data_2H5E
#
_model_server_result.job_id            DxNyyPWtc0OZNa5aL55m5w 
_model_server_result.datetime_utc      '2024-11-16 17:32:59' 
_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          2h5e 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":2567}' 
#
_entry.id    2H5E 
#
_exptl.entry_id    2H5E 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              443.201 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "GUANOSINE-5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    2 
_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            2H5E 
_cell.length_a            73.174 
_cell.length_b            239.781 
_cell.length_c            69.677 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2H5E 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,E 1 1 
B,D,F 2 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
? 2 C N N 
? 2 D N 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                     2H5E 
_atom_sites.fract_transf_matrix[1][1]    0.013666 
_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]    0.00417 
_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]    0.014352 
_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 2 GDP A 1 2567 2567 GDP GDP . 
D 2 GDP B 1 3567 2567 GDP GDP . 
E 3 HOH A 1 2568 39 HOH HOH . 
E 3 HOH A 2 2569 40 HOH HOH . 
E 3 HOH A 3 2570 42 HOH HOH . 
E 3 HOH A 4 2571 43 HOH HOH . 
E 3 HOH A 5 2572 44 HOH HOH . 
E 3 HOH A 6 2573 45 HOH HOH . 
E 3 HOH A 7 2574 46 HOH HOH . 
E 3 HOH A 8 2575 47 HOH HOH . 
E 3 HOH A 9 2576 50 HOH HOH . 
E 3 HOH A 10 2577 53 HOH HOH . 
E 3 HOH A 11 2578 55 HOH HOH . 
E 3 HOH A 12 2579 58 HOH HOH . 
E 3 HOH A 13 2580 61 HOH HOH . 
E 3 HOH A 14 2581 63 HOH HOH . 
E 3 HOH A 15 2582 66 HOH HOH . 
E 3 HOH A 16 2583 69 HOH HOH . 
E 3 HOH A 17 2584 70 HOH HOH . 
E 3 HOH A 18 2585 71 HOH HOH . 
E 3 HOH A 19 2586 72 HOH HOH . 
E 3 HOH A 20 2587 73 HOH HOH . 
E 3 HOH A 21 2588 74 HOH HOH . 
E 3 HOH A 22 2589 75 HOH HOH . 
E 3 HOH A 23 2590 77 HOH HOH . 
E 3 HOH A 24 2591 79 HOH HOH . 
E 3 HOH A 25 2592 80 HOH HOH . 
E 3 HOH A 26 2593 84 HOH HOH . 
E 3 HOH A 27 2594 86 HOH HOH . 
E 3 HOH A 28 2595 87 HOH HOH . 
E 3 HOH A 29 2596 91 HOH HOH . 
E 3 HOH A 30 2597 92 HOH HOH . 
E 3 HOH A 31 2598 94 HOH HOH . 
E 3 HOH A 32 2599 96 HOH HOH . 
E 3 HOH A 33 2600 98 HOH HOH . 
E 3 HOH A 34 2601 107 HOH HOH . 
E 3 HOH A 35 2602 108 HOH HOH . 
E 3 HOH A 36 2603 109 HOH HOH . 
E 3 HOH A 37 2604 110 HOH HOH . 
E 3 HOH A 38 2605 111 HOH HOH . 
E 3 HOH A 39 2606 113 HOH HOH . 
E 3 HOH A 40 2607 117 HOH HOH . 
E 3 HOH A 41 2608 124 HOH HOH . 
E 3 HOH A 42 2609 126 HOH HOH . 
E 3 HOH A 43 2610 135 HOH HOH . 
E 3 HOH A 44 2611 136 HOH HOH . 
E 3 HOH A 45 2612 144 HOH HOH . 
E 3 HOH A 46 2613 145 HOH HOH . 
E 3 HOH A 47 2614 147 HOH HOH . 
E 3 HOH A 48 2615 148 HOH HOH . 
E 3 HOH A 49 2616 151 HOH HOH . 
E 3 HOH A 50 2617 152 HOH HOH . 
E 3 HOH A 51 2618 155 HOH HOH . 
E 3 HOH A 52 2619 156 HOH HOH . 
E 3 HOH A 53 2620 160 HOH HOH . 
E 3 HOH A 54 2621 164 HOH HOH . 
E 3 HOH A 55 2622 168 HOH HOH . 
E 3 HOH A 56 2623 169 HOH HOH . 
E 3 HOH A 57 2624 170 HOH HOH . 
F 3 HOH B 1 3568 41 HOH HOH . 
F 3 HOH B 2 3569 49 HOH HOH . 
F 3 HOH B 3 3570 51 HOH HOH . 
F 3 HOH B 4 3571 52 HOH HOH . 
F 3 HOH B 5 3572 54 HOH HOH . 
F 3 HOH B 6 3573 57 HOH HOH . 
F 3 HOH B 7 3574 59 HOH HOH . 
F 3 HOH B 8 3575 68 HOH HOH . 
F 3 HOH B 9 3576 81 HOH HOH . 
F 3 HOH B 10 3577 85 HOH HOH . 
F 3 HOH B 11 3578 93 HOH HOH . 
F 3 HOH B 12 3579 97 HOH HOH . 
F 3 HOH B 13 3580 100 HOH HOH . 
F 3 HOH B 14 3581 101 HOH HOH . 
