data_5KMG
#
_model_server_result.job_id            MvNIy3fCSvAs_lYkr92KYw 
_model_server_result.datetime_utc      '2025-07-16 11:17:31' 
_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          5kmg 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":501}' 
#
_entry.id    5KMG 
#
_exptl.entry_id    5KMG 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              443.201 
_entity.id                          6 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "GUANOSINE-5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    1 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? 42-meric 42 'representative helical assembly' 1 
? trimeric 3 'helical asymmetric unit' 2 
? trimeric 3 'helical asymmetric unit, std helical frame' 3 
#
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,G 1 (1-14) 
A,B,C,D,E,F,G 2 8 
A,B,C,D,E,F,G 3 H 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
H 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'helical symmetry operation' ? ? -0.898181 0.439626 0 -0.439626 -0.898181 0 0 0 1 492.99173 790.17869 -69.36 
3 'helical symmetry operation' ? ? -0.999984 0.005585 0 -0.005585 -0.999984 0 0 0 1 674.10699 677.88247 -60.69 
4 'helical symmetry operation' ? ? -0.903036 -0.429566 0 0.429566 -0.903036 0 0 0 1 788.41924 498.03284 -52.02 
5 'helical symmetry operation' ? ? -0.626604 -0.779338 0 0.779338 -0.626604 0 0 0 1 813.20832 286.37586 -43.35 
6 'helical symmetry operation' ? ? -0.225631 -0.974213 0 0.974213 -0.225631 0 0 0 1 743.54728 84.97944 -34.68 
7 'helical symmetry operation' ? ? 0.220187 -0.975458 0 0.975458 0.220187 0 0 0 1 593.28161 -66.12783 -26.01 
8 'helical symmetry operation' ? ? 0.622241 -0.782825 0 0.782825 0.622241 0 0 0 1 392.27739 -136.91259 -17.34 
9 'helical symmetry operation' ? ? 0.900622 -0.434602 0 0.434602 0.900622 0 0 0 1 180.48526 -113.306 -8.67 
10 'helical symmetry operation' ? ? 0.900622 0.434602 0 -0.434602 0.900622 0 0 0 1 -113.306 180.48526 8.67 
11 'helical symmetry operation' ? ? 0.622241 0.782825 0 -0.782825 0.622241 0 0 0 1 -136.91259 392.27739 17.34 
12 'helical symmetry operation' ? ? 0.220187 0.975458 0 -0.975458 0.220187 0 0 0 1 -66.12783 593.28161 26.01 
13 'helical symmetry operation' ? ? -0.225631 0.974213 0 -0.974213 -0.225631 0 0 0 1 84.97944 743.54728 34.68 
14 'helical symmetry operation' ? ? -0.626604 0.779338 0 -0.779338 -0.626604 0 0 0 1 286.37586 813.20832 43.35 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      6 
_struct_asym.id                             F 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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 D O1G GTP . A GTP 501 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.564 ? 
metalc ? metalc2 D O1B GTP . A GTP 501 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.895 ? 
#
_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                     5KMG 
_atom_sites.fract_transf_matrix[1][1]    1 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    1 
_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]    1 
_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 4 GTP A 1 501 1 GTP GTP . 
E 5 MG A 1 502 2 MG MG . 
F 6 GDP B 1 501 1 GDP GDP . 
G 7 POU B 1 502 3 POU POU . 
