data_6MZG
#
_model_server_result.job_id            iTY3wB-HD-MjrSmp3g6vIA 
_model_server_result.datetime_utc      '2025-01-03 03:40:00' 
_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          6mzg 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"S","auth_seq_id":600}' 
#
_entry.id    6MZG 
#
_exptl.entry_id    6MZG 
_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    4 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          90.19 
_cell.angle_gamma         90 
_cell.entry_id            6MZG 
_cell.length_a            115.13 
_cell.length_b            194.99 
_cell.length_c            149.57 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6MZG 
_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
? hexameric 6 author_defined_assembly 1 
? hexameric 6 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,E,F,M,N,O,P,Q,R,S,T 1 1 
G,H,I,J,K,L,U,V,W,X,Y,Z,AA,BA 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 O N N 
? 7 S N N 
? 7 W N N 
? 7 AA 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 M O1G GTP . A GTP 600 1_555 N MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.498 ? 
metalc ? metalc2 M O1B GTP . A GTP 600 1_555 N MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.111 ? 
metalc ? metalc3 B OE1 GLN 11 B GLN 11 1_555 P MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.254 ? 
metalc ? metalc4 O O1A GDP . B GDP 600 1_555 P MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.124 ? 
metalc ? metalc5 Q O1G GTP . C GTP 600 1_555 R MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.645 ? 
metalc ? metalc6 Q O1B GTP . C GTP 600 1_555 R MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.266 ? 
metalc ? metalc7 S O1A GDP . D GDP 600 1_555 T MG MG . D MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.349 ? 
metalc ? metalc8 U O3G GTP . G GTP 600 1_555 V MG MG . G MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.106 ? 
metalc ? metalc9 U O2B GTP . G GTP 600 1_555 V MG MG . G MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.6 ? 
metalc ? metalc10 H OD2 ASP 177 H ASP 179 1_555 X MG MG . H MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.884 ? 
metalc ? metalc11 W O2A GDP . H GDP 600 1_555 X MG MG . H MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.544 ? 
metalc ? metalc12 Y O3G GTP . I GTP 600 1_555 Z MG MG . I MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.281 ? 
metalc ? metalc13 Y O2B GTP . I GTP 600 1_555 Z MG MG . I MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.733 ? 
metalc ? metalc14 J OE1 GLN 11 J GLN 11 1_555 BA MG MG . J MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.57 ? 
metalc ? metalc15 AA O2A GDP . J GDP 600 1_555 BA MG MG . J MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.268 ? 
#
_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                     6MZG 
_atom_sites.fract_transf_matrix[1][1]    0.008686 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000029 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.005128 
_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]    0.006686 
_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
M 5 GTP A 1 600 600 GTP GTP . 
N 6 MG A 1 601 601 MG MG . 
O 7 GDP B 1 600 600 GDP GDP . 
P 6 MG B 1 601 601 MG MG . 
Q 5 GTP C 1 600 600 GTP GTP . 
R 6 MG C 1 601 601 MG MG . 
S 7 GDP D 1 600 600 GDP GDP . 
T 6 MG D 1 601 601 MG MG . 
U 5 GTP G 1 600 600 GTP GTP . 
V 6 MG G 1 601 601 MG MG . 
W 7 GDP H 1 600 600 GDP GDP . 
X 6 MG H 1 601 601 MG MG . 
Y 5 GTP I 1 600 600 GTP GTP . 
Z 6 MG I 1 601 601 MG MG . 
AA 7 GDP J 1 600 600 GDP GDP . 
BA 6 MG J 1 601 601 MG MG . 
