data_8VWN
#
_model_server_result.job_id            bgYDqrqJKAo4BUsGR8wGkw 
_model_server_result.datetime_utc      '2024-11-28 05:43:41' 
_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          8vwn 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"G","auth_seq_id":301}' 
#
_entry.id    8VWN 
#
_exptl.entry_id    8VWN 
_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    4 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          95.88 
_cell.angle_gamma         90 
_cell.entry_id            8VWN 
_cell.length_a            194.27 
_cell.length_b            155.309 
_cell.length_c            50.916 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8VWN 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    'C 2y' 
_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 
? monomeric 1 author_defined_assembly 4 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,E,F,L 1 1 
B,G,H,M 2 1 
C,I 3 1 
D,J,K,N 4 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 E N N 
? 2 G N N 
? 2 I N N 
? 2 J 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 F MG MG . A MG 302 1_555 L O HOH . A HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? 
metalc ? metalc2 F MG MG . A MG 302 1_555 L O HOH . A HOH 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? 
metalc ? metalc3 F MG MG . A MG 302 1_555 L O HOH . A HOH 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? 
metalc ? metalc4 F MG MG . A MG 302 1_555 L O HOH . A HOH 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? 
metalc ? metalc5 F MG MG . A MG 302 1_555 L O HOH . A HOH 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? 
metalc ? metalc6 F MG MG . A MG 302 1_555 L O HOH . A HOH 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? 
metalc ? metalc7 H MG MG . B MG 302 1_555 M O HOH . B HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? 
metalc ? metalc8 H MG MG . B MG 302 1_555 M O HOH . B HOH 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? 
metalc ? metalc9 H MG MG . B MG 302 1_555 M O HOH . B HOH 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? 
metalc ? metalc10 H MG MG . B MG 302 1_555 M O HOH . B HOH 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? 
metalc ? metalc11 H MG MG . B MG 302 1_555 M O HOH . B HOH 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? 
metalc ? metalc12 H MG MG . B MG 302 1_555 M O HOH . B HOH 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? 
metalc ? metalc13 K MG MG . D MG 302 1_555 N O HOH . D HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? 
metalc ? metalc14 K MG MG . D MG 302 1_555 N O HOH . D HOH 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? 
metalc ? metalc15 K MG MG . D MG 302 1_555 N O HOH . D HOH 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? 
metalc ? metalc16 K MG MG . D MG 302 1_555 N O HOH . D HOH 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? 
metalc ? metalc17 K MG MG . D MG 302 1_555 N O HOH . D HOH 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? 
metalc ? metalc18 K MG MG . D MG 302 1_555 N O HOH . D HOH 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? 
#
_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                     8VWN 
_atom_sites.fract_transf_matrix[1][1]    0.005147 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.00053 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.006439 
_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]    0.019744 
_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
E 2 GDP A 1 301 1 GDP GDP . 
F 3 MG A 1 302 1 MG MO6 . 
G 2 GDP B 1 301 2 GDP GDP . 
H 3 MG B 1 302 2 MG MO6 . 
I 2 GDP C 1 301 3 GDP GDP . 
J 2 GDP D 1 301 4 GDP GDP . 
K 3 MG D 1 302 3 MG MO6 . 
L 4 HOH A 1 401 1 HOH MO6 . 
L 4 HOH A 2 402 1 HOH MO6 . 
L 4 HOH A 3 403 1 HOH MO6 . 
L 4 HOH A 4 404 1 HOH MO6 . 
L 4 HOH A 5 405 1 HOH MO6 . 
L 4 HOH A 6 406 1 HOH MO6 . 
M 4 HOH B 1 401 2 HOH MO6 . 
M 4 HOH B 2 402 2 HOH MO6 . 
M 4 HOH B 3 403 2 HOH MO6 . 
M 4 HOH B 4 404 2 HOH MO6 . 
M 4 HOH B 5 405 2 HOH MO6 . 
M 4 HOH B 6 406 2 HOH MO6 . 
M 4 HOH B 7 407 1 HOH HOH . 
N 4 HOH D 1 401 3 HOH MO6 . 
N 4 HOH D 2 402 3 HOH MO6 . 
N 4 HOH D 3 403 3 HOH MO6 . 
N 4 HOH D 4 404 3 HOH MO6 . 
