data_6MHE
#
_model_server_result.job_id            oEOEb0gs7E-K_WmzMZupvA 
_model_server_result.datetime_utc      '2024-12-26 15:46:16' 
_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          6mhe 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":402}' 
#
_entry.id    6MHE 
#
_exptl.entry_id    6MHE 
_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            6MHE 
_cell.length_a            83.24 
_cell.length_b            83.24 
_cell.length_c            133.83 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6MHE 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        96 
_symmetry.space_group_name_Hall    'P 4nw 2abw' 
_symmetry.space_group_name_H-M     'P 43 21 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                      4 
_struct_asym.id                             D 
_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                     6MHE 
_atom_sites.fract_transf_matrix[1][1]    0.012013 
_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]    0.012013 
_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]    0.007472 
_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 GOL A 1 401 3 GOL GOL . 
D 4 GDP A 1 402 401 GDP GDP . 
E 5 HOH A 1 501 13 HOH HOH . 
E 5 HOH A 2 502 80 HOH HOH . 
E 5 HOH A 3 503 44 HOH HOH . 
E 5 HOH A 4 504 64 HOH HOH . 
E 5 HOH A 5 505 30 HOH HOH . 
E 5 HOH A 6 506 24 HOH HOH . 
E 5 HOH A 7 507 21 HOH HOH . 
E 5 HOH A 8 508 33 HOH HOH . 
E 5 HOH A 9 509 95 HOH HOH . 
E 5 HOH A 10 510 32 HOH HOH . 
E 5 HOH A 11 511 42 HOH HOH . 
E 5 HOH A 12 512 103 HOH HOH . 
E 5 HOH A 13 513 94 HOH HOH . 
E 5 HOH A 14 514 15 HOH HOH . 
E 5 HOH A 15 515 6 HOH HOH . 
E 5 HOH A 16 516 74 HOH HOH . 
E 5 HOH A 17 517 16 HOH HOH . 
E 5 HOH A 18 518 29 HOH HOH . 
E 5 HOH A 19 519 99 HOH HOH . 
E 5 HOH A 20 520 69 HOH HOH . 
E 5 HOH A 21 521 68 HOH HOH . 
E 5 HOH A 22 522 59 HOH HOH . 
E 5 HOH A 23 523 54 HOH HOH . 
E 5 HOH A 24 524 66 HOH HOH . 
E 5 HOH A 25 525 97 HOH HOH . 
E 5 HOH A 26 526 31 HOH HOH . 
E 5 HOH A 27 527 104 HOH HOH . 
E 5 HOH A 28 528 37 HOH HOH . 
E 5 HOH A 29 529 83 HOH HOH . 
E 5 HOH A 30 530 48 HOH HOH . 
E 5 HOH A 31 531 93 HOH HOH . 
E 5 HOH A 32 532 50 HOH HOH . 
E 5 HOH A 33 533 105 HOH HOH . 
E 5 HOH A 34 534 17 HOH HOH . 
E 5 HOH A 35 535 81 HOH HOH . 
E 5 HOH A 36 536 36 HOH HOH . 
E 5 HOH A 37 537 18 HOH HOH . 
E 5 HOH A 38 538 39 HOH HOH . 
E 5 HOH A 39 539 14 HOH HOH . 
E 5 HOH A 40 540 11 HOH HOH . 
E 5 HOH A 41 541 52 HOH HOH . 
E 5 HOH A 42 542 89 HOH HOH . 
E 5 HOH A 43 543 53 HOH HOH . 
E 5 HOH A 44 544 77 HOH HOH . 
E 5 HOH A 45 545 35 HOH HOH . 
E 5 HOH A 46 546 41 HOH HOH . 
E 5 HOH A 47 547 82 HOH HOH . 
E 5 HOH A 48 548 84 HOH HOH . 
E 5 HOH A 49 549 38 HOH HOH . 
E 5 HOH A 50 550 98 HOH HOH . 
E 5 HOH A 51 551 20 HOH HOH . 
E 5 HOH A 52 552 65 HOH HOH . 
E 5 HOH A 53 553 55 HOH HOH . 
E 5 HOH A 54 554 43 HOH HOH . 
E 5 HOH A 55 555 61 HOH HOH . 
E 5 HOH A 56 556 26 HOH HOH . 
E 5 HOH A 57 557 46 HOH HOH . 
E 5 HOH A 58 558 49 HOH HOH . 
E 5 HOH A 59 559 90 HOH HOH . 
E 5 HOH A 60 560 25 HOH HOH . 
E 5 HOH A 61 561 72 HOH HOH . 
E 5 HOH A 62 562 28 HOH HOH . 
E 5 HOH A 63 563 40 HOH HOH . 
E 5 HOH A 64 564 5 HOH HOH . 
E 5 HOH A 65 565 100 HOH HOH . 
E 5 HOH A 66 566 101 HOH HOH . 
E 5 HOH A 67 567 91 HOH HOH . 
E 5 HOH A 68 568 60 HOH HOH . 
E 5 HOH A 69 569 92 HOH HOH . 
E 5 HOH A 70 570 70 HOH HOH . 
E 5 HOH A 71 571 79 HOH HOH . 
E 5 HOH A 72 572 102 HOH HOH . 
E 5 HOH A 73 573 96 HOH HOH . 
E 5 HOH A 74 574 4 HOH HOH . 
E 5 HOH A 75 575 67 HOH HOH . 
F 5 HOH C 1 101 7 HOH HOH . 