#
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 . . . F 6 351.524 456.869 266.144 1 20 ? PB GDP 501 B 1 
HETATM 2 O O1B GDP . . . F 6 351.221 458.055 265.251 1 20 ? O1B GDP 501 B 1 
HETATM 3 O O2B GDP . . . F 6 351.465 457.344 267.572 1 20 ? O2B GDP 501 B 1 
HETATM 4 O O3B GDP . . . F 6 350.664 455.67 265.903 1 20 ? O3B GDP 501 B 1 
HETATM 5 O O3A GDP . . . F 6 353.074 456.563 265.874 1 20 ? O3A GDP 501 B 1 
HETATM 6 P PA GDP . . . F 6 353.943 455.481 266.683 1 20 ? PA GDP 501 B 1 
HETATM 7 O O1A GDP . . . F 6 354.105 454.218 265.867 1 20 ? O1A GDP 501 B 1 
HETATM 8 O O2A GDP . . . F 6 353.322 455.126 268.004 1 20 ? O2A GDP 501 B 1 
HETATM 9 O O5' GDP . . . F 6 355.224 456.367 266.828 1 20 ? O5' GDP 501 B 1 
HETATM 10 C C5' GDP . . . F 6 356.551 456.022 266.401 1 20 ? C5' GDP 501 B 1 
HETATM 11 C C4' GDP . . . F 6 357.475 455.99 267.617 1 20 ? C4' GDP 501 B 1 
HETATM 12 O O4' GDP . . . F 6 357.094 454.937 268.51 1 20 ? O4' GDP 501 B 1 
HETATM 13 C C3' GDP . . . F 6 358.868 455.64 267.168 1 20 ? C3' GDP 501 B 1 
HETATM 14 O O3' GDP . . . F 6 359.812 456.295 267.999 1 20 ? O3' GDP 501 B 1 
HETATM 15 C C2' GDP . . . F 6 358.982 454.144 267.271 1 20 ? C2' GDP 501 B 1 
HETATM 16 O O2' GDP . . . F 6 360.325 453.696 267.463 1 20 ? O2' GDP 501 B 1 
HETATM 17 C C1' GDP . . . F 6 358.147 453.899 268.488 1 20 ? C1' GDP 501 B 1 
HETATM 18 N N9 GDP . . . F 6 357.455 452.639 268.527 1 20 ? N9 GDP 501 B 1 
HETATM 19 C C8 GDP . . . F 6 356.499 452.152 267.719 1 20 ? C8 GDP 501 B 1 
HETATM 20 N N7 GDP . . . F 6 356.097 450.939 268.189 1 20 ? N7 GDP 501 B 1 
HETATM 21 C C5 GDP . . . F 6 356.797 450.711 269.317 1 20 ? C5 GDP 501 B 1 
HETATM 22 C C6 GDP . . . F 6 356.868 449.649 270.314 1 20 ? C6 GDP 501 B 1 
HETATM 23 O O6 GDP . . . F 6 356.132 448.659 270.203 1 20 ? O6 GDP 501 B 1 
HETATM 24 N N1 GDP . . . F 6 357.722 449.787 271.314 1 20 ? N1 GDP 501 B 1 
HETATM 25 C C2 GDP . . . F 6 358.519 450.836 271.454 1 20 ? C2 GDP 501 B 1 
HETATM 26 N N2 GDP . . . F 6 359.337 450.856 272.528 1 20 ? N2 GDP 501 B 1 
HETATM 27 N N3 GDP . . . F 6 358.526 451.867 270.59 1 20 ? N3 GDP 501 B 1 
HETATM 28 C C4 GDP . . . F 6 357.68 451.825 269.527 1 20 ? C4 GDP 501 B 1 
HETATM 29 H H4' GDP . . . F 6 357.477 456.966 268.125 1 24 ? H4' GDP 501 B 1 
HETATM 30 H H3' GDP . . . F 6 358.998 455.945 266.119 1 24 ? H3' GDP 501 B 1 
HETATM 31 H HO3' GDP . . . F 6 360.692 456.181 267.602 1 24 ? HO3' GDP 501 B 1 
HETATM 32 H H2' GDP . . . F 6 358.523 453.67 266.394 1 24 ? H2' GDP 501 B 1 
HETATM 33 H HO2' GDP . . . F 6 360.927 454.324 267.031 1 24 ? HO2' GDP 501 B 1 
HETATM 34 H H1' GDP . . . F 6 358.782 454.003 269.378 1 24 ? H1' GDP 501 B 1 
HETATM 35 H H8 GDP . . . F 6 356.106 452.643 266.836 1 24 ? H8 GDP 501 B 1 
HETATM 36 H HN1 GDP . . . F 6 357.773 449.035 272.032 1 24 ? HN1 GDP 501 B 1 
HETATM 37 H HN21 GDP . . . F 6 359.145 450.242 273.306 1 24 ? HN21 GDP 501 B 1 
HETATM 38 H HN22 GDP . . . F 6 360.226 451.328 272.474 1 24 ? HN22 GDP 501 B 1 
#
_model_server_stats.io_time_ms              72 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           276 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           38 
#