data_8QW6
#
_model_server_result.job_id            P7CdCcl1d-c0gmCnJGAovw 
_model_server_result.datetime_utc      '2025-01-10 13:05:43' 
_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          8qw6 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":201}' 
#
_entry.id    8QW6 
#
_exptl.entry_id    8QW6 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              443.201 
_entity.id                          5 
_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         112.25 
_cell.angle_beta          100.61 
_cell.angle_gamma         100.57 
_cell.entry_id            8QW6 
_cell.length_a            70.207 
_cell.length_b            72.298 
_cell.length_c            80.794 
_cell.Z_PDB               2 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8QW6 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    'P 1' 
_symmetry.space_group_name_H-M     'P 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? tetrameric 4 author_defined_assembly 1 
? tetrameric 4 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,B,C,D,I,J,K,O,P,Q,R 1 1 
E,F,G,H,L,M,N,S,T,U 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
? 5 I N N 
? 5 L 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 D OG SER 18 E SER 17 1_555 K MG MG . E MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.422 ? 
metalc ? metalc2 D O ASP 34 E ASP 33 1_555 K MG MG . E MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.344 ? 
metalc ? metalc3 L O2B GDP . A GDP 201 1_555 N MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.963 ? 
#
_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                     8QW6 
_atom_sites.fract_transf_matrix[1][1]    0.014244 
_atom_sites.fract_transf_matrix[1][2]    0.002658 
_atom_sites.fract_transf_matrix[1][3]    0.004205 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.01407 
_atom_sites.fract_transf_matrix[2][3]    0.006641 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.013925 
_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
I 5 GDP E 1 201 201 GDP GDP . 
J 6 X4R E 1 202 301 X4R LIG . 
K 7 MG E 1 203 501 MG MG . 
L 5 GDP A 1 201 201 GDP GDP . 
M 6 X4R A 1 202 301 X4R LIG . 
N 7 MG A 1 203 501 MG MG . 
O 8 HOH H 1 201 64 HOH HOH . 
O 8 HOH H 2 202 34 HOH HOH . 
O 8 HOH H 3 203 38 HOH HOH . 
P 8 HOH G 1 201 10 HOH HOH . 
P 8 HOH G 2 202 19 HOH HOH . 
P 8 HOH G 3 203 4 HOH HOH . 
P 8 HOH G 4 204 6 HOH HOH . 
P 8 HOH G 5 205 5 HOH HOH . 
P 8 HOH G 6 206 54 HOH HOH . 
P 8 HOH G 7 207 35 HOH HOH . 
Q 8 HOH F 1 301 2 HOH HOH . 
Q 8 HOH F 2 302 24 HOH HOH . 
Q 8 HOH F 3 303 9 HOH HOH . 
Q 8 HOH F 4 304 1 HOH HOH . 
Q 8 HOH F 5 305 63 HOH HOH . 
Q 8 HOH F 6 306 18 HOH HOH . 
Q 8 HOH F 7 307 25 HOH HOH . 
Q 8 HOH F 8 308 17 HOH HOH . 
Q 8 HOH F 9 309 21 HOH HOH . 
Q 8 HOH F 10 310 14 HOH HOH . 
Q 8 HOH F 11 311 23 HOH HOH . 
Q 8 HOH F 12 312 52 HOH HOH . 
Q 8 HOH F 13 313 58 HOH HOH . 
Q 8 HOH F 14 314 44 HOH HOH . 
Q 8 HOH F 15 315 41 HOH HOH . 
Q 8 HOH F 16 316 56 HOH HOH . 
R 8 HOH E 1 301 55 HOH HOH . 
R 8 HOH E 2 302 16 HOH HOH . 
R 8 HOH E 3 303 47 HOH HOH . 
S 8 HOH C 1 201 27 HOH HOH . 
S 8 HOH C 2 202 15 HOH HOH . 
S 8 HOH C 3 203 13 HOH HOH . 
S 8 HOH C 4 204 33 HOH HOH . 
T 8 HOH B 1 301 48 HOH HOH . 
T 8 HOH B 2 302 39 HOH HOH . 
T 8 HOH B 3 303 20 HOH HOH . 
T 8 HOH B 4 304 59 HOH HOH . 
T 8 HOH B 5 305 11 HOH HOH . 
T 8 HOH B 6 306 28 HOH HOH . 
T 8 HOH B 7 307 3 HOH HOH . 
T 8 HOH B 8 308 32 HOH HOH . 
T 8 HOH B 9 309 60 HOH HOH . 
T 8 HOH B 10 310 46 HOH HOH . 