F 5 HOH C 2 102 34 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 . . . D 4 -14.139 -14.949 -16.482 1 28.62 ? PB GDP 402 A 1 
HETATM 2 O O1B GDP . . . D 4 -15.526 -15.475 -16.856 1 31.85 ? O1B GDP 402 A 1 
HETATM 3 O O2B GDP . . . D 4 -14.176 -13.456 -16.33 1 39.51 ? O2B GDP 402 A 1 
HETATM 4 O O3B GDP . . . D 4 -13.695 -15.601 -15.17 1 32.96 ? O3B GDP 402 A 1 
HETATM 5 O O3A GDP . . . D 4 -13.076 -15.349 -17.669 1 28.98 ? O3A GDP 402 A 1 
HETATM 6 P PA GDP . . . D 4 -11.955 -14.33 -18.299 1 29.92 ? PA GDP 402 A 1 
HETATM 7 O O1A GDP . . . D 4 -12.607 -13.325 -19.229 1 28.54 ? O1A GDP 402 A 1 
HETATM 8 O O2A GDP . . . D 4 -11.214 -13.615 -17.205 1 30.91 ? O2A GDP 402 A 1 
HETATM 9 O O5' GDP . . . D 4 -10.893 -15.281 -19.147 1 29.55 ? O5' GDP 402 A 1 
HETATM 10 C C5' GDP . . . D 4 -10.01 -16.087 -18.378 1 36.22 ? C5' GDP 402 A 1 
HETATM 11 C C4' GDP . . . D 4 -8.698 -16.158 -19.096 1 31.26 ? C4' GDP 402 A 1 
HETATM 12 O O4' GDP . . . D 4 -8.989 -16.806 -20.55 1 29.74 ? O4' GDP 402 A 1 
HETATM 13 C C3' GDP . . . D 4 -8.21 -14.972 -19.29 1 28.99 ? C3' GDP 402 A 1 
HETATM 14 O O3' GDP . . . D 4 -6.741 -15.025 -19.212 1 33.25 ? O3' GDP 402 A 1 
HETATM 15 C C2' GDP . . . D 4 -8.621 -14.581 -20.752 1 34.94 ? C2' GDP 402 A 1 
HETATM 16 O O2' GDP . . . D 4 -7.72 -13.731 -21.303 1 39.05 ? O2' GDP 402 A 1 
HETATM 17 C C1' GDP . . . D 4 -8.537 -15.93 -21.44 1 34.47 ? C1' GDP 402 A 1 
HETATM 18 N N9 GDP . . . D 4 -9.322 -16.055 -22.688 1 30.94 ? N9 GDP 402 A 1 
HETATM 19 C C8 GDP . . . D 4 -10.593 -15.643 -22.581 1 29.76 ? C8 GDP 402 A 1 
HETATM 20 N N7 GDP . . . D 4 -11.169 -15.836 -23.782 1 23.07 ? N7 GDP 402 A 1 
HETATM 21 C C5 GDP . . . D 4 -10.254 -16.369 -24.601 1 33.34 ? C5 GDP 402 A 1 
HETATM 22 C C6 GDP . . . D 4 -10.301 -16.811 -26.068 1 28.77 ? C6 GDP 402 A 1 
HETATM 23 O O6 GDP . . . D 4 -11.283 -16.7 -26.68 1 36.82 ? O6 GDP 402 A 1 
HETATM 24 N N1 GDP . . . D 4 -9.13 -17.362 -26.681 1 39.01 ? N1 GDP 402 A 1 
HETATM 25 C C2 GDP . . . D 4 -7.926 -17.496 -25.925 1 31.06 ? C2 GDP 402 A 1 
HETATM 26 N N2 GDP . . . D 4 -6.716 -18.055 -26.529 1 34.38 ? N2 GDP 402 A 1 
HETATM 27 N N3 GDP . . . D 4 -7.885 -17.076 -24.532 1 32.01 ? N3 GDP 402 A 1 
HETATM 28 C C4 GDP . . . D 4 -9.108 -16.508 -23.91 1 31.3 ? C4 GDP 402 A 1 
HETATM 29 H H5' GDP . . . D 4 -9.884 -15.69 -17.501 1 43.52 ? H5' GDP 402 A 1 
HETATM 30 H "H5''" GDP . . . D 4 -10.381 -16.978 -18.28 1 43.52 ? "H5''" GDP 402 A 1 
HETATM 31 H H4' GDP . . . D 4 -8.034 -16.668 -18.606 1 37.56 ? H4' GDP 402 A 1 
HETATM 32 H H3' GDP . . . D 4 -8.584 -14.347 -18.65 1 34.84 ? H3' GDP 402 A 1 
HETATM 33 H HO3' GDP . . . D 4 -6.458 -14.379 -18.737 1 39.95 ? HO3' GDP 402 A 1 
HETATM 34 H H2' GDP . . . D 4 -9.501 -14.175 -20.792 1 41.98 ? H2' GDP 402 A 1 
HETATM 35 H HO2' GDP . . . D 4 -8.046 -12.946 -21.325 1 46.91 ? HO2' GDP 402 A 1 
HETATM 36 H H1' GDP . . . D 4 -7.602 -16.063 -21.662 1 41.41 ? H1' GDP 402 A 1 
HETATM 37 H H8 GDP . . . D 4 -11 -15.291 -21.822 1 35.76 ? H8 GDP 402 A 1 
HETATM 38 H HN1 GDP . . . D 4 -9.151 -17.611 -27.504 1 46.86 ? HN1 GDP 402 A 1 
HETATM 39 H HN21 GDP . . . D 4 -6.721 -18.308 -27.35 1 41.3 ? HN21 GDP 402 A 1 
HETATM 40 H HN22 GDP . . . D 4 -6.001 -18.129 -26.058 1 41.3 ? HN22 GDP 402 A 1 
#
_model_server_stats.io_time_ms              31 
_model_server_stats.parse_time_ms           18 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           615 
_model_server_stats.encode_time_ms          14 
_model_server_stats.element_count           40 
#