data_7D72
#
_model_server_result.job_id            ttKs8bV-cks8X0sh8RCHrw 
_model_server_result.datetime_utc      '2024-11-26 12:56:19' 
_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          7d72 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"Q","auth_seq_id":501}' 
#
_entry.id    7D72 
#
_exptl.entry_id    7D72 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              605.341 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE" 
_entity.pdbx_number_of_molecules    12 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          90 
_cell.angle_gamma         90 
_cell.entry_id            7D72 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7D72 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    dodecameric 
_pdbx_struct_assembly.oligomeric_count      12 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    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    ? 
_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 M N N 
? 3 N N N 
? 3 O N N 
? 3 P N N 
? 3 Q N N 
? 3 R N N 
? 3 S N N 
? 3 U N N 
? 3 W N N 
? 3 Y N N 
? 3 Z N N 
? 3 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
disulf ? disulf1 G SG CYS 289 E CYS 289 1_555 G SG CYS 306 E CYS 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf2 I SG CYS 289 G CYS 289 1_555 I SG CYS 306 G CYS 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf3 K SG CYS 289 J CYS 289 1_555 K SG CYS 306 J CYS 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf4 L SG CYS 289 L CYS 289 1_555 L SG CYS 306 L CYS 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
metalc ? metalc1 G OD1 ASP 110 E ASP 110 1_555 T MG MG . E MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? 
metalc ? metalc2 G OD1 ASP 218 E ASP 218 1_555 T MG MG . E MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.82 ? 
metalc ? metalc3 S O2A GDD . E GDD 401 1_555 T MG MG . E MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.45 ? 
metalc ? metalc4 S O3B GDD . E GDD 401 1_555 T MG MG . E MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.126 ? 
metalc ? metalc5 T MG MG . E MG 402 1_555 BA O HOH . E HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.645 ? 
metalc ? metalc6 T MG MG . E MG 402 1_555 BA O HOH . E HOH 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.138 ? 
metalc ? metalc7 H OD1 ASP 110 F ASP 110 1_555 V MG MG . F MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.281 ? 
metalc ? metalc8 U O2A GDD . F GDD 401 1_555 V MG MG . F MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.335 ? 
metalc ? metalc9 U O3B GDD . F GDD 401 1_555 V MG MG . F MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.002 ? 
metalc ? metalc10 V MG MG . F MG 402 1_555 CA O HOH . F HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? 
metalc ? metalc11 V MG MG . F MG 402 1_555 CA O HOH . F HOH 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.689 ? 
metalc ? metalc12 I OD1 ASP 218 G ASP 218 1_555 X MG MG . G MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.413 ? 
metalc ? metalc13 X MG MG . G MG 402 1_555 DA O HOH . G HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.271 ? 
