data_1BOF
#
_model_server_result.job_id            DO0lAn2fYzbypuZcEmI79A 
_model_server_result.datetime_utc      '2024-11-15 07:34:09' 
_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          1bof 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":355}' 
#
_entry.id    1BOF 
#
_exptl.entry_id    1BOF 
_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    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            1BOF 
_cell.length_a            121.747 
_cell.length_b            121.747 
_cell.length_c            68.929 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1BOF 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        79 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'I 4' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      4 
_struct_asym.id                             E 
_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 46 A SER 47 1_555 C MG MG . A MG 800 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.223 ? 
metalc ? metalc2 A OG1 THR 180 A THR 181 1_555 C MG MG . A MG 800 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? 
metalc ? metalc3 E O3B GDP . A GDP 355 1_555 C MG MG . A MG 800 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.237 ? 
metalc ? metalc4 C MG MG . A MG 800 1_555 F O HOH . A HOH 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.405 ? 
metalc ? metalc5 C MG MG . A MG 800 1_555 F O HOH . A HOH 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.092 ? 
metalc ? metalc6 C MG MG . A MG 800 1_555 F O HOH . A HOH 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.495 ? 
#
_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                     1BOF 
_atom_sites.fract_transf_matrix[1][1]    0.008214 
_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]    0.008214 
_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]    0.014508 
_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 SO4 A 1 356 356 SO4 SO4 . 
C 3 MG A 1 800 800 MG MG . 
D 2 SO4 A 1 804 804 SO4 SO4 . 
E 4 GDP A 1 355 355 GDP GDP . 
F 5 HOH A 1 401 401 HOH HOH . 
F 5 HOH A 2 402 402 HOH HOH . 
F 5 HOH A 3 403 403 HOH HOH . 
F 5 HOH A 4 404 404 HOH HOH . 
F 5 HOH A 5 405 405 HOH HOH . 
F 5 HOH A 6 406 406 HOH HOH . 
F 5 HOH A 7 407 407 HOH HOH . 
F 5 HOH A 8 408 408 HOH HOH . 
F 5 HOH A 9 409 409 HOH HOH . 
F 5 HOH A 10 410 410 HOH HOH . 
F 5 HOH A 11 411 411 HOH HOH . 
F 5 HOH A 12 412 412 HOH HOH . 
F 5 HOH A 13 413 413 HOH HOH . 
F 5 HOH A 14 414 414 HOH HOH . 
F 5 HOH A 15 415 415 HOH HOH . 
F 5 HOH A 16 416 416 HOH HOH . 
F 5 HOH A 17 417 417 HOH HOH . 
F 5 HOH A 18 418 418 HOH HOH . 
F 5 HOH A 19 419 419 HOH HOH . 
F 5 HOH A 20 420 420 HOH HOH . 
F 5 HOH A 21 421 421 HOH HOH . 
F 5 HOH A 22 422 422 HOH HOH . 
F 5 HOH A 23 423 423 HOH HOH . 
F 5 HOH A 24 424 424 HOH HOH . 
F 5 HOH A 25 425 425 HOH HOH . 
F 5 HOH A 26 426 426 HOH HOH . 
F 5 HOH A 27 427 427 HOH HOH . 
F 5 HOH A 28 428 428 HOH HOH . 
F 5 HOH A 29 429 429 HOH HOH . 
F 5 HOH A 30 431 431 HOH HOH . 
F 5 HOH A 31 432 432 HOH HOH . 
F 5 HOH A 32 433 433 HOH HOH . 
F 5 HOH A 33 434 434 HOH HOH . 
F 5 HOH A 34 435 435 HOH HOH . 
F 5 HOH A 35 436 436 HOH HOH . 
F 5 HOH A 36 437 437 HOH HOH . 
F 5 HOH A 37 438 438 HOH HOH . 
F 5 HOH A 38 439 439 HOH HOH . 
F 5 HOH A 39 440 440 HOH HOH . 
F 5 HOH A 40 441 441 HOH HOH . 
F 5 HOH A 41 442 442 HOH HOH . 
F 5 HOH A 42 443 443 HOH HOH . 
F 5 HOH A 43 600 600 HOH HOH . 
F 5 HOH A 44 601 601 HOH HOH . 
