data_1TUI
#
_model_server_result.job_id            CT81dzkqxyogzbxi2AmYAQ 
_model_server_result.datetime_utc      '2024-10-19 17:30:15' 
_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          1tui 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"G","auth_seq_id":407}' 
#
_entry.id    1TUI 
#
_exptl.entry_id    1TUI 
_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    3 
_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            1TUI 
_cell.length_a            175.9 
_cell.length_b            175.9 
_cell.length_c            223.8 
_cell.Z_PDB               36 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1TUI 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        182 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 63 2 2' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_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,G,H,I,J,K,L 
_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 E N N 
? 3 G N N 
? 3 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 OG1 THR 25 A THR 25 1_555 D MG MG . A MG 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.139 ? 
metalc ? metalc2 A O CYS 82 A CYS 82 1_555 D MG MG . A MG 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.13 ? 
metalc ? metalc3 E O2B GDP . A GDP 407 1_555 D MG MG . A MG 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? 
metalc ? metalc4 D MG MG . A MG 408 1_555 J O HOH . A HOH 419 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.328 ? 
metalc ? metalc5 B OG1 THR 25 B THR 25 1_555 F MG MG . B MG 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? 
metalc ? metalc6 G O2B GDP . B GDP 407 1_555 F MG MG . B MG 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.452 ? 
metalc ? metalc7 F MG MG . B MG 408 1_555 K O HOH . B HOH 419 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.332 ? 
metalc ? metalc8 C OG1 THR 25 C THR 25 1_555 H MG MG . C MG 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? 
metalc ? metalc9 I O2B GDP . C GDP 407 1_555 H MG MG . C MG 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.294 ? 
metalc ? metalc10 H MG MG . C MG 408 1_555 L O HOH . C HOH 419 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? 
#
_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                     1TUI 
_atom_sites.fract_transf_matrix[1][1]    0.005685 
_atom_sites.fract_transf_matrix[1][2]    0.003282 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.006565 
_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]    0.004468 
_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
D 2 MG A 1 408 408 MG MG . 
E 3 GDP A 1 407 407 GDP GDP . 
F 2 MG B 1 408 408 MG MG . 
G 3 GDP B 1 407 407 GDP GDP . 
H 2 MG C 1 408 408 MG MG . 
I 3 GDP C 1 407 407 GDP GDP . 
J 4 HOH A 1 409 1 HOH HOH . 
J 4 HOH A 2 410 2 HOH HOH . 
J 4 HOH A 3 411 3 HOH HOH . 
J 4 HOH A 4 412 4 HOH HOH . 
J 4 HOH A 5 413 5 HOH HOH . 
J 4 HOH A 6 414 6 HOH HOH . 
J 4 HOH A 7 415 8 HOH HOH . 
J 4 HOH A 8 416 9 HOH HOH . 
J 4 HOH A 9 417 10 HOH HOH . 
J 4 HOH A 10 418 11 HOH HOH . 
J 4 HOH A 11 419 12 HOH HOH . 
J 4 HOH A 12 420 13 HOH HOH . 
J 4 HOH A 13 421 14 HOH HOH . 
J 4 HOH A 14 422 20 HOH HOH . 
J 4 HOH A 15 423 22 HOH HOH . 
J 4 HOH A 16 424 24 HOH HOH . 
J 4 HOH A 17 425 25 HOH HOH . 
J 4 HOH A 18 426 26 HOH HOH . 
J 4 HOH A 19 427 29 HOH HOH . 
J 4 HOH A 20 428 30 HOH HOH . 
J 4 HOH A 21 429 31 HOH HOH . 
J 4 HOH A 22 430 32 HOH HOH . 
J 4 HOH A 23 431 33 HOH HOH . 
J 4 HOH A 24 432 36 HOH HOH . 
J 4 HOH A 25 433 46 HOH HOH . 
J 4 HOH A 26 434 47 HOH HOH . 
J 4 HOH A 27 435 48 HOH HOH . 
J 4 HOH A 28 436 53 HOH HOH . 