F 3 HOH B 15 3582 103 HOH HOH . 
F 3 HOH B 16 3583 104 HOH HOH . 
F 3 HOH B 17 3584 105 HOH HOH . 
F 3 HOH B 18 3585 106 HOH HOH . 
F 3 HOH B 19 3586 115 HOH HOH . 
F 3 HOH B 20 3587 120 HOH HOH . 
F 3 HOH B 21 3588 123 HOH HOH . 
F 3 HOH B 22 3589 128 HOH HOH . 
F 3 HOH B 23 3590 129 HOH HOH . 
F 3 HOH B 24 3591 131 HOH HOH . 
F 3 HOH B 25 3592 132 HOH HOH . 
F 3 HOH B 26 3593 140 HOH HOH . 
F 3 HOH B 27 3594 141 HOH HOH . 
F 3 HOH B 28 3595 143 HOH HOH . 
F 3 HOH B 29 3596 153 HOH HOH . 
F 3 HOH B 30 3597 158 HOH HOH . 
F 3 HOH B 31 3598 159 HOH HOH . 
F 3 HOH B 32 3599 163 HOH HOH . 
F 3 HOH B 33 3600 166 HOH HOH . 
F 3 HOH B 34 3601 172 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 2 -2.782 26.713 -1.186 1 25.98 ? PB GDP 2567 A 1 
HETATM 2 O O1B GDP . . . C 2 -3.37 27.058 -2.5 1 24.23 ? O1B GDP 2567 A 1 
HETATM 3 O O2B GDP . . . C 2 -1.304 27.147 -1.222 1 25.32 ? O2B GDP 2567 A 1 
HETATM 4 O O3B GDP . . . C 2 -3.577 27.454 -0.1 1 24.36 ? O3B GDP 2567 A 1 
HETATM 5 O O3A GDP . . . C 2 -2.86 25.109 -0.901 1 24.81 ? O3A GDP 2567 A 1 
HETATM 6 P PA GDP . . . C 2 -4.055 24.474 -0.038 1 24.51 ? PA GDP 2567 A 1 
HETATM 7 O O1A GDP . . . C 2 -3.776 24.703 1.368 1 21.97 ? O1A GDP 2567 A 1 
HETATM 8 O O2A GDP . . . C 2 -5.406 25.086 -0.439 1 26.22 ? O2A GDP 2567 A 1 
HETATM 9 O O5' GDP . . . C 2 -4.001 22.888 -0.375 1 25.31 ? O5' GDP 2567 A 1 
HETATM 10 C C5' GDP . . . C 2 -4.084 22.454 -1.717 1 25.06 ? C5' GDP 2567 A 1 
HETATM 11 C C4' GDP . . . C 2 -4.494 20.995 -1.776 1 25.74 ? C4' GDP 2567 A 1 
HETATM 12 O O4' GDP . . . C 2 -3.45 20.2 -1.24 1 25.88 ? O4' GDP 2567 A 1 
HETATM 13 C C3' GDP . . . C 2 -5.769 20.726 -0.977 1 26.49 ? C3' GDP 2567 A 1 
HETATM 14 O O3' GDP . . . C 2 -6.649 19.821 -1.672 1 27.14 ? O3' GDP 2567 A 1 
HETATM 15 C C2' GDP . . . C 2 -5.206 20.178 0.328 1 26.15 ? C2' GDP 2567 A 1 
HETATM 16 O O2' GDP . . . C 2 -6.089 19.267 0.934 1 27.09 ? O2' GDP 2567 A 1 
HETATM 17 C C1' GDP . . . C 2 -3.914 19.499 -0.107 1 26.31 ? C1' GDP 2567 A 1 
HETATM 18 N N9 GDP . . . C 2 -2.808 19.512 0.871 1 27.04 ? N9 GDP 2567 A 1 
HETATM 19 C C8 GDP . . . C 2 -2.3 20.598 1.541 1 27.5 ? C8 GDP 2567 A 1 
HETATM 20 N N7 GDP . . . C 2 -1.264 20.183 2.314 1 27.24 ? N7 GDP 2567 A 1 
HETATM 21 C C5 GDP . . . C 2 -1.097 18.856 2.126 1 27.35 ? C5 GDP 2567 A 1 
HETATM 22 C C6 GDP . . . C 2 -0.204 17.932 2.67 1 28.35 ? C6 GDP 2567 A 1 
HETATM 23 O O6 GDP . . . C 2 0.324 18.149 3.766 1 30.05 ? O6 GDP 2567 A 1 
HETATM 24 N N1 GDP . . . C 2 -0.306 16.615 2.277 1 28.93 ? N1 GDP 2567 A 1 
HETATM 25 C C2 GDP . . . C 2 -1.261 16.213 1.357 1 27.93 ? C2 GDP 2567 A 1 
HETATM 26 N N2 GDP . . . C 2 -1.408 14.917 1.109 1 27.54 ? N2 GDP 2567 A 1 
HETATM 27 N N3 GDP . . . C 2 -2.144 17.125 0.828 1 26.82 ? N3 GDP 2567 A 1 
HETATM 28 C C4 GDP . . . C 2 -2.06 18.421 1.214 1 26.89 ? C4 GDP 2567 A 1 
#
_model_server_stats.io_time_ms              65 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    11 
_model_server_stats.query_time_ms           277 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           28 
#