F 5 HOH A 45 603 603 HOH HOH . 
F 5 HOH A 46 629 629 HOH HOH . 
F 5 HOH A 47 801 801 HOH HOH . 
F 5 HOH A 48 802 802 HOH HOH . 
F 5 HOH A 49 803 803 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 . . . E 4 38.443 22.121 36.152 1 23.53 ? PB GDP 355 A 1 
HETATM 2 O O1B GDP . . . E 4 38.83 21.674 37.512 1 22.81 ? O1B GDP 355 A 1 
HETATM 3 O O2B GDP . . . E 4 37.618 21.166 35.391 1 21.29 ? O2B GDP 355 A 1 
HETATM 4 O O3B GDP . . . E 4 37.952 23.481 36.037 1 21.34 ? O3B GDP 355 A 1 
HETATM 5 O O3A GDP . . . E 4 39.845 22.114 35.26 1 23.63 ? O3A GDP 355 A 1 
HETATM 6 P PA GDP . . . E 4 40.865 23.265 34.605 1 22.23 ? PA GDP 355 A 1 
HETATM 7 O O1A GDP . . . E 4 41.374 24.007 35.742 1 24.28 ? O1A GDP 355 A 1 
HETATM 8 O O2A GDP . . . E 4 40.215 24.012 33.525 1 21.83 ? O2A GDP 355 A 1 
HETATM 9 O O5' GDP . . . E 4 42.021 22.414 34.013 1 17.17 ? O5' GDP 355 A 1 
HETATM 10 C C5' GDP . . . E 4 42.961 21.906 34.929 1 17.38 ? C5' GDP 355 A 1 
HETATM 11 C C4' GDP . . . E 4 44.394 21.993 34.414 1 18.69 ? C4' GDP 355 A 1 
HETATM 12 O O4' GDP . . . E 4 44.56 21.149 33.25 1 23.7 ? O4' GDP 355 A 1 
HETATM 13 C C3' GDP . . . E 4 44.856 23.426 34.043 1 19.84 ? C3' GDP 355 A 1 
HETATM 14 O O3' GDP . . . E 4 46.209 23.543 34.418 1 18.89 ? O3' GDP 355 A 1 
HETATM 15 C C2' GDP . . . E 4 44.726 23.378 32.544 1 19.63 ? C2' GDP 355 A 1 
HETATM 16 O O2' GDP . . . E 4 45.601 24.296 31.989 1 17.07 ? O2' GDP 355 A 1 
HETATM 17 C C1' GDP . . . E 4 45.048 21.948 32.132 1 20.15 ? C1' GDP 355 A 1 
HETATM 18 N N9 GDP . . . E 4 44.334 21.527 30.892 1 23.38 ? N9 GDP 355 A 1 
HETATM 19 C C8 GDP . . . E 4 42.971 21.541 30.601 1 25.54 ? C8 GDP 355 A 1 
HETATM 20 N N7 GDP . . . E 4 42.59 21.011 29.457 1 23.34 ? N7 GDP 355 A 1 
HETATM 21 C C5 GDP . . . E 4 43.837 20.565 28.949 1 22 ? C5 GDP 355 A 1 
HETATM 22 C C6 GDP . . . E 4 44.139 19.887 27.709 1 23.28 ? C6 GDP 355 A 1 
HETATM 23 O O6 GDP . . . E 4 43.376 19.503 26.808 1 25.72 ? O6 GDP 355 A 1 
HETATM 24 N N1 GDP . . . E 4 45.514 19.665 27.573 1 22.08 ? N1 GDP 355 A 1 
HETATM 25 C C2 GDP . . . E 4 46.475 20.017 28.492 1 25.36 ? C2 GDP 355 A 1 
HETATM 26 N N2 GDP . . . E 4 47.736 19.731 28.207 1 22.86 ? N2 GDP 355 A 1 
HETATM 27 N N3 GDP . . . E 4 46.188 20.617 29.658 1 26.65 ? N3 GDP 355 A 1 
HETATM 28 C C4 GDP . . . E 4 44.869 20.883 29.817 1 21.9 ? C4 GDP 355 A 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    11 
_model_server_stats.query_time_ms           298 
_model_server_stats.encode_time_ms          16 
_model_server_stats.element_count           28 
#