data_1GDD
#
_model_server_result.job_id            rwDQ91s2cs8utvX7lQ3v6w 
_model_server_result.datetime_utc      '2024-11-15 15:34:09' 
_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          1gdd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":355}' 
#
_entry.id    1GDD 
#
_exptl.entry_id    1GDD 
_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    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            1GDD 
_cell.length_a            121.84 
_cell.length_b            121.84 
_cell.length_c            68.39 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1GDD 
_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 
_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                     1GDD 
_atom_sites.fract_transf_matrix[1][1]    0.008207 
_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]    0.008207 
_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]    0.014622 
_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 GDP A 1 355 355 GDP GDP . 
D 4 HOH A 1 401 401 HOH HOH . 
D 4 HOH A 2 402 402 HOH HOH . 
D 4 HOH A 3 403 403 HOH HOH . 
D 4 HOH A 4 404 404 HOH HOH . 
D 4 HOH A 5 407 407 HOH HOH . 
D 4 HOH A 6 410 410 HOH HOH . 
D 4 HOH A 7 411 411 HOH HOH . 
D 4 HOH A 8 415 415 HOH HOH . 
D 4 HOH A 9 416 416 HOH HOH . 
D 4 HOH A 10 417 417 HOH HOH . 
D 4 HOH A 11 418 418 HOH HOH . 
D 4 HOH A 12 421 421 HOH HOH . 
D 4 HOH A 13 422 422 HOH HOH . 
D 4 HOH A 14 434 434 HOH HOH . 
D 4 HOH A 15 439 439 HOH HOH . 
D 4 HOH A 16 453 453 HOH HOH . 
D 4 HOH A 17 459 459 HOH HOH . 
D 4 HOH A 18 460 460 HOH HOH . 
D 4 HOH A 19 472 472 HOH HOH . 
D 4 HOH A 20 477 477 HOH HOH . 
D 4 HOH A 21 481 481 HOH HOH . 
D 4 HOH A 22 484 484 HOH HOH . 
D 4 HOH A 23 489 489 HOH HOH . 
D 4 HOH A 24 491 491 HOH HOH . 
D 4 HOH A 25 499 499 HOH HOH . 
D 4 HOH A 26 508 508 HOH HOH . 
D 4 HOH A 27 516 516 HOH HOH . 
D 4 HOH A 28 600 600 HOH HOH . 
D 4 HOH A 29 601 601 HOH HOH . 
D 4 HOH A 30 602 602 HOH HOH . 
D 4 HOH A 31 603 603 HOH HOH . 
D 4 HOH A 32 604 604 HOH HOH . 
D 4 HOH A 33 605 605 HOH HOH . 
D 4 HOH A 34 606 606 HOH HOH . 
D 4 HOH A 35 607 607 HOH HOH . 
D 4 HOH A 36 608 608 HOH HOH . 
D 4 HOH A 37 609 609 HOH HOH . 
D 4 HOH A 38 610 610 HOH HOH . 
D 4 HOH A 39 611 611 HOH HOH . 
D 4 HOH A 40 612 612 HOH HOH . 
D 4 HOH A 41 613 613 HOH HOH . 
D 4 HOH A 42 614 614 HOH HOH . 
D 4 HOH A 43 615 615 HOH HOH . 
D 4 HOH A 44 616 616 HOH HOH . 
D 4 HOH A 45 617 617 HOH HOH . 
D 4 HOH A 46 618 618 HOH HOH . 
D 4 HOH A 47 619 619 HOH HOH . 
D 4 HOH A 48 620 620 HOH HOH . 
D 4 HOH A 49 621 621 HOH HOH . 
D 4 HOH A 50 622 622 HOH HOH . 
D 4 HOH A 51 623 623 HOH HOH . 
D 4 HOH A 52 624 624 HOH HOH . 
D 4 HOH A 53 625 625 HOH HOH . 
D 4 HOH A 54 626 626 HOH HOH . 
D 4 HOH A 55 627 627 HOH HOH . 
D 4 HOH A 56 628 628 HOH HOH . 
D 4 HOH A 57 629 629 HOH HOH . 
D 4 HOH A 58 630 630 HOH HOH . 
D 4 HOH A 59 631 631 HOH HOH . 
D 4 HOH A 60 632 632 HOH HOH . 
D 4 HOH A 61 633 633 HOH HOH . 
D 4 HOH A 62 634 634 HOH HOH . 