J 4 HOH A 29 437 56 HOH HOH . 
J 4 HOH A 30 438 58 HOH HOH . 
J 4 HOH A 31 439 66 HOH HOH . 
J 4 HOH A 32 440 68 HOH HOH . 
J 4 HOH A 33 441 71 HOH HOH . 
K 4 HOH B 1 409 1 HOH HOH . 
K 4 HOH B 2 410 2 HOH HOH . 
K 4 HOH B 3 411 3 HOH HOH . 
K 4 HOH B 4 412 4 HOH HOH . 
K 4 HOH B 5 413 5 HOH HOH . 
K 4 HOH B 6 414 6 HOH HOH . 
K 4 HOH B 7 415 8 HOH HOH . 
K 4 HOH B 8 416 9 HOH HOH . 
K 4 HOH B 9 417 10 HOH HOH . 
K 4 HOH B 10 418 11 HOH HOH . 
K 4 HOH B 11 419 12 HOH HOH . 
K 4 HOH B 12 420 13 HOH HOH . 
K 4 HOH B 13 421 22 HOH HOH . 
K 4 HOH B 14 422 41 HOH HOH . 
K 4 HOH B 15 423 42 HOH HOH . 
K 4 HOH B 16 424 43 HOH HOH . 
K 4 HOH B 17 425 76 HOH HOH . 
K 4 HOH B 18 426 77 HOH HOH . 
K 4 HOH B 19 427 78 HOH HOH . 
K 4 HOH B 20 428 80 HOH HOH . 
K 4 HOH B 21 429 82 HOH HOH . 
K 4 HOH B 22 430 83 HOH HOH . 
K 4 HOH B 23 431 84 HOH HOH . 
L 4 HOH C 1 409 75 HOH HOH . 
L 4 HOH C 2 410 1 HOH HOH . 
L 4 HOH C 3 411 2 HOH HOH . 
L 4 HOH C 4 412 3 HOH HOH . 
L 4 HOH C 5 413 5 HOH HOH . 
L 4 HOH C 6 414 6 HOH HOH . 
L 4 HOH C 7 415 8 HOH HOH . 
L 4 HOH C 8 416 9 HOH HOH . 
L 4 HOH C 9 417 10 HOH HOH . 
L 4 HOH C 10 418 11 HOH HOH . 
L 4 HOH C 11 419 12 HOH HOH . 
L 4 HOH C 12 420 13 HOH HOH . 
L 4 HOH C 13 421 14 HOH HOH . 
L 4 HOH C 14 422 20 HOH HOH . 
L 4 HOH C 15 423 24 HOH HOH . 
L 4 HOH C 16 424 25 HOH HOH . 
L 4 HOH C 17 425 26 HOH HOH . 
L 4 HOH C 18 426 28 HOH HOH . 
L 4 HOH C 19 427 30 HOH HOH . 
L 4 HOH C 20 428 31 HOH HOH . 
L 4 HOH C 21 429 32 HOH HOH . 
L 4 HOH C 22 430 33 HOH HOH . 
L 4 HOH C 23 431 39 HOH HOH . 
L 4 HOH C 24 432 42 HOH HOH . 
L 4 HOH C 25 433 43 HOH HOH . 
L 4 HOH C 26 434 90 HOH HOH . 
L 4 HOH C 27 435 91 HOH HOH . 
L 4 HOH C 28 436 92 HOH HOH . 
L 4 HOH C 29 437 95 HOH HOH . 
L 4 HOH C 30 438 97 HOH HOH . 
L 4 HOH C 31 439 99 HOH HOH . 
L 4 HOH C 32 440 102 HOH HOH . 
L 4 HOH C 33 441 103 HOH HOH . 
L 4 HOH C 34 442 104 HOH HOH . 
L 4 HOH C 35 443 105 HOH HOH . 
L 4 HOH C 36 444 108 HOH HOH . 
L 4 HOH C 37 445 111 HOH HOH . 
L 4 HOH C 38 446 114 HOH HOH . 
