data_5IZK
#
_model_server_result.job_id            uPSMefpJbQUbNB3H5i00zQ 
_model_server_result.datetime_utc      '2024-11-22 08:59:48' 
_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          5izk 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":1001}' 
#
_entry.id    5IZK 
#
_exptl.entry_id    5IZK 
_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          90.25 
_cell.angle_gamma         90 
_cell.entry_id            5IZK 
_cell.length_a            58.691 
_cell.length_b            96.861 
_cell.length_c            125.408 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5IZK 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_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
PISA monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 author_and_software_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                     5IZK 
_atom_sites.fract_transf_matrix[1][1]    0.017038 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000074 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.010324 
_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]    0.007974 
_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 1001 1001 GDP GDP . 
D 2 GDP B 1 1001 1001 GDP GDP . 
E 3 HOH A 1 1101 9 HOH HOH . 
E 3 HOH A 2 1102 4 HOH HOH . 
E 3 HOH A 3 1103 19 HOH HOH . 
E 3 HOH A 4 1104 10 HOH HOH . 
E 3 HOH A 5 1105 14 HOH HOH . 
E 3 HOH A 6 1106 11 HOH HOH . 
E 3 HOH A 7 1107 3 HOH HOH . 
E 3 HOH A 8 1108 6 HOH HOH . 
E 3 HOH A 9 1109 5 HOH HOH . 
E 3 HOH A 10 1110 7 HOH HOH . 
E 3 HOH A 11 1111 1 HOH HOH . 
E 3 HOH A 12 1112 20 HOH HOH . 
E 3 HOH A 13 1113 2 HOH HOH . 
E 3 HOH A 14 1114 8 HOH HOH . 
E 3 HOH A 15 1115 15 HOH HOH . 
F 3 HOH B 1 1101 17 HOH HOH . 
F 3 HOH B 2 1102 12 HOH HOH . 
F 3 HOH B 3 1103 21 HOH HOH . 
F 3 HOH B 4 1104 13 HOH HOH . 
F 3 HOH B 5 1105 16 HOH HOH . 
F 3 HOH B 6 1106 18 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 . . . D 2 -0.015 -17.621 222.531 1 148.12 ? PB GDP 1001 B 1 
HETATM 2 O O1B GDP . . . D 2 0.031 -16.372 221.738 1 154.57 ? O1B GDP 1001 B 1 
HETATM 3 O O2B GDP . . . D 2 0.624 -18.776 221.887 1 158.28 ? O2B GDP 1001 B 1 
HETATM 4 O O3B GDP . . . D 2 -1.301 -17.876 223.194 1 148.08 ? O3B GDP 1001 B 1 
HETATM 5 O O3A GDP . . . D 2 0.966 -17.262 223.727 1 139.72 ? O3A GDP 1001 B 1 
HETATM 6 P PA GDP . . . D 2 0.42 -16.43 224.993 1 131.88 ? PA GDP 1001 B 1 
HETATM 7 O O1A GDP . . . D 2 0.2 -15.032 224.565 1 129.28 ? O1A GDP 1001 B 1 
HETATM 8 O O2A GDP . . . D 2 -0.693 -17.192 225.599 1 135.62 ? O2A GDP 1001 B 1 
HETATM 9 O O5' GDP . . . D 2 1.683 -16.477 225.985 1 138.54 ? O5' GDP 1001 B 1 
HETATM 10 C C5' GDP . . . D 2 1.559 -17.085 227.274 1 128.3 ? C5' GDP 1001 B 1 
HETATM 11 C C4' GDP . . . D 2 2.718 -16.635 228.165 1 135.9 ? C4' GDP 1001 B 1 
HETATM 12 O O4' GDP . . . D 2 2.57 -15.242 228.476 1 130.81 ? O4' GDP 1001 B 1 
HETATM 13 C C3' GDP . . . D 2 2.618 -17.325 229.516 1 135.87 ? C3' GDP 1001 B 1 
HETATM 14 O O3' GDP . . . D 2 3.526 -18.435 229.554 1 148.16 ? O3' GDP 1001 B 1 
HETATM 15 C C2' GDP . . . D 2 3.068 -16.265 230.508 1 137 ? C2' GDP 1001 B 1 
HETATM 16 O O2' GDP . . . D 2 4.262 -16.707 231.171 1 122.5 ? O2' GDP 1001 B 1 
HETATM 17 C C1' GDP . . . D 2 3.386 -15.058 229.641 1 134.52 ? C1' GDP 1001 B 1 
HETATM 18 N N9 GDP . . . D 2 3.001 -13.801 230.32 1 134.02 ? N9 GDP 1001 B 1 
HETATM 19 C C8 GDP . . . D 2 1.918 -13.076 230.058 1 126.6 ? C8 GDP 1001 B 1 
HETATM 20 N N7 GDP . . . D 2 1.923 -12.027 230.874 1 128.52 ? N7 GDP 1001 B 1 
HETATM 21 C C5 GDP . . . D 2 3.008 -12.102 231.64 1 134.56 ? C5 GDP 1001 B 1 
HETATM 22 C C6 GDP . . . D 2 3.459 -11.301 232.603 1 132.64 ? C6 GDP 1001 B 1 
HETATM 23 O O6 GDP . . . D 2 2.839 -10.286 232.917 1 126.98 ? O6 GDP 1001 B 1 
HETATM 24 N N1 GDP . . . D 2 4.648 -11.616 233.264 1 134.73 ? N1 GDP 1001 B 1 
HETATM 25 C C2 GDP . . . D 2 5.328 -12.773 232.885 1 142.1 ? C2 GDP 1001 B 1 
HETATM 26 N N2 GDP . . . D 2 6.465 -13.112 233.486 1 153.41 ? N2 GDP 1001 B 1 
HETATM 27 N N3 GDP . . . D 2 4.824 -13.539 231.909 1 144.63 ? N3 GDP 1001 B 1 
HETATM 28 C C4 GDP . . . D 2 3.678 -13.204 231.297 1 142.28 ? C4 GDP 1001 B 1 
#
_model_server_stats.io_time_ms              74 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           296 
_model_server_stats.encode_time_ms          13 
_model_server_stats.element_count           28 
#