data_4XC8
#
_model_server_result.job_id            vnVERnZV1UmO151q0vh46A 
_model_server_result.datetime_utc      '2024-11-24 13:36:41' 
_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          4xc8 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":1102}' 
#
_entry.id    4XC8 
#
_exptl.entry_id    4XC8 
_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    2 
_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            4XC8 
_cell.length_a            316.51 
_cell.length_b            316.51 
_cell.length_c            342.27 
_cell.Z_PDB               36 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4XC8 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        155 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'H 3 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H,I,J 
_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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 D N N 
? 3 H 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 OG SER 243 A SER 223 1_555 E MG MG . A MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.72 ? 
metalc ? metalc2 A O ILE 268 A ILE 248 1_555 F MG MG . A MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.501 ? 
metalc ? metalc3 A OD1 ASP 269 A ASP 249 1_555 F MG MG . A MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.653 ? 
metalc ? metalc4 A OD1 ASP 282 A ASP 262 1_555 E MG MG . A MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? 
metalc ? metalc5 A OD1 ASP 282 A ASP 262 1_555 F MG MG . A MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.982 ? 
metalc ? metalc6 A OD2 ASP 282 A ASP 262 1_555 F MG MG . A MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.396 ? 
metalc ? metalc7 A OE1 GLU 330 A GLU 310 1_555 F MG MG . A MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.878 ? 
metalc ? metalc8 D O2B GDP . A GDP 1102 1_555 E MG MG . A MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? 
metalc ? metalc9 B OG SER 243 B SER 223 1_555 I MG MG . B MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.511 ? 
metalc ? metalc10 B O ILE 268 B ILE 248 1_555 J MG MG . B MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.909 ? 
metalc ? metalc11 B OD1 ASP 269 B ASP 249 1_555 J MG MG . B MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.872 ? 
metalc ? metalc12 B OD1 ASP 282 B ASP 262 1_555 I MG MG . B MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? 
metalc ? metalc13 B OD1 ASP 282 B ASP 262 1_555 J MG MG . B MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.928 ? 
metalc ? metalc14 B OD2 ASP 282 B ASP 262 1_555 J MG MG . B MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.695 ? 
metalc ? metalc15 B OE1 GLU 330 B GLU 310 1_555 J MG MG . B MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.532 ? 
#
_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 180 n n 
PB O2B GDP sing 181 n n 
PB O3B GDP sing 182 n n 
PB O3A GDP sing 183 n n 
O2B HOB2 GDP sing 184 n n 
O3B HOB3 GDP sing 185 n n 
O3A PA GDP sing 186 n n 
PA O1A GDP doub 187 n n 
PA O2A GDP sing 188 n n 
PA O5' GDP sing 189 n n 
O2A HOA2 GDP sing 190 n n 
O5' C5' GDP sing 191 n n 
C5' C4' GDP sing 192 n n 
C5' H5' GDP sing 193 n n 
C5' "H5''" GDP sing 194 n n 
C4' O4' GDP sing 195 n n 
C4' C3' GDP sing 196 n n 
C4' H4' GDP sing 197 n n 
O4' C1' GDP sing 198 n n 
C3' O3' GDP sing 199 n n 
C3' C2' GDP sing 200 n n 
C3' H3' GDP sing 201 n n 
O3' HO3' GDP sing 202 n n 
C2' O2' GDP sing 203 n n 
C2' C1' GDP sing 204 n n 
C2' H2' GDP sing 205 n n 
O2' HO2' GDP sing 206 n n 
C1' N9 GDP sing 207 n n 
C1' H1' GDP sing 208 n n 
N9 C8 GDP sing 209 n y 
N9 C4 GDP sing 210 n y 
C8 N7 GDP doub 211 n y 
C8 H8 GDP sing 212 n n 
N7 C5 GDP sing 213 n y 
C5 C6 GDP sing 214 n n 
C5 C4 GDP doub 215 n y 
C6 O6 GDP doub 216 n n 
C6 N1 GDP sing 217 n n 
N1 C2 GDP sing 218 n n 
N1 HN1 GDP sing 219 n n 
C2 N2 GDP sing 220 n n 
C2 N3 GDP doub 221 n n 
N2 HN21 GDP sing 222 n n 
N2 HN22 GDP sing 223 n n 
N3 C4 GDP sing 224 n n 
#
_atom_sites.entry_id                     4XC8 
_atom_sites.fract_transf_matrix[1][1]    0.003159 
_atom_sites.fract_transf_matrix[1][2]    0.001824 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.003648 
_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]    0.002922 
_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 BCO A 1 1101 1211 BCO BCO . 
D 3 GDP A 1 1102 1200 GDP GDP . 