#
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 . . . S 7 11.841 -87.34 -69.979 1 55.68 ? PB GDP 600 D 1 
HETATM 2 O O1B GDP . . . S 7 12.181 -87.067 -71.426 1 44.48 ? O1B GDP 600 D 1 
HETATM 3 O O2B GDP . . . S 7 11.294 -86.097 -69.318 1 68.55 ? O2B GDP 600 D 1 
HETATM 4 O O3B GDP . . . S 7 13.092 -87.774 -69.26 1 60 ? O3B GDP 600 D 1 
HETATM 5 O O3A GDP . . . S 7 10.778 -88.544 -69.877 1 46.66 ? O3A GDP 600 D 1 
HETATM 6 P PA GDP . . . S 7 9.215 -88.334 -70.19 1 25.41 ? PA GDP 600 D 1 
HETATM 7 O O1A GDP . . . S 7 8.796 -89.236 -71.324 1 29.7 ? O1A GDP 600 D 1 
HETATM 8 O O2A GDP . . . S 7 8.908 -86.889 -70.501 1 25.11 ? O2A GDP 600 D 1 
HETATM 9 O O5' GDP . . . S 7 8.49 -88.78 -68.827 1 21.8 ? O5' GDP 600 D 1 
HETATM 10 C C5' GDP . . . S 7 7.605 -89.893 -68.813 1 33.22 ? C5' GDP 600 D 1 
HETATM 11 C C4' GDP . . . S 7 6.332 -89.503 -68.083 1 34.61 ? C4' GDP 600 D 1 
HETATM 12 O O4' GDP . . . S 7 5.845 -88.307 -68.689 1 20.08 ? O4' GDP 600 D 1 
HETATM 13 C C3' GDP . . . S 7 5.269 -90.573 -68.256 1 46.04 ? C3' GDP 600 D 1 
HETATM 14 O O3' GDP . . . S 7 4.738 -90.937 -66.978 1 51.07 ? O3' GDP 600 D 1 
HETATM 15 C C2' GDP . . . S 7 4.192 -89.955 -69.126 1 40.56 ? C2' GDP 600 D 1 
HETATM 16 O O2' GDP . . . S 7 2.889 -90.197 -68.586 1 48.84 ? O2' GDP 600 D 1 
HETATM 17 C C1' GDP . . . S 7 4.497 -88.468 -69.134 1 32.55 ? C1' GDP 600 D 1 
HETATM 18 N N9 GDP . . . S 7 4.354 -87.908 -70.499 1 46.18 ? N9 GDP 600 D 1 
HETATM 19 C C8 GDP . . . S 7 5.212 -88.078 -71.524 1 49.17 ? C8 GDP 600 D 1 
HETATM 20 N N7 GDP . . . S 7 4.783 -87.419 -72.631 1 46.78 ? N7 GDP 600 D 1 
HETATM 21 C C5 GDP . . . S 7 3.627 -86.807 -72.311 1 52.63 ? C5 GDP 600 D 1 
HETATM 22 C C6 GDP . . . S 7 2.643 -85.946 -73.008 1 63.01 ? C6 GDP 600 D 1 
HETATM 23 O O6 GDP . . . S 7 2.807 -85.627 -74.206 1 64.51 ? O6 GDP 600 D 1 
HETATM 24 N N1 GDP . . . S 7 1.575 -85.522 -72.314 1 61.38 ? N1 GDP 600 D 1 
HETATM 25 C C2 GDP . . . S 7 1.373 -85.851 -71.023 1 53.28 ? C2 GDP 600 D 1 
HETATM 26 N N2 GDP . . . S 7 0.268 -85.382 -70.392 1 56.38 ? N2 GDP 600 D 1 
HETATM 27 N N3 GDP . . . S 7 2.233 -86.635 -70.325 1 44.31 ? N3 GDP 600 D 1 
HETATM 28 C C4 GDP . . . S 7 3.351 -87.131 -70.905 1 47.34 ? C4 GDP 600 D 1 
#
_model_server_stats.io_time_ms              76 
_model_server_stats.parse_time_ms           18 
_model_server_stats.create_model_time_ms    86 
_model_server_stats.query_time_ms           481 
_model_server_stats.encode_time_ms          12 
_model_server_stats.element_count           28 
#