data_7D73
#
_model_server_result.job_id            qZzsaqw94yEF1sH2YCYdcQ 
_model_server_result.datetime_utc      '2024-11-22 21:13:24' 
_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          7d73 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"M","auth_seq_id":501}' 
#
_entry.id    7D73 
#
_exptl.entry_id    7D73 
_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    2 
_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            7D73 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7D73 
_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 
_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 P 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 I SG CYS 289 J CYS 289 1_555 I SG CYS 306 J CYS 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf2 K SG CYS 289 L CYS 289 1_555 K SG CYS 306 L CYS 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
covale ? covale1 G O ALA 52 G ALA 52 1_555 S N2 GTP . G GTP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.296 ? 
covale ? covale2 J O ALA 52 K ALA 52 1_555 V N2 GTP . K GTP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.295 ? 
covale ? covale3 L O ALA 52 H ALA 52 1_555 X N2 GTP . H GTP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.342 ? 
#
_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     ? 
#
_atom_sites.entry_id                     7D73 
_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 A 1 501 501 GDD GDD . 
N 4 GTP B 1 501 501 GTP GTP . 
O 4 GTP E 1 401 401 GTP GTP . 
P 3 GDD C 1 501 501 GDD GDD . 
Q 4 GTP D 1 501 501 GTP GTP . 
R 4 GTP F 1 401 401 GTP GTP . 
S 4 GTP G 1 401 401 GTP GTP . 
T 4 GTP I 1 401 401 GTP GTP . 
U 4 GTP J 1 401 401 GTP GTP . 
V 4 GTP K 1 401 401 GTP GTP . 
W 4 GTP L 1 401 401 GTP GTP . 
X 4 GTP H 1 401 401 GTP GTP . 
#
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 . . . M 3 149.49 135.548 120.848 1 8.88 ? N2 GDD 501 A 1 
HETATM 2 C C2 GDD . . . M 3 149.004 136.759 120.468 1 8.88 ? C2 GDD 501 A 1 
HETATM 3 N N1 GDD . . . M 3 148.637 