data_1U0L
#
_model_server_result.job_id            r3RSxDJuMyXIzk_dGktDWw 
_model_server_result.datetime_utc      '2024-10-11 06:22:03' 
_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          1u0l 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"G","auth_seq_id":599}' 
#
_entry.id    1U0L 
#
_exptl.entry_id    1U0L 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              443.201 
_entity.id                          3 
_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          105.72 
_cell.angle_gamma         90 
_cell.entry_id            1U0L 
_cell.length_a            142.819 
_cell.length_b            114.798 
_cell.length_c            77.088 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1U0L 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 1 2 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
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
? monomeric 1 author_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,D,E,J 1 1 
B,F,G,K 2 1 
C,H,I,L 3 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
? 3 E N N 
? 3 G N N 
? 3 I 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 SG CYS 256 A CYS 250 1_555 D ZN ZN . A ZN 298 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.259 ? 
metalc ? metalc2 A SG CYS 261 A CYS 255 1_555 D ZN ZN . A ZN 298 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.315 ? 
metalc ? metalc3 A ND1 HIS 263 A HIS 257 1_555 D ZN ZN . A ZN 298 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.388 ? 
metalc ? metalc4 A SG CYS 269 A CYS 263 1_555 D ZN ZN . A ZN 298 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.38 ? 
metalc ? metalc5 B SG CYS 256 B CYS 550 1_555 F ZN ZN . B ZN 598 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.461 ? 
metalc ? metalc6 B SG CYS 261 B CYS 555 1_555 F ZN ZN . B ZN 598 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.48 ? 
metalc ? metalc7 B ND1 HIS 263 B HIS 557 1_555 F ZN ZN . B ZN 598 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.217 ? 
metalc ? metalc8 B SG CYS 269 B CYS 563 1_555 F ZN ZN . B ZN 598 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? 
metalc ? metalc9 C SG CYS 256 C CYS 850 1_555 H ZN ZN . C ZN 898 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.426 ? 
metalc ? metalc10 C SG CYS 261 C CYS 855 1_555 H ZN ZN . C ZN 898 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.346 ? 
metalc ? metalc11 C ND1 HIS 263 C HIS 857 1_555 H ZN ZN . C ZN 898 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.278 ? 
metalc ? metalc12 C SG CYS 269 C CYS 863 1_555 H ZN ZN . C ZN 898 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.28 ? 
#
_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                     1U0L 
_atom_sites.fract_transf_matrix[1][1]    0.007002 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.001971 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.008711 
_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]    0.013476 
_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
D 2 ZN A 1 298 298 ZN ZN . 
E 3 GDP A 1 299 299 GDP GDP . 
F 2 ZN B 1 598 598 ZN ZN . 
G 3 GDP B 1 599 599 GDP GDP . 
H 2 ZN C 1 898 898 ZN ZN . 
I 3 GDP C 1 899 899 GDP GDP . 
J 4 HOH A 1 300 1 HOH TIP . 
J 4 HOH A 2 301 3 HOH TIP . 
J 4 HOH A 3 302 4 HOH TIP . 
J 4 HOH A 4 303 7 HOH TIP . 
J 4 HOH A 5 304 10 HOH TIP . 
J 4 HOH A 6 305 11 HOH TIP . 
J 4 HOH A 7 306 13 HOH TIP . 
J 4 HOH A 8 307 15 HOH TIP . 
J 4 HOH A 9 308 16 HOH TIP . 
J 4 HOH A 10 309 17 HOH TIP . 
J 4 HOH A 11 310 19 HOH TIP . 
J 4 HOH A 12 311 20 HOH TIP . 
J 4 HOH A 13 312 21 HOH TIP . 
J 4 HOH A 14 313 23 HOH TIP . 
J 4 HOH A 15 314 27 HOH TIP . 
J 4 HOH A 16 315 31 HOH TIP . 
J 4 HOH A 17 316 35 HOH TIP . 
J 4 HOH A 18 317 43 HOH TIP . 
J 4 HOH A 19 318 47 HOH TIP . 
J 4 HOH A 20 319 48 HOH TIP . 
J 4 HOH A 21 320 50 HOH TIP . 
J 4 HOH A 22 321 53 HOH TIP . 
K 4 HOH B 1 5 5 HOH TIP . 
K 4 HOH B 2 6 6 HOH TIP . 
K 4 HOH B 3 8 8 HOH TIP . 
K 4 HOH B 4 25 25 HOH TIP . 
K 4 HOH B 5 28 28 HOH TIP . 
K 4 HOH B 6 34 34 HOH TIP . 
K 4 HOH B 7 36 36 HOH TIP . 
K 4 HOH B 8 38 38 HOH TIP . 
K 4 HOH B 9 39 39 HOH TIP . 
K 4 HOH B 10 42 42 HOH TIP . 
K 4 HOH B 11 45 45 HOH TIP . 
K 4 HOH B 12 46 46 HOH TIP . 
K 4 HOH B 13 49 49 HOH TIP . 
K 4 HOH B 14 52 52 HOH TIP . 
K 4 HOH B 15 54 54 HOH TIP . 