metalc ? metalc14 X MG MG . G MG 402 1_555 DA O HOH . G HOH 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.262 ? 
#
_chem_comp.formula           'C16 H25 N5 O16 P2' 
_chem_comp.formula_weight    605.341 
_chem_comp.id                GDD 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE" 
_chem_comp.type              non-polymer 
_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
N2 C2 GDD sing 83 n n 
N2 H2N1 GDD sing 84 n n 
N2 H2N2 GDD sing 85 n n 
C2 N1 GDD sing 86 n n 
C2 N3 GDD doub 87 n n 
N1 C6 GDD sing 88 n n 
N1 H1 GDD sing 89 n n 
N3 C4 GDD sing 90 n n 
C4 C5 GDD doub 91 n y 
C4 N9 GDD sing 92 n y 
C5 C6 GDD sing 93 n n 
C5 N7 GDD sing 94 n y 
C6 O6 GDD doub 95 n n 
N7 C8 GDD doub 96 n y 
C8 N9 GDD sing 97 n y 
C8 H8 GDD sing 98 n n 
N9 C1' GDD sing 99 n n 
C1' C2' GDD sing 100 n n 
C1' O4' GDD sing 101 n n 
C1' H1' GDD sing 102 n n 
C2' O2' GDD sing 103 n n 
C2' C3' GDD sing 104 n n 
C2' H2' GDD sing 105 n n 
O2' HA GDD sing 106 n n 
C3' O3' GDD sing 107 n n 
C3' C4' GDD sing 108 n n 
C3' H3' GDD sing 109 n n 
O3' HB GDD sing 110 n n 
C4' O4' GDD sing 111 n n 
C4' C5' GDD sing 112 n n 
C4' H4' GDD sing 113 n n 
C5' O5' GDD sing 114 n n 
C5' "H5'1" GDD sing 115 n n 
C5' "H5'2" GDD sing 116 n n 
O5' PA GDD sing 117 n n 
PA O1A GDD doub 118 n n 
PA O2A GDD sing 119 n n 
PA O3A GDD sing 120 n n 
O2A HO2A GDD sing 121 n n 
O3A PB GDD sing 122 n n 
PB O2B GDD sing 123 n n 
PB O3B GDD doub 124 n n 
PB O1B GDD sing 125 n n 
O2B HO2B GDD sing 126 n n 
O1B C11 GDD sing 127 n n 
C11 O51 GDD sing 128 n n 
C11 C21 GDD sing 129 n n 
C11 H11 GDD sing 130 n n 
O51 C51 GDD sing 131 n n 
C51 C61 GDD sing 132 n n 
C51 C41 GDD sing 133 n n 
C51 H51 GDD sing 134 n n 
C61 O6A GDD sing 135 n n 
C61 H611 GDD sing 136 n n 
C61 H612 GDD sing 137 n n 
O6A H6A GDD sing 138 n n 
C21 O21 GDD sing 139 n n 
C21 C31 GDD sing 140 n n 
C21 H21 GDD sing 141 n n 
O21 HC GDD sing 142 n n 
C31 O31 GDD sing 143 n n 
C31 C41 GDD sing 144 n n 
C31 H31 GDD sing 145 n n 
O31 HD GDD sing 146 n n 
C41 O41 GDD sing 147 n n 
C41 H41 GDD sing 148 n n 
O41 HE GDD sing 149 n n 
#
_atom_sites.entry_id                     7D72 
_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
M 3 GDD K 1 401 401 GDD GDD . 
N 3 GDD I 1 401 401 GDD GDD . 
O 3 GDD A 1 501 501 GDD GDD . 
P 3 GDD B 1 501 501 GDD GDD . 
Q 3 GDD C 1 501 501 GDD GDD . 
R 3 GDD D 1 501 501 GDD GDD . 
S 3 GDD E 1 401 401 GDD GDD . 
T 4 MG E 1 402 402 MG MG . 
U 3 GDD F 1 401 401 GDD GDD . 
V 4 MG F 1 402 402 MG MG . 
W 3 GDD G 1 401 401 GDD GDD . 
X 4 MG G 1 402 402 MG MG . 
Y 3 GDD H 1 401 401 GDD GDD . 
Z 3 GDD J 1 401 401 GDD GDD . 
AA 3 GDD L 1 401 401 GDD GDD . 
BA 5 HOH E 1 501 404 HOH HOH . 
BA 5 HOH E 2 502 403 HOH HOH . 
CA 5 HOH F 1 501 403 HOH HOH . 
CA 5 HOH F 2 502 404 HOH HOH . 
DA 5 HOH G 1 501 404 HOH HOH . 
DA 5 HOH G 2 502 403 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 N N2 GDD . . . Q 3 106.389 110.071 124.39 1 30.6 ? N2 GDD 501 C 1 
HETATM 2 C C2 GDD . . . Q 3 106.589 109.339 125.518 1 30.6 ? C2 GDD 501 C 1 
HETATM 3 N N1 GDD . . . Q 3 106.211 109.906 126.689 1 30.6 ? N1 GDD 501 C 1 
