data_3KUD
#
_model_server_result.job_id            Ba61a-Jtr_ttZrHh88P82w 
_model_server_result.datetime_utc      '2024-12-26 17:54:33' 
_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          3kud 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":170}' 
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_entry.id    3KUD 
#
_exptl.entry_id    3KUD 
_exptl.method      'X-RAY DIFFRACTION' 
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_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            3KUD 
_cell.length_a            91.13 
_cell.length_b            91.13 
_cell.length_c            277.98 
_cell.Z_PDB               18 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3KUD 
_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 
_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                      3 
_struct_asym.id                             C 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_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                     3KUD 
_atom_sites.fract_transf_matrix[1][1]    0.010973 
_atom_sites.fract_transf_matrix[1][2]    0.006335 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.012671 
_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]    0.003597 
_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 3 GDP A 1 170 170 GDP GDP . 
D 4 MG A 1 171 171 MG MG . 
E 5 HOH A 1 500 500 HOH HOH . 
E 5 HOH A 2 501 501 HOH HOH . 
E 5 HOH A 3 503 503 HOH HOH . 
E 5 HOH A 4 506 506 HOH HOH . 
E 5 HOH A 5 507 507 HOH HOH . 
E 5 HOH A 6 509 509 HOH HOH . 
E 5 HOH A 7 510 510 HOH HOH . 
E 5 HOH A 8 511 511 HOH HOH . 
E 5 HOH A 9 512 512 HOH HOH . 
E 5 HOH A 10 515 515 HOH HOH . 
E 5 HOH A 11 516 516 HOH HOH . 
E 5 HOH A 12 517 517 HOH HOH . 
E 5 HOH A 13 518 518 HOH HOH . 
E 5 HOH A 14 519 519 HOH HOH . 
E 5 HOH A 15 522 522 HOH HOH . 
E 5 HOH A 16 525 525 HOH HOH . 
E 5 HOH A 17 533 533 HOH HOH . 
E 5 HOH A 18 537 537 HOH HOH . 
E 5 HOH A 19 539 539 HOH HOH . 
E 5 HOH A 20 541 541 HOH HOH . 
E 5 HOH A 21 542 542 HOH HOH . 
E 5 HOH A 22 544 544 HOH HOH . 
E 5 HOH A 23 545 545 HOH HOH . 
E 5 HOH A 24 546 546 HOH HOH . 
E 5 HOH A 25 547 547 HOH HOH . 
E 5 HOH A 26 548 548 HOH HOH . 
F 5 HOH B 1 502 502 HOH HOH . 
F 5 HOH B 2 504 504 HOH HOH . 
F 5 HOH B 3 505 505 HOH HOH . 
F 5 HOH B 4 513 513 HOH HOH . 
F 5 HOH B 5 514 514 HOH HOH . 
F 5 HOH B 6 521 521 HOH HOH . 
F 5 HOH B 7 524 524 HOH HOH . 
F 5 HOH B 8 526 526 HOH HOH . 
F 5 HOH B 9 528 528 HOH HOH . 
F 5 HOH B 10 529 529 HOH HOH . 
F 5 HOH B 11 531 531 HOH HOH . 
F 5 HOH B 12 534 534 HOH HOH . 
F 5 HOH B 13 535 535 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 -29.105 -24.542 -27.31 1 22.96 ? PB GDP 170 A 1 
HETATM 2 O O1B GDP . . . C 3 -29.831 -23.611 -28.225 1 25.62 ? O1B GDP 170 A 1 
HETATM 3 O O2B GDP . . . C 3 -27.696 -24.023 -26.966 1 19.31 ? O2B GDP 170 A 1 
HETATM 4 O O3B GDP . . . C 3 -30.053 -24.672 -26.113 1 23.72 ? O3B GDP 170 A 1 
HETATM 5 O O3A GDP . . . C 3 -29.011 -26.036 -27.821 1 27.53 ? O3A GDP 170 A 1 
HETATM 6 P PA GDP . . . C 3 -27.705 -26.956 -27.728 1 27.32 ? PA GDP 170 A 1 
HETATM 7 O O1A GDP . . . C 3 -27.545 -27.203 -26.307 1 31.37 ? O1A GDP 170 A 1 
HETATM 8 O O2A GDP . . . C 3 -26.552 -26.292 -28.486 1 29.17 ? O2A GDP 170 A 1 
HETATM 9 O O5' GDP . . . C 3 -28.169 -28.312 -28.455 1 28.36 ? O5' GDP 170 A 1 
HETATM 10 C C5' GDP . . . C 3 -29.52 -28.81 -28.246 1 25.36 ? C5' GDP 170 A 1 
HETATM 11 C C4' GDP . . . C 3 -29.496 -30.304 -28.614 1 25.24 ? C4' GDP 170 A 1 
HETATM 12 O O4' GDP . . . C 3 -29.579 -30.415 -30.052 1 24.75 ? O4' GDP 170 A 1 
HETATM 13 C C3' GDP . . . C 3 -28.161 -30.97 -28.229 1 24.97 ? C3' GDP 170 A 1 
HETATM 14 O O3' GDP . . . C 3 -28.371 -32.363 -28.146 1 26.6 ? O3' GDP 170 A 1 
HETATM 15 C C2' GDP . . . C 3 -27.357 -30.838 -29.491 1 27.05 ? C2' GDP 170 A 1 
HETATM 16 O O2' GDP . . . C 3 -26.485 -31.938 -29.616 1 29.13 ? O2' GDP 170 A 1 
HETATM 17 C C1' GDP . . . C 3 -28.405 -31.044 -30.578 1 24.86 ? C1' GDP 170 A 1 
HETATM 18 N N9 GDP . . . C 3 -27.96 -30.303 -31.772 1 24.46 ? N9 GDP 170 A 1 
HETATM 19 C C8 GDP . . . C 3 -27.479 -29.039 -31.774 1 21.34 ? C8 GDP 170 A 1 
HETATM 20 N N7 GDP . . . C 3 -27.149 -28.661 -33.032 1 18.95 ? N7 GDP 170 A 1 
HETATM 21 C C5 GDP . . . C 3 -27.462 -29.69 -33.864 1 17.36 ? C5 GDP 170 A 1 
HETATM 22 C C6 GDP . . . C 3 -27.364 -29.959 -35.311 1 17.03 ? C6 GDP 170 A 1 
HETATM 23 O O6 GDP . . . C 3 -26.956 -29.115 -36.139 1 21.39 ? O6 GDP 170 A 1 
HETATM 24 N N1 GDP . . . C 3 -27.766 -31.159 -35.745 1 20.55 ? N1 GDP 170 A 1 
HETATM 25 C C2 GDP . . . C 3 -28.24 -32.103 -34.896 1 21.91 ? C2 GDP 170 A 1 
HETATM 26 N N2 GDP . . . C 3 -28.589 -33.284 -35.422 1 21 ? N2 GDP 170 A 1 
HETATM 27 N N3 GDP . . . C 3 -28.366 -31.957 -33.57 1 17.87 ? N3 GDP 170 A 1 
HETATM 28 C C4 GDP . . . C 3 -27.997 -30.774 -33.021 1 21.86 ? C4 GDP 170 A 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           14 
_model_server_stats.create_model_time_ms    15 
_model_server_stats.query_time_ms           320 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           28 
#