E 4 MG A 1 1103 1 MG MG . 
F 4 MG A 1 1104 3 MG MG . 
G 2 BCO B 1 1101 1212 BCO BCO . 
H 3 GDP B 1 1102 1201 GDP GDP . 
I 4 MG B 1 1103 2 MG MG . 
J 4 MG B 1 1104 4 MG MG . 
#
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 . . . H 3 -275.833 -105.334 -47.139 1 72.31 ? PB GDP 1102 B 1 
HETATM 2 O O1B GDP . . . H 3 -276.419 -105.252 -48.55 1 68.44 ? O1B GDP 1102 B 1 
HETATM 3 O O2B GDP . . . H 3 -275.103 -106.693 -46.987 1 73.52 ? O2B GDP 1102 B 1 
HETATM 4 O O3B GDP . . . H 3 -276.92 -105.253 -46.165 1 74.22 ? O3B GDP 1102 B 1 
HETATM 5 O O3A GDP . . . H 3 -274.834 -104.149 -46.907 1 66.56 ? O3A GDP 1102 B 1 
HETATM 6 P PA GDP . . . H 3 -274.597 -103.494 -45.474 1 74.96 ? PA GDP 1102 B 1 
HETATM 7 O O1A GDP . . . H 3 -275.862 -102.838 -44.986 1 74.82 ? O1A GDP 1102 B 1 
HETATM 8 O O2A GDP . . . H 3 -274.224 -104.482 -44.516 1 76.86 ? O2A GDP 1102 B 1 
HETATM 9 O O5' GDP . . . H 3 -273.469 -102.408 -45.589 1 52.65 ? O5' GDP 1102 B 1 
HETATM 10 C C5' GDP . . . H 3 -272.26 -102.761 -45.894 1 52.85 ? C5' GDP 1102 B 1 
HETATM 11 C C4' GDP . . . H 3 -271.283 -101.559 -45.896 1 54.96 ? C4' GDP 1102 B 1 
HETATM 12 O O4' GDP . . . H 3 -271.72 -100.477 -46.813 1 53.8 ? O4' GDP 1102 B 1 
HETATM 13 C C3' GDP . . . H 3 -271.023 -100.897 -44.6 1 60.46 ? C3' GDP 1102 B 1 
HETATM 14 O O3' GDP . . . H 3 -269.689 -100.457 -44.454 1 63.86 ? O3' GDP 1102 B 1 
HETATM 15 C C2' GDP . . . H 3 -271.864 -99.713 -44.648 1 60.66 ? C2' GDP 1102 B 1 
HETATM 16 O O2' GDP . . . H 3 -271.411 -98.673 -43.757 1 59.12 ? O2' GDP 1102 B 1 
HETATM 17 C C1' GDP . . . H 3 -271.729 -99.298 -46.068 1 58.75 ? C1' GDP 1102 B 1 
HETATM 18 N N9 GDP . . . H 3 -272.751 -98.326 -46.575 1 60.51 ? N9 GDP 1102 B 1 
HETATM 19 C C8 GDP . . . H 3 -274.023 -98.377 -46.398 1 60.56 ? C8 GDP 1102 B 1 
HETATM 20 N N7 GDP . . . H 3 -274.591 -97.337 -46.995 1 59.97 ? N7 GDP 1102 B 1 
HETATM 21 C C5 GDP . . . H 3 -273.623 -96.608 -47.567 1 59.12 ? C5 GDP 1102 B 1 
HETATM 22 C C6 GDP . . . H 3 -273.61 -95.391 -48.345 1 56.6 ? C6 GDP 1102 B 1 
HETATM 23 O O6 GDP . . . H 3 -274.781 -94.743 -48.627 1 57.09 ? O6 GDP 1102 B 1 
HETATM 24 N N1 GDP . . . H 3 -272.439 -94.903 -48.788 1 55.19 ? N1 GDP 1102 B 1 
HETATM 25 C C2 GDP . . . H 3 -271.346 -95.513 -48.521 1 53.8 ? C2 GDP 1102 B 1 
HETATM 26 N N2 GDP . . . H 3 -270.073 -94.951 -49.022 1 61.79 ? N2 GDP 1102 B 1 
HETATM 27 N N3 GDP . . . H 3 -271.321 -96.686 -47.78 1 53.43 ? N3 GDP 1102 B 1 
HETATM 28 C C4 GDP . . . H 3 -272.466 -97.213 -47.314 1 58.17 ? C4 GDP 1102 B 1 
#
_model_server_stats.io_time_ms              114 
_model_server_stats.parse_time_ms           43 
_model_server_stats.create_model_time_ms    81 
_model_server_stats.query_time_ms           991 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           28 
#