HETATM 4 N N3 GDD . . . Q 3 107.12 108.157 125.357 1 30.6 ? N3 GDD 501 C 1 
HETATM 5 C C4 GDD . . . Q 3 107.319 107.423 126.445 1 30.6 ? C4 GDD 501 C 1 
HETATM 6 C C5 GDD . . . Q 3 106.973 107.891 127.688 1 30.6 ? C5 GDD 501 C 1 
HETATM 7 C C6 GDD . . . Q 3 106.415 109.157 127.783 1 30.6 ? C6 GDD 501 C 1 
HETATM 8 O O6 GDD . . . Q 3 106.108 109.571 128.878 1 30.6 ? O6 GDD 501 C 1 
HETATM 9 N N7 GDD . . . Q 3 107.28 106.96 128.605 1 30.6 ? N7 GDD 501 C 1 
HETATM 10 C C8 GDD . . . Q 3 107.812 105.91 127.976 1 30.6 ? C8 GDD 501 C 1 
HETATM 11 N N9 GDD . . . Q 3 107.834 106.196 126.659 1 30.6 ? N9 GDD 501 C 1 
HETATM 12 C C1' GDD . . . Q 3 108.374 105.189 125.766 1 30.6 ? C1' GDD 501 C 1 
HETATM 13 C C2' GDD . . . Q 3 109.627 104.571 126.384 1 30.6 ? C2' GDD 501 C 1 
HETATM 14 O O2' GDD . . . Q 3 110.791 105.159 125.846 1 30.6 ? O2' GDD 501 C 1 
HETATM 15 C C3' GDD . . . Q 3 109.616 103.182 125.784 1 30.6 ? C3' GDD 501 C 1 
HETATM 16 O O3' GDD . . . Q 3 110.309 103.274 124.552 1 30.6 ? O3' GDD 501 C 1 
HETATM 17 C C4' GDD . . . Q 3 108.134 102.902 125.545 1 30.6 ? C4' GDD 501 C 1 
HETATM 18 O O4' GDD . . . Q 3 107.439 104.153 125.673 1 30.6 ? O4' GDD 501 C 1 
HETATM 19 C C5' GDD . . . Q 3 107.667 101.993 126.667 1 30.6 ? C5' GDD 501 C 1 
HETATM 20 O O5' GDD . . . Q 3 107.562 102.796 127.833 1 30.6 ? O5' GDD 501 C 1 
HETATM 21 P PA GDD . . . Q 3 107.517 102.09 129.26 1 30.6 ? PA GDD 501 C 1 
HETATM 22 O O1A GDD . . . Q 3 106.475 102.717 130.091 1 30.6 ? O1A GDD 501 C 1 
HETATM 23 O O2A GDD . . . Q 3 108.945 102.209 129.972 1 30.6 ? O2A GDD 501 C 1 
HETATM 24 O O3A GDD . . . Q 3 107.186 100.549 129.082 1 30.6 ? O3A GDD 501 C 1 
HETATM 25 P PB GDD . . . Q 3 108.007 99.294 129.604 1 30.6 ? PB GDD 501 C 1 
HETATM 26 O O2B GDD . . . Q 3 108.072 99.277 131.202 1 30.6 ? O2B GDD 501 C 1 
HETATM 27 O O3B GDD . . . Q 3 109.346 99.358 129.016 1 30.6 ? O3B GDD 501 C 1 
HETATM 28 O O1B GDD . . . Q 3 107.177 98.05 129.043 1 30.6 ? O1B GDD 501 C 1 
HETATM 29 C C11 GDD . . . Q 3 106.407 98.267 127.871 1 30.6 ? C11 GDD 501 C 1 
HETATM 30 O O51 GDD . . . Q 3 107.066 97.684 126.758 1 30.6 ? O51 GDD 501 C 1 
HETATM 31 C C51 GDD . . . Q 3 107.269 96.292 126.938 1 30.6 ? C51 GDD 501 C 1 
HETATM 32 C C61 GDD . . . Q 3 108.187 95.782 125.842 1 30.6 ? C61 GDD 501 C 1 
HETATM 33 O O6A GDD . . . Q 3 109.247 96.728 125.722 1 30.6 ? O6A GDD 501 C 1 
HETATM 34 C C21 GDD . . . Q 3 105.026 97.659 128.068 1 30.6 ? C21 GDD 501 C 1 
HETATM 35 O O21 GDD . . . Q 3 104.229 98.023 126.953 1 30.6 ? O21 GDD 501 C 1 
HETATM 36 C C31 GDD . . . Q 3 105.1 96.144 128.066 1 30.6 ? C31 GDD 501 C 1 
HETATM 37 O O31 GDD . . . Q 3 103.776 95.677 127.904 1 30.6 ? O31 GDD 501 C 1 
HETATM 38 C C41 GDD . . . Q 3 105.914 95.611 126.899 1 30.6 ? C41 GDD 501 C 1 
HETATM 39 O O41 GDD . . . Q 3 106.074 94.215 127.062 1 30.6 ? O41 GDD 501 C 1 
#
_model_server_stats.io_time_ms              26 
_model_server_stats.parse_time_ms           19 
_model_server_stats.create_model_time_ms    93 
_model_server_stats.query_time_ms           809 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           39 
#