K 4 HOH B 16 56 56 HOH TIP . 
L 4 HOH C 1 2 2 HOH TIP . 
L 4 HOH C 2 9 9 HOH TIP . 
L 4 HOH C 3 12 12 HOH TIP . 
L 4 HOH C 4 14 14 HOH TIP . 
L 4 HOH C 5 18 18 HOH TIP . 
L 4 HOH C 6 22 22 HOH TIP . 
L 4 HOH C 7 24 24 HOH TIP . 
L 4 HOH C 8 26 26 HOH TIP . 
L 4 HOH C 9 29 29 HOH TIP . 
L 4 HOH C 10 30 30 HOH TIP . 
L 4 HOH C 11 32 32 HOH TIP . 
L 4 HOH C 12 33 33 HOH TIP . 
L 4 HOH C 13 37 37 HOH TIP . 
L 4 HOH C 14 40 40 HOH TIP . 
L 4 HOH C 15 41 41 HOH TIP . 
L 4 HOH C 16 44 44 HOH TIP . 
L 4 HOH C 17 51 51 HOH TIP . 
L 4 HOH C 18 55 55 HOH TIP . 
#
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 . . . G 3 95.104 57.645 27.683 1 30.12 ? PB GDP 599 B 1 
HETATM 2 O O1B GDP . . . G 3 94.139 56.616 27.175 1 26.2 ? O1B GDP 599 B 1 
HETATM 3 O O2B GDP . . . G 3 94.472 58.966 28.111 1 26.72 ? O2B GDP 599 B 1 
HETATM 4 O O3B GDP . . . G 3 96.29 57.874 26.699 1 24.46 ? O3B GDP 599 B 1 
HETATM 5 O O3A GDP . . . G 3 95.736 57.011 29.109 1 33.51 ? O3A GDP 599 B 1 
HETATM 6 P PA GDP . . . G 3 97.194 56.534 29.473 1 33.03 ? PA GDP 599 B 1 
HETATM 7 O O1A GDP . . . G 3 98.126 57.683 29.611 1 28.56 ? O1A GDP 599 B 1 
HETATM 8 O O2A GDP . . . G 3 97.649 55.484 28.485 1 33.08 ? O2A GDP 599 B 1 
HETATM 9 O O5' GDP . . . G 3 96.953 55.796 30.893 1 33.63 ? O5' GDP 599 B 1 
HETATM 10 C C5' GDP . . . G 3 96.518 56.535 32.047 1 38.7 ? C5' GDP 599 B 1 
HETATM 11 C C4' GDP . . . G 3 96.953 55.819 33.318 1 40.93 ? C4' GDP 599 B 1 
HETATM 12 O O4' GDP . . . G 3 96.611 54.398 33.176 1 40.77 ? O4' GDP 599 B 1 
HETATM 13 C C3' GDP . . . G 3 98.482 55.909 33.647 1 42.32 ? C3' GDP 599 B 1 
HETATM 14 O O3' GDP . . . G 3 98.608 56.05 35.128 1 43.88 ? O3' GDP 599 B 1 
HETATM 15 C C2' GDP . . . G 3 99.003 54.577 33.189 1 40.58 ? C2' GDP 599 B 1 
HETATM 16 O O2' GDP . . . G 3 100.189 54.251 33.849 1 43.11 ? O2' GDP 599 B 1 
HETATM 17 C C1' GDP . . . G 3 97.766 53.647 33.402 1 40.16 ? C1' GDP 599 B 1 
HETATM 18 N N9 GDP . . . G 3 97.78 52.444 32.41 1 38.56 ? N9 GDP 599 B 1 
HETATM 19 C C8 GDP . . . G 3 97.85 52.533 31.057 1 38.52 ? C8 GDP 599 B 1 
HETATM 20 N N7 GDP . . . G 3 97.85 51.313 30.501 1 38.12 ? N7 GDP 599 B 1 
HETATM 21 C C5 GDP . . . G 3 97.777 50.422 31.566 1 40.59 ? C5 GDP 599 B 1 
HETATM 22 C C6 GDP . . . G 3 97.744 48.99 31.58 1 41.26 ? C6 GDP 599 B 1 
HETATM 23 O O6 GDP . . . G 3 97.787 48.243 30.582 1 42.05 ? O6 GDP 599 B 1 
HETATM 24 N N1 GDP . . . G 3 97.666 48.441 32.886 1 40.46 ? N1 GDP 599 B 1 
HETATM 25 C C2 GDP . . . G 3 97.619 49.229 34.036 1 41.62 ? C2 GDP 599 B 1 
HETATM 26 N N2 GDP . . . G 3 97.545 48.602 35.223 1 42.07 ? N2 GDP 599 B 1 
HETATM 27 N N3 GDP . . . G 3 97.651 50.589 34.013 1 40.34 ? N3 GDP 599 B 1 
HETATM 28 C C4 GDP . . . G 3 97.724 51.108 32.755 1 39.97 ? C4 GDP 599 B 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           20 
_model_server_stats.create_model_time_ms    8 
_model_server_stats.query_time_ms           310 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           28 
#