N 4 HOH D 5 405 3 HOH MO6 . 
N 4 HOH D 6 406 3 HOH MO6 . 
#
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 2 61.398 -1.314 -26.691 1 176.89 ? PB GDP 301 B 1 
HETATM 2 O O1B GDP . . . G 2 61.741 -0.512 -27.926 1 172.61 ? O1B GDP 301 B 1 
HETATM 3 O O2B GDP . . . G 2 60.612 -2.572 -26.979 1 154.18 ? O2B GDP 301 B 1 
HETATM 4 O O3B GDP . . . G 2 60.86 -0.469 -25.561 1 162.38 ? O3B GDP 301 B 1 
HETATM 5 O O3A GDP . . . G 2 62.815 -1.811 -26.1 1 151.3 ? O3A GDP 301 B 1 
HETATM 6 P PA GDP . . . G 2 63.988 -2.438 -27.01 1 143.33 ? PA GDP 301 B 1 
HETATM 7 O O1A GDP . . . G 2 63.547 -2.468 -28.454 1 171.39 ? O1A GDP 301 B 1 
HETATM 8 O O2A GDP . . . G 2 64.442 -3.718 -26.354 1 140.43 ? O2A GDP 301 B 1 
HETATM 9 O O5' GDP . . . G 2 65.179 -1.364 -26.874 1 147.22 ? O5' GDP 301 B 1 
HETATM 10 C C5' GDP . . . G 2 66.473 -1.821 -26.494 1 154.36 ? C5' GDP 301 B 1 
HETATM 11 C C4' GDP . . . G 2 67.589 -1.16 -27.289 1 157.16 ? C4' GDP 301 B 1 
HETATM 12 O O4' GDP . . . G 2 68.619 -0.797 -26.371 1 154.01 ? O4' GDP 301 B 1 
HETATM 13 C C3' GDP . . . G 2 68.176 -2.166 -28.266 1 163.45 ? C3' GDP 301 B 1 
HETATM 14 O O3' GDP . . . G 2 68.317 -1.58 -29.565 1 175.03 ? O3' GDP 301 B 1 
HETATM 15 C C2' GDP . . . G 2 69.539 -2.54 -27.719 1 157.72 ? C2' GDP 301 B 1 
HETATM 16 O O2' GDP . . . G 2 70.542 -2.37 -28.725 1 150.28 ? O2' GDP 301 B 1 
HETATM 17 C C1' GDP . . . G 2 69.791 -1.592 -26.558 1 157.59 ? C1' GDP 301 B 1 
HETATM 18 N N9 GDP . . . G 2 70.053 -2.361 -25.316 1 162.25 ? N9 GDP 301 B 1 
HETATM 19 C C8 GDP . . . G 2 69.135 -3.054 -24.616 1 158.51 ? C8 GDP 301 B 1 
HETATM 20 N N7 GDP . . . G 2 69.689 -3.646 -23.529 1 160.22 ? N7 GDP 301 B 1 
HETATM 21 C C5 GDP . . . G 2 70.998 -3.33 -23.524 1 164.91 ? C5 GDP 301 B 1 
HETATM 22 C C6 GDP . . . G 2 72.164 -3.623 -22.658 1 164.78 ? C6 GDP 301 B 1 
HETATM 23 O O6 GDP . . . G 2 72.049 -4.335 -21.637 1 161.3 ? O6 GDP 301 B 1 
HETATM 24 N N1 GDP . . . G 2 73.349 -3.101 -23.004 1 168.75 ? N1 GDP 301 B 1 
HETATM 25 C C2 GDP . . . G 2 73.508 -2.331 -24.1 1 172.88 ? C2 GDP 301 B 1 
HETATM 26 N N2 GDP . . . G 2 74.742 -1.843 -24.38 1 173.31 ? N2 GDP 301 B 1 
HETATM 27 N N3 GDP . . . G 2 72.484 -2.022 -24.937 1 172.22 ? N3 GDP 301 B 1 
HETATM 28 C C4 GDP . . . G 2 71.232 -2.485 -24.704 1 167.86 ? C4 GDP 301 B 1 
#
_model_server_stats.io_time_ms              15 
_model_server_stats.parse_time_ms           34 
_model_server_stats.create_model_time_ms    65 
_model_server_stats.query_time_ms           368 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           28 
#