG 197 1_555 L O HOH . A HOH 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.695 ? 
metalc ? metalc10 B O VAL 81 B VAL 79 1_555 J MG MG . B MG 197 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.642 ? 
metalc ? metalc11 B O GLY 83 B GLY 81 1_555 J MG MG . B MG 197 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.806 ? 
#
_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 70 n n 
PB O2B GDP sing 71 n n 
PB O3B GDP sing 72 n n 
PB O3A GDP sing 73 n n 
O2B HOB2 GDP sing 74 n n 
O3B HOB3 GDP sing 75 n n 
O3A PA GDP sing 76 n n 
PA O1A GDP doub 77 n n 
PA O2A GDP sing 78 n n 
PA O5' GDP sing 79 n n 
O2A HOA2 GDP sing 80 n n 
O5' C5' GDP sing 81 n n 
C5' C4' GDP sing 82 n n 
C5' H5' GDP sing 83 n n 
C5' "H5''" GDP sing 84 n n 
C4' O4' GDP sing 85 n n 
C4' C3' GDP sing 86 n n 
C4' H4' GDP sing 87 n n 
O4' C1' GDP sing 88 n n 
C3' O3' GDP sing 89 n n 
C3' C2' GDP sing 90 n n 
C3' H3' GDP sing 91 n n 
O3' HO3' GDP sing 92 n n 
C2' O2' GDP sing 93 n n 
C2' C1' GDP sing 94 n n 
C2' H2' GDP sing 95 n n 
O2' HO2' GDP sing 96 n n 
C1' N9 GDP sing 97 n n 
C1' H1' GDP sing 98 n n 
N9 C8 GDP sing 99 n y 
N9 C4 GDP sing 100 n y 
C8 N7 GDP doub 101 n y 
C8 H8 GDP sing 102 n n 
N7 C5 GDP sing 103 n y 
C5 C6 GDP sing 104 n n 
C5 C4 GDP doub 105 n y 
C6 O6 GDP doub 106 n n 
C6 N1 GDP sing 107 n n 
N1 C2 GDP sing 108 n n 
N1 HN1 GDP sing 109 n n 
C2 N2 GDP sing 110 n n 
C2 N3 GDP doub 111 n n 
N2 HN21 GDP sing 112 n n 
N2 HN22 GDP sing 113 n n 
N3 C4 GDP sing 114 n n 
#
_atom_sites.entry_id                     3T1O 
_atom_sites.fract_transf_matrix[1][1]    0.022075 
_atom_sites.fract_transf_matrix[1][2]    0.001126 
_atom_sites.fract_transf_matrix[1][3]    0.004558 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.020926 
_atom_sites.fract_transf_matrix[2][3]    0.007306 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.020269 
_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 2 GDP A 1 274 274 GDP GDP . 
D 3 MPD A 1 5276 5276 MPD MPD . 
E 4 MG A 1 197 197 MG MG . 
F 4 MG A 1 198 198 MG MG . 
G 4 MG A 1 199 199 MG MG . 
H 4 MG A 1 200 200 MG MG . 
I 2 GDP B 1 274 274 GDP GDP . 
J 4 MG B 1 197 197 MG MG . 
K 4 MG B 1 198 198 MG MG . 
L 5 HOH A 1 201 201 HOH HOH . 
L 5 HOH A 2 202 202 HOH HOH . 
L 5 HOH A 3 203 203 HOH HOH . 
L 5 HOH A 4 204 204 HOH HOH . 
L 5 HOH A 5 205 205 HOH HOH . 
L 5 HOH A 6 206 206 HOH HOH . 
L 5 HOH A 7 207 207 HOH HOH . 
L 5 HOH A 8 208 208 HOH HOH . 
L 5 HOH A 9 209 209 HOH HOH . 
L 5 HOH A 10 210 210 HOH HOH . 
L 5 HOH A 11 211 211 HOH HOH . 
L 5 HOH A 12 212 212 HOH HOH . 
L 5 HOH A 13 213 213 HOH HOH . 
L 5 HOH A 14 214 214 HOH HOH . 
L 5 HOH A 15 215 215 HOH HOH . 
L 5 HOH A 16 216 216 HOH HOH . 
L 5 HOH A 17 218 218 HOH HOH . 