L 4 HOH C 39 447 115 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 . . . G 3 26.997 94.331 126.462 1 36.8 ? PB GDP 407 B 1 
HETATM 2 O O1B GDP . . . G 3 26.599 94.743 127.893 1 10.17 ? O1B GDP 407 B 1 
HETATM 3 O O2B GDP . . . G 3 27.637 93.141 126.206 1 20.59 ? O2B GDP 407 B 1 
HETATM 4 O O3B GDP . . . G 3 25.786 94.083 125.477 1 48.78 ? O3B GDP 407 B 1 
HETATM 5 O O3A GDP . . . G 3 27.924 95.26 125.787 1 14.97 ? O3A GDP 407 B 1 
HETATM 6 P PA GDP . . . G 3 29.083 95.134 124.843 1 29.96 ? PA GDP 407 B 1 
HETATM 7 O O1A GDP . . . G 3 28.545 94.394 123.724 1 9.27 ? O1A GDP 407 B 1 
HETATM 8 O O2A GDP . . . G 3 30.248 94.601 125.576 1 25.05 ? O2A GDP 407 B 1 
HETATM 9 O O5' GDP . . . G 3 29.416 96.515 124.167 1 20.32 ? O5' GDP 407 B 1 
HETATM 10 C C5' GDP . . . G 3 28.373 97.341 123.602 1 1.95 ? C5' GDP 407 B 1 
HETATM 11 C C4' GDP . . . G 3 29.024 98.502 122.849 1 5.42 ? C4' GDP 407 B 1 
HETATM 12 O O4' GDP . . . G 3 29.881 99.156 123.836 1 17.12 ? O4' GDP 407 B 1 
HETATM 13 C C3' GDP . . . G 3 29.967 98.049 121.756 1 13.06 ? C3' GDP 407 B 1 
HETATM 14 O O3' GDP . . . G 3 29.719 98.676 120.565 1 19.62 ? O3' GDP 407 B 1 
HETATM 15 C C2' GDP . . . G 3 31.388 98.256 122.334 1 5.73 ? C2' GDP 407 B 1 
HETATM 16 O O2' GDP . . . G 3 32.279 98.684 121.352 1 37.33 ? O2' GDP 407 B 1 
HETATM 17 C C1' GDP . . . G 3 31.133 99.442 123.246 1 37.99 ? C1' GDP 407 B 1 
HETATM 18 N N9 GDP . . . G 3 32.176 99.67 124.255 1 16.2 ? N9 GDP 407 B 1 
HETATM 19 C C8 GDP . . . G 3 32.487 98.704 125.159 1 20.41 ? C8 GDP 407 B 1 
HETATM 20 N N7 GDP . . . G 3 33.318 99.095 126.105 1 29.6 ? N7 GDP 407 B 1 
HETATM 21 C C5 GDP . . . G 3 33.656 100.386 125.779 1 15.76 ? C5 GDP 407 B 1 
HETATM 22 C C6 GDP . . . G 3 34.518 101.283 126.428 1 44.12 ? C6 GDP 407 B 1 
HETATM 23 O O6 GDP . . . G 3 35.266 101.07 127.375 1 58.64 ? O6 GDP 407 B 1 
HETATM 24 N N1 GDP . . . G 3 34.395 102.563 125.941 1 41.52 ? N1 GDP 407 B 1 
HETATM 25 C C2 GDP . . . G 3 33.619 102.873 124.861 1 38.9 ? C2 GDP 407 B 1 
HETATM 26 N N2 GDP . . . G 3 33.754 104.097 124.336 1 28.03 ? N2 GDP 407 B 1 
HETATM 27 N N3 GDP . . . G 3 32.783 102.044 124.269 1 16.41 ? N3 GDP 407 B 1 
HETATM 28 C C4 GDP . . . G 3 32.875 100.785 124.731 1 43.85 ? C4 GDP 407 B 1 
#
_model_server_stats.io_time_ms              0 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    11 
_model_server_stats.query_time_ms           290 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           28 
#