data_6GWD
#
_model_server_result.job_id            aRzgGFhqDQ-NrY_2vFRlLA 
_model_server_result.datetime_utc      '2024-10-19 03:50:06' 
_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          6gwd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":600}' 
#
_entry.id    6GWD 
#
_exptl.entry_id    6GWD 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              443.201 
_entity.id                          6 
_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          118.76 
_cell.angle_gamma         90 
_cell.entry_id            6GWD 
_cell.length_a            450.8 
_cell.length_b            53.84 
_cell.length_c            229.62 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6GWD 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    nonameric 
_pdbx_struct_assembly.oligomeric_count      9 
_pdbx_struct_assembly.details               software_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,M,N,O,P,Q,R 
_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
? 6 L N N 
? 6 O N N 
? 6 R 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 OE1 GLU 71 A GLU 71 1_555 K MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.453 ? 
metalc ? metalc2 J O1G GTP . A GTP 600 1_555 K MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? 
metalc ? metalc3 J O2G GTP . A GTP 600 1_555 K MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.707 ? 
metalc ? metalc4 J O2B GTP . A GTP 600 1_555 K MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.183 ? 
metalc ? metalc5 M O3G GTP . C GTP 600 1_555 N MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.354 ? 
metalc ? metalc6 M O2B GTP . C GTP 600 1_555 N MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.229 ? 
metalc ? metalc7 E OE1 GLU 71 E GLU 71 1_555 Q MG MG . E MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.407 ? 
metalc ? metalc8 E OE2 GLU 71 E GLU 71 1_555 Q MG MG . E MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.168 ? 
metalc ? metalc9 P O2B GTP . E GTP 600 1_555 Q MG MG . E MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.734 ? 
#
_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                     6GWD 
_atom_sites.fract_transf_matrix[1][1]    0.002218 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.001217 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.018574 
_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]    0.004968 
_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
J 4 GTP A 1 600 600 GTP GTP . 
K 5 MG A 1 601 601 MG MG . 
L 6 GDP B 1 600 600 GDP GDP . 
M 4 GTP C 1 600 600 GTP GTP . 
N 5 MG C 1 601 601 MG MG . 
O 6 GDP D 1 600 600 GDP GDP . 
P 4 GTP E 1 600 600 GTP GTP . 
Q 5 MG E 1 601 601 MG MG . 
R 6 GDP F 1 600 600 GDP GDP . 
#
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 . . . L 6 -85.174 -12.142 135.111 1 147.04 ? PB GDP 600 B 1 
HETATM 2 O O1B GDP . . . L 6 -85.56 -12.47 133.652 1 142.77 ? O1B GDP 600 B 1 
HETATM 3 O O2B GDP . . . L 6 -84.015 -11.268 135.207 1 148.13 ? O2B GDP 600 B 1 
HETATM 4 O O3B GDP . . . L 6 -86.355 -11.546 135.87 1 148.77 ? O3B GDP 600 B 1 
HETATM 5 O O3A GDP . . . L 6 -84.923 -13.541 135.829 1 147.98 ? O3A GDP 600 B 1 
