data_8QVU
#
_model_server_result.job_id            4ozOT31EQ6nVhvIidrsE9Q 
_model_server_result.datetime_utc      '2025-03-21 06:40:43' 
_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          8qvu 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":202}' 
#
_entry.id    8QVU 
#
_exptl.entry_id    8QVU 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              443.201 
_entity.id                          7 
_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          111.673 
_cell.angle_gamma         90 
_cell.entry_id            8QVU 
_cell.length_a            72.253 
_cell.length_b            120.9 
_cell.length_c            81.016 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8QVU 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    'P 2yb' 
_symmetry.space_group_name_H-M     'P 1 21 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,G,K,L,M,P,Q,R,V 1 1 
D,E,F,H,I,J,N,O,S,T,U,W 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
? 7 L N N 
? 7 N 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 G OG SER 17 E SER 17 1_555 M MG MG . E MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.992 ? 
metalc ? metalc2 G OD1 ASP 57 E ASP 57 1_555 M MG MG . E MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.746 ? 
metalc ? metalc3 G OD2 ASP 57 E ASP 57 1_555 M MG MG . E MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.725 ? 
metalc ? metalc4 L O2B GDP . E GDP 202 1_555 M MG MG . E MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.658 ? 
metalc ? metalc5 H OG SER 17 A SER 17 1_555 O MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.839 ? 
metalc ? metalc6 N O1B GDP . A GDP 201 1_555 O MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.244 ? 
#
_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                     8QVU 
_atom_sites.fract_transf_matrix[1][1]    0.01384 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.0055 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.008271 
_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]    0.013282 
_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 PO4 B 1 301 300 PO4 PO4 . 
J 6 WYL B 1 302 200 WYL LIG . 
K 6 WYL E 1 201 200 WYL LIG . 
L 7 GDP E 1 202 201 GDP GDP . 
M 8 MG E 1 203 301 MG MG . 
N 7 GDP A 1 201 201 GDP GDP . 
O 8 MG A 1 202 202 MG MG . 
P 9 HOH H 1 201 52 HOH HOH . 
Q 9 HOH G 1 201 54 HOH HOH . 
Q 9 HOH G 2 202 65 HOH HOH . 
Q 9 HOH G 3 203 32 HOH HOH . 
Q 9 HOH G 4 204 55 HOH HOH . 
Q 9 HOH G 5 205 30 HOH HOH . 
Q 9 HOH G 6 206 53 HOH HOH . 
Q 9 HOH G 7 207 21 HOH HOH . 
Q 9 HOH G 8 208 48 HOH HOH . 
R 9 HOH F 1 301 22 HOH HOH . 
R 9 HOH F 2 302 20 HOH HOH . 
R 9 HOH F 3 303 57 HOH HOH . 
R 9 HOH F 4 304 10 HOH HOH . 
R 9 HOH F 5 305 59 HOH HOH . 
R 9 HOH F 6 306 24 HOH HOH . 
R 9 HOH F 7 307 44 HOH HOH . 
R 9 HOH F 8 308 23 HOH HOH . 
R 9 HOH F 9 309 29 HOH HOH . 
R 9 HOH F 10 310 8 HOH HOH . 
R 9 HOH F 11 311 12 HOH HOH . 
R 9 HOH F 12 312 40 HOH HOH . 
R 9 HOH F 13 313 56 HOH HOH . 
R 9 HOH F 14 314 37 HOH HOH . 
R 9 HOH F 15 315 11 HOH HOH . 
R 9 HOH F 16 316 58 HOH HOH . 
R 9 HOH F 17 317 7 HOH HOH . 
R 9 HOH F 18 318 9 HOH HOH . 
R 9 HOH F 19 319 49 HOH HOH . 
S 9 HOH D 1 201 60 HOH HOH . 
S 9 HOH D 2 202 35 HOH HOH . 
S 9 HOH D 3 203 18 HOH HOH . 
T 9 HOH C 1 201 36 HOH HOH . 
T 9 HOH C 2 202 13 HOH HOH . 
T 9 HOH C 3 203 61 HOH HOH . 
T 9 HOH C 4 204 62 HOH HOH . 
T 9 HOH C 5 205 28 HOH HOH . 
T 9 HOH C 6 206 14 HOH HOH . 
T 9 HOH C 7 207 51 HOH HOH . 
T 9 HOH C 8 208 15 HOH HOH . 
U 9 HOH B 1 401 26 HOH HOH . 
U 9 HOH B 2 402 34 HOH HOH . 
U 9 HOH B 3 403 31 HOH HOH . 
U 9 HOH B 4 404 47 HOH HOH . 
U 9 HOH B 5 405 27 HOH HOH . 
U 9 HOH B 6 406 66 HOH HOH . 
U 9 HOH B 7 407 17 HOH HOH . 
U 9 HOH B 8 408 33 HOH HOH . 
U 9 HOH B 9 409 64 HOH HOH . 
U 9 HOH B 10 410 16 HOH HOH . 