L 5 HOH A 18 219 219 HOH HOH . 
L 5 HOH A 19 221 221 HOH HOH . 
L 5 HOH A 20 222 222 HOH HOH . 
L 5 HOH A 21 223 223 HOH HOH . 
L 5 HOH A 22 224 224 HOH HOH . 
L 5 HOH A 23 225 225 HOH HOH . 
L 5 HOH A 24 226 226 HOH HOH . 
L 5 HOH A 25 227 227 HOH HOH . 
L 5 HOH A 26 228 228 HOH HOH . 
L 5 HOH A 27 229 229 HOH HOH . 
L 5 HOH A 28 230 230 HOH HOH . 
L 5 HOH A 29 231 231 HOH HOH . 
L 5 HOH A 30 232 232 HOH HOH . 
L 5 HOH A 31 233 233 HOH HOH . 
L 5 HOH A 32 234 234 HOH HOH . 
L 5 HOH A 33 235 235 HOH HOH . 
L 5 HOH A 34 236 236 HOH HOH . 
L 5 HOH A 35 237 237 HOH HOH . 
L 5 HOH A 36 238 238 HOH HOH . 
L 5 HOH A 37 239 239 HOH HOH . 
L 5 HOH A 38 240 240 HOH HOH . 
L 5 HOH A 39 241 241 HOH HOH . 
L 5 HOH A 40 242 242 HOH HOH . 
L 5 HOH A 41 243 243 HOH HOH . 
L 5 HOH A 42 244 244 HOH HOH . 
L 5 HOH A 43 245 245 HOH HOH . 
L 5 HOH A 44 247 247 HOH HOH . 
L 5 HOH A 45 250 250 HOH HOH . 
L 5 HOH A 46 251 251 HOH HOH . 
M 5 HOH B 1 199 199 HOH HOH . 
M 5 HOH B 2 200 200 HOH HOH . 
M 5 HOH B 3 201 201 HOH HOH . 
M 5 HOH B 4 202 202 HOH HOH . 
M 5 HOH B 5 203 203 HOH HOH . 
M 5 HOH B 6 204 204 HOH HOH . 
M 5 HOH B 7 205 205 HOH HOH . 
M 5 HOH B 8 206 206 HOH HOH . 
M 5 HOH B 9 207 207 HOH HOH . 
M 5 HOH B 10 208 208 HOH HOH . 
M 5 HOH B 11 209 209 HOH HOH . 
M 5 HOH B 12 210 210 HOH HOH . 
M 5 HOH B 13 211 211 HOH HOH . 
M 5 HOH B 14 212 212 HOH HOH . 
M 5 HOH B 15 213 213 HOH HOH . 
M 5 HOH B 16 214 214 HOH HOH . 
M 5 HOH B 17 215 215 HOH HOH . 
M 5 HOH B 18 216 216 HOH HOH . 
M 5 HOH B 19 217 217 HOH HOH . 
M 5 HOH B 20 218 218 HOH HOH . 
M 5 HOH B 21 219 219 HOH HOH . 
M 5 HOH B 22 220 220 HOH HOH . 
M 5 HOH B 23 221 221 HOH HOH . 
M 5 HOH B 24 222 222 HOH HOH . 
M 5 HOH B 25 223 223 HOH HOH . 
M 5 HOH B 26 224 224 HOH HOH . 
M 5 HOH B 27 225 225 HOH HOH . 
M 5 HOH B 28 226 226 HOH HOH . 
M 5 HOH B 29 227 227 HOH HOH . 
M 5 HOH B 30 228 228 HOH HOH . 
M 5 HOH B 31 229 229 HOH HOH . 
M 5 HOH B 32 230 230 HOH HOH . 
M 5 HOH B 33 231 231 HOH HOH . 
M 5 HOH B 34 232 232 HOH HOH . 
M 5 HOH B 35 233 233 HOH HOH . 
M 5 HOH B 36 234 234 HOH HOH . 
M 5 HOH B 37 235 235 HOH HOH . 
M 5 HOH B 38 236 236 HOH HOH . 
M 5 HOH B 39 237 237 HOH HOH . 
M 5 HOH B 40 238 238 HOH HOH . 
M 5 HOH B 41 239 239 HOH HOH . 
M 5 HOH B 42 240 240 HOH HOH . 