HETATM 6 P PA GDP . . . L 6 -83.911 -14.743 135.586 1 146.34 ? PA GDP 600 B 1 
HETATM 7 O O1A GDP . . . L 6 -83.041 -14.43 134.434 1 144.19 ? O1A GDP 600 B 1 
HETATM 8 O O2A GDP . . . L 6 -83.067 -14.868 136.855 1 147.39 ? O2A GDP 600 B 1 
HETATM 9 O O5' GDP . . . L 6 -84.791 -16.064 135.339 1 150.02 ? O5' GDP 600 B 1 
HETATM 10 C C5' GDP . . . L 6 -84.757 -17.256 136.151 1 157.63 ? C5' GDP 600 B 1 
HETATM 11 C C4' GDP . . . L 6 -84.726 -18.454 135.235 1 149.93 ? C4' GDP 600 B 1 
HETATM 12 O O4' GDP . . . L 6 -83.596 -18.345 134.342 1 145.63 ? O4' GDP 600 B 1 
HETATM 13 C C3' GDP . . . L 6 -84.545 -19.796 135.933 1 156.58 ? C3' GDP 600 B 1 
HETATM 14 O O3' GDP . . . L 6 -85.108 -20.843 135.149 1 152.33 ? O3' GDP 600 B 1 
HETATM 15 C C2' GDP . . . L 6 -83.026 -19.902 136.031 1 156.81 ? C2' GDP 600 B 1 
HETATM 16 O O2' GDP . . . L 6 -82.617 -21.26 136.171 1 161.39 ? O2' GDP 600 B 1 
HETATM 17 C C1' GDP . . . L 6 -82.616 -19.311 134.679 1 143.7 ? C1' GDP 600 B 1 
HETATM 18 N N9 GDP . . . L 6 -81.289 -18.658 134.662 1 140.27 ? N9 GDP 600 B 1 
HETATM 19 C C8 GDP . . . L 6 -80.865 -17.568 135.381 1 145.62 ? C8 GDP 600 B 1 
HETATM 20 N N7 GDP . . . L 6 -79.628 -17.212 135.117 1 140.39 ? N7 GDP 600 B 1 
HETATM 21 C C5 GDP . . . L 6 -79.211 -18.124 134.162 1 133.07 ? C5 GDP 600 B 1 
HETATM 22 C C6 GDP . . . L 6 -77.954 -18.276 133.467 1 127.8 ? C6 GDP 600 B 1 
HETATM 23 O O6 GDP . . . L 6 -76.948 -17.577 133.58 1 128.97 ? O6 GDP 600 B 1 
HETATM 24 N N1 GDP . . . L 6 -77.966 -19.357 132.604 1 121.83 ? N1 GDP 600 B 1 
HETATM 25 C C2 GDP . . . L 6 -79.024 -20.205 132.413 1 119.25 ? C2 GDP 600 B 1 
HETATM 26 N N2 GDP . . . L 6 -78.807 -21.288 131.664 1 112.19 ? N2 GDP 600 B 1 
HETATM 27 N N3 GDP . . . L 6 -80.199 -20.059 133.019 1 124.45 ? N3 GDP 600 B 1 
HETATM 28 C C4 GDP . . . L 6 -80.225 -19.022 133.876 1 131.89 ? C4 GDP 600 B 1 
HETATM 29 H H5' GDP . . . L 6 -83.919 -17.25 136.845 1 164.83 ? H5' GDP 600 B 1 
HETATM 30 H "H5''" GDP . . . L 6 -85.668 -17.204 136.746 1 165.2 ? "H5''" GDP 600 B 1 
HETATM 31 H H4' GDP . . . L 6 -85.588 -18.448 134.57 1 140.33 ? H4' GDP 600 B 1 
HETATM 32 H H3' GDP . . . L 6 -85.006 -19.803 136.918 1 166.25 ? H3' GDP 600 B 1 
HETATM 33 H HO3' GDP . . . L 6 -84.874 -21.699 135.595 1 151.19 ? HO3' GDP 600 B 1 
HETATM 34 H H2' GDP . . . L 6 -82.647 -19.29 136.849 1 164.81 ? H2' GDP 600 B 1 
HETATM 35 H HO2' GDP . . . L 6 -82.21 -21.317 137.075 1 168.76 ? HO2' GDP 600 B 1 
HETATM 36 H H1' GDP . . . L 6 -82.638 -20.065 133.894 1 132.5 ? H1' GDP 600 B 1 
HETATM 37 H H8 GDP . . . L 6 -81.492 -17.03 136.09 1 155.26 ? H8 GDP 600 B 1 
HETATM 38 H HN1 GDP . . . L 6 -77.102 -19.511 132.095 1 119.89 ? HN1 GDP 600 B 1 
HETATM 39 H HN21 GDP . . . L 6 -79.557 -21.951 131.494 1 107.03 ? HN21 GDP 600 B 1 
HETATM 40 H HN22 GDP . . . L 6 -77.904 -21.533 131.274 1 108.89 ? HN22 GDP 600 B 1 
#
_model_server_stats.io_time_ms              49 
_model_server_stats.parse_time_ms           24 
_model_server_stats.create_model_time_ms    26 
_model_server_stats.query_time_ms           308 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           40 
#