D 4 HOH A 63 635 635 HOH HOH . 
D 4 HOH A 64 636 636 HOH HOH . 
D 4 HOH A 65 637 637 HOH HOH . 
D 4 HOH A 66 638 638 HOH HOH . 
D 4 HOH A 67 639 639 HOH HOH . 
D 4 HOH A 68 640 640 HOH HOH . 
D 4 HOH A 69 641 641 HOH HOH . 
D 4 HOH A 70 642 642 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 38.14 21.754 36 1 28.58 ? PB GDP 355 A 1 
HETATM 2 O O1B GDP . . . C 3 38.519 21.398 37.344 1 31.27 ? O1B GDP 355 A 1 
HETATM 3 O O2B GDP . . . C 3 37.226 20.791 35.356 1 31.36 ? O2B GDP 355 A 1 
HETATM 4 O O3B GDP . . . C 3 37.759 23.111 35.814 1 31.58 ? O3B GDP 355 A 1 
HETATM 5 O O3A GDP . . . C 3 39.581 21.699 35.158 1 28.55 ? O3A GDP 355 A 1 
HETATM 6 P PA GDP . . . C 3 40.604 22.865 34.571 1 25.26 ? PA GDP 355 A 1 
HETATM 7 O O1A GDP . . . C 3 41.037 23.662 35.664 1 25.03 ? O1A GDP 355 A 1 
HETATM 8 O O2A GDP . . . C 3 39.877 23.52 33.46 1 28.55 ? O2A GDP 355 A 1 
HETATM 9 O O5' GDP . . . C 3 41.737 21.995 34.002 1 22.73 ? O5' GDP 355 A 1 
HETATM 10 C C5' GDP . . . C 3 42.748 21.605 34.937 1 19.79 ? C5' GDP 355 A 1 
HETATM 11 C C4' GDP . . . C 3 44.117 21.647 34.474 1 22.06 ? C4' GDP 355 A 1 
HETATM 12 O O4' GDP . . . C 3 44.315 20.784 33.32 1 30.11 ? O4' GDP 355 A 1 
HETATM 13 C C3' GDP . . . C 3 44.59 23.062 34.058 1 26.34 ? C3' GDP 355 A 1 
HETATM 14 O O3' GDP . . . C 3 45.915 23.254 34.284 1 27.67 ? O3' GDP 355 A 1 
HETATM 15 C C2' GDP . . . C 3 44.42 22.982 32.564 1 26.8 ? C2' GDP 355 A 1 
HETATM 16 O O2' GDP . . . C 3 45.088 24.07 31.969 1 22.64 ? O2' GDP 355 A 1 
HETATM 17 C C1' GDP . . . C 3 44.855 21.59 32.213 1 28.62 ? C1' GDP 355 A 1 
HETATM 18 N N9 GDP . . . C 3 44.029 21.247 31.035 1 31.56 ? N9 GDP 355 A 1 
HETATM 19 C C8 GDP . . . C 3 42.628 21.319 30.856 1 32.62 ? C8 GDP 355 A 1 
HETATM 20 N N7 GDP . . . C 3 42.175 20.862 29.695 1 35.31 ? N7 GDP 355 A 1 
HETATM 21 C C5 GDP . . . C 3 43.413 20.305 29.1 1 31.51 ? C5 GDP 355 A 1 
HETATM 22 C C6 GDP . . . C 3 43.682 19.599 27.849 1 25.81 ? C6 GDP 355 A 1 
HETATM 23 O O6 GDP . . . C 3 42.921 19.197 26.956 1 32.04 ? O6 GDP 355 A 1 
HETATM 24 N N1 GDP . . . C 3 45.001 19.404 27.648 1 25.02 ? N1 GDP 355 A 1 
HETATM 25 C C2 GDP . . . C 3 46.016 19.775 28.469 1 26.25 ? C2 GDP 355 A 1 
HETATM 26 N N2 GDP . . . C 3 47.268 19.612 28.086 1 21.61 ? N2 GDP 355 A 1 
HETATM 27 N N3 GDP . . . C 3 45.808 20.309 29.658 1 31.77 ? N3 GDP 355 A 1 
HETATM 28 C C4 GDP . . . C 3 44.504 20.629 29.889 1 31.19 ? C4 GDP 355 A 1 
#
_model_server_stats.io_time_ms              47 
_model_server_stats.parse_time_ms           5 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           309 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           28 
#