M 5 HOH B 43 241 241 HOH HOH . 
M 5 HOH B 44 242 242 HOH HOH . 
M 5 HOH B 45 243 243 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 . . . I 2 -7.6 -16.768 -14.53 1 16.16 ? PB GDP 274 B 1 
HETATM 2 O O1B GDP . . . I 2 -6.468 -16.147 -13.824 1 12.96 ? O1B GDP 274 B 1 
HETATM 3 O O2B GDP . . . I 2 -7.186 -17.478 -15.718 1 13.94 ? O2B GDP 274 B 1 
HETATM 4 O O3B GDP . . . I 2 -8.825 -16.008 -14.806 1 16.1 ? O3B GDP 274 B 1 
HETATM 5 O O3A GDP . . . I 2 -8.076 -17.961 -13.454 1 14.36 ? O3A GDP 274 B 1 
HETATM 6 P PA GDP . . . I 2 -9.496 -18.063 -12.777 1 16.3 ? PA GDP 274 B 1 
HETATM 7 O O1A GDP . . . I 2 -10.437 -18.46 -13.829 1 18.08 ? O1A GDP 274 B 1 
HETATM 8 O O2A GDP . . . I 2 -9.95 -16.928 -11.93 1 16.15 ? O2A GDP 274 B 1 
HETATM 9 O O5' GDP . . . I 2 -9.221 -19.315 -11.796 1 18.21 ? O5' GDP 274 B 1 
HETATM 10 C C5' GDP . . . I 2 -8.572 -20.451 -12.278 1 17.55 ? C5' GDP 274 B 1 
HETATM 11 C C4' GDP . . . I 2 -9.02 -21.593 -11.313 1 19.45 ? C4' GDP 274 B 1 
HETATM 12 O O4' GDP . . . I 2 -8.417 -21.335 -10.049 1 21.16 ? O4' GDP 274 B 1 
HETATM 13 C C3' GDP . . . I 2 -10.521 -21.698 -11.027 1 23.89 ? C3' GDP 274 B 1 
HETATM 14 O O3' GDP . . . I 2 -10.719 -23.095 -10.7 1 30 ? O3' GDP 274 B 1 
HETATM 15 C C2' GDP . . . I 2 -10.709 -20.922 -9.74 1 25.72 ? C2' GDP 274 B 1 
HETATM 16 O O2' GDP . . . I 2 -11.833 -21.34 -8.92 1 25.11 ? O2' GDP 274 B 1 
HETATM 17 C C1' GDP . . . I 2 -9.449 -21.298 -9.029 1 22.23 ? C1' GDP 274 B 1 
HETATM 18 N N9 GDP . . . I 2 -9.091 -20.308 -7.971 1 23.7 ? N9 GDP 274 B 1 
HETATM 19 C C8 GDP . . . I 2 -9.051 -18.928 -8.109 1 22.73 ? C8 GDP 274 B 1 
HETATM 20 N N7 GDP . . . I 2 -8.638 -18.36 -6.963 1 20.5 ? N7 GDP 274 B 1 
HETATM 21 C C5 GDP . . . I 2 -8.435 -19.396 -6.094 1 21.25 ? C5 GDP 274 B 1 
HETATM 22 C C6 GDP . . . I 2 -7.995 -19.493 -4.699 1 24.44 ? C6 GDP 274 B 1 
HETATM 23 O O6 GDP . . . I 2 -7.733 -18.449 -4.045 1 23 ? O6 GDP 274 B 1 
HETATM 24 N N1 GDP . . . I 2 -7.9 -20.728 -4.139 1 21.44 ? N1 GDP 274 B 1 
HETATM 25 C C2 GDP . . . I 2 -8.17 -21.873 -4.828 1 25.09 ? C2 GDP 274 B 1 
HETATM 26 N N2 GDP . . . I 2 -8.031 -23.068 -4.141 1 23.29 ? N2 GDP 274 B 1 
HETATM 27 N N3 GDP . . . I 2 -8.604 -21.878 -6.126 1 21.33 ? N3 GDP 274 B 1 
HETATM 28 C C4 GDP . . . I 2 -8.703 -20.666 -6.776 1 21.04 ? C4 GDP 274 B 1 
#
_model_server_stats.io_time_ms              62 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           298 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           28 
#