T 8 HOH B 11 311 57 HOH HOH . 
U 8 HOH A 1 301 12 HOH HOH . 
U 8 HOH A 2 302 29 HOH HOH . 
U 8 HOH A 3 303 53 HOH HOH . 
U 8 HOH A 4 304 26 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 . . . L 5 -31.83 -37.076 -8.732 1 58.75 ? PB GDP 201 A 1 
HETATM 2 O O1B GDP . . . L 5 -30.674 -37.992 -8.48 1 62.36 -1 O1B GDP 201 A 1 
HETATM 3 O O2B GDP . . . L 5 -33.121 -37.632 -8.223 1 56.85 ? O2B GDP 201 A 1 
HETATM 4 O O3B GDP . . . L 5 -31.573 -35.674 -8.279 1 47.39 ? O3B GDP 201 A 1 
HETATM 5 O O3A GDP . . . L 5 -31.972 -37.013 -10.325 1 64.11 ? O3A GDP 201 A 1 
HETATM 6 P PA GDP . . . L 5 -31.836 -38.202 -11.383 1 64.47 ? PA GDP 201 A 1 
HETATM 7 O O1A GDP . . . L 5 -30.409 -38.618 -11.447 1 57.38 -1 O1A GDP 201 A 1 
HETATM 8 O O2A GDP . . . L 5 -32.865 -39.227 -11.058 1 54.22 ? O2A GDP 201 A 1 
HETATM 9 O O5' GDP . . . L 5 -32.233 -37.462 -12.739 1 62.06 ? O5' GDP 201 A 1 
HETATM 10 C C5' GDP . . . L 5 -33.638 -37.269 -13.027 1 68.47 ? C5' GDP 201 A 1 
HETATM 11 C C4' GDP . . . L 5 -33.832 -37.357 -14.518 1 63.41 ? C4' GDP 201 A 1 
HETATM 12 O O4' GDP . . . L 5 -33.106 -36.27 -15.135 1 59.42 ? O4' GDP 201 A 1 
HETATM 13 C C3' GDP . . . L 5 -33.296 -38.635 -15.169 1 67.43 ? C3' GDP 201 A 1 
HETATM 14 O O3' GDP . . . L 5 -34.342 -39.586 -15.324 1 64.03 ? O3' GDP 201 A 1 
HETATM 15 C C2' GDP . . . L 5 -32.755 -38.173 -16.526 1 70.95 ? C2' GDP 201 A 1 
HETATM 16 O O2' GDP . . . L 5 -33.666 -38.418 -17.575 1 65.02 ? O2' GDP 201 A 1 
HETATM 17 C C1' GDP . . . L 5 -32.499 -36.678 -16.337 1 67.93 ? C1' GDP 201 A 1 
HETATM 18 N N9 GDP . . . L 5 -31.087 -36.332 -16.251 1 56.27 ? N9 GDP 201 A 1 
HETATM 19 C C8 GDP . . . L 5 -30.228 -36.623 -15.224 1 55.5 ? C8 GDP 201 A 1 
HETATM 20 N N7 GDP . . . L 5 -29.009 -36.196 -15.435 1 60.42 ? N7 GDP 201 A 1 
HETATM 21 C C5 GDP . . . L 5 -29.067 -35.598 -16.686 1 54.47 ? C5 GDP 201 A 1 
HETATM 22 C C6 GDP . . . L 5 -28.054 -34.959 -17.439 1 62.2 ? C6 GDP 201 A 1 
HETATM 23 O O6 GDP . . . L 5 -26.867 -34.786 -17.141 1 68.97 ? O6 GDP 201 A 1 
HETATM 24 N N1 GDP . . . L 5 -28.545 -34.491 -18.655 1 56.99 ? N1 GDP 201 A 1 
HETATM 25 C C2 GDP . . . L 5 -29.837 -34.621 -19.09 1 65.55 ? C2 GDP 201 A 1 
HETATM 26 N N2 GDP . . . L 5 -30.113 -34.11 -20.294 1 66.55 ? N2 GDP 201 A 1 
HETATM 27 N N3 GDP . . . L 5 -30.795 -35.219 -18.387 1 64.05 ? N3 GDP 201 A 1 
HETATM 28 C C4 GDP . . . L 5 -30.337 -35.693 -17.206 1 56.67 ? C4 GDP 201 A 1 
#
_model_server_stats.io_time_ms              56 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    23 
_model_server_stats.query_time_ms           311 
_model_server_stats.encode_time_ms          9 
_model_server_stats.element_count           28 
#