U 9 HOH B 11 411 42 HOH HOH . 
U 9 HOH B 12 412 46 HOH HOH . 
U 9 HOH B 13 413 63 HOH HOH . 
U 9 HOH B 14 414 50 HOH HOH . 
V 9 HOH E 1 301 6 HOH HOH . 
V 9 HOH E 2 302 1 HOH HOH . 
V 9 HOH E 3 303 3 HOH HOH . 
V 9 HOH E 4 304 4 HOH HOH . 
V 9 HOH E 5 305 43 HOH HOH . 
V 9 HOH E 6 306 5 HOH HOH . 
V 9 HOH E 7 307 25 HOH HOH . 
V 9 HOH E 8 308 39 HOH HOH . 
V 9 HOH E 9 309 38 HOH HOH . 
V 9 HOH E 10 310 45 HOH HOH . 
W 9 HOH A 1 301 41 HOH HOH . 
W 9 HOH A 2 302 19 HOH HOH . 
W 9 HOH A 3 303 2 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 7 -15.886 57.083 -5.074 1 94.26 ? PB GDP 202 E 1 
HETATM 2 O O1B GDP . . . L 7 -14.592 56.369 -5.341 1 78.89 ? O1B GDP 202 E 1 
HETATM 3 O O2B GDP . . . L 7 -17.067 56.176 -4.92 1 84.63 ? O2B GDP 202 E 1 
HETATM 4 O O3B GDP . . . L 7 -15.815 58.126 -3.992 1 78.92 ? O3B GDP 202 E 1 
HETATM 5 O O3A GDP . . . L 7 -16.158 57.888 -6.44 1 83.78 ? O3A GDP 202 E 1 
HETATM 6 P PA GDP . . . L 7 -17.624 58.239 -6.997 1 80.91 ? PA GDP 202 E 1 
HETATM 7 O O1A GDP . . . L 7 -18.173 57.079 -7.775 1 63.45 ? O1A GDP 202 E 1 
HETATM 8 O O2A GDP . . . L 7 -18.444 58.874 -5.904 1 75.66 ? O2A GDP 202 E 1 
HETATM 9 O O5' GDP . . . L 7 -17.266 59.371 -8.066 1 85.46 ? O5' GDP 202 E 1 
HETATM 10 C C5' GDP . . . L 7 -16.028 59.305 -8.76 1 81.11 ? C5' GDP 202 E 1 
HETATM 11 C C4' GDP . . . L 7 -16.113 60.134 -10.025 1 98.16 ? C4' GDP 202 E 1 
HETATM 12 O O4' GDP . . . L 7 -15.465 59.439 -11.087 1 95.21 ? O4' GDP 202 E 1 
HETATM 13 C C3' GDP . . . L 7 -17.559 60.351 -10.434 1 104.04 ? C3' GDP 202 E 1 
HETATM 14 O O3' GDP . . . L 7 -17.776 61.735 -10.702 1 103.31 ? O3' GDP 202 E 1 
HETATM 15 C C2' GDP . . . L 7 -17.744 59.588 -11.718 1 86.3 ? C2' GDP 202 E 1 
HETATM 16 O O2' GDP . . . L 7 -18.469 60.396 -12.641 1 88.73 ? O2' GDP 202 E 1 
HETATM 17 C C1' GDP . . . L 7 -16.333 59.353 -12.213 1 89.8 ? C1' GDP 202 E 1 
HETATM 18 N N9 GDP . . . L 7 -16.23 58.011 -12.809 1 97.91 ? N9 GDP 202 E 1 
HETATM 19 C C8 GDP . . . L 7 -16.423 56.84 -12.187 1 98.07 ? C8 GDP 202 E 1 
HETATM 20 N N7 GDP . . . L 7 -16.248 55.798 -13.032 1 89.67 ? N7 GDP 202 E 1 
HETATM 21 C C5 GDP . . . L 7 -15.936 56.32 -14.225 1 93.18 ? C5 GDP 202 E 1 
HETATM 22 C C6 GDP . . . L 7 -15.615 55.799 -15.56 1 91.76 ? C6 GDP 202 E 1 
HETATM 23 O O6 GDP . . . L 7 -15.597 54.577 -15.767 1 99.75 ? O6 GDP 202 E 1 
HETATM 24 N N1 GDP . . . L 7 -15.336 56.673 -16.525 1 81.96 ? N1 GDP 202 E 1 
HETATM 25 C C2 GDP . . . L 7 -15.343 57.995 -16.323 1 80.62 ? C2 GDP 202 E 1 
HETATM 26 N N2 GDP . . . L 7 -15.052 58.814 -17.354 1 86.4 ? N2 GDP 202 E 1 
HETATM 27 N N3 GDP . . . L 7 -15.625 58.551 -15.129 1 89.41 ? N3 GDP 202 E 1 
HETATM 28 C C4 GDP . . . L 7 -15.918 57.775 -14.069 1 97.11 ? C4 GDP 202 E 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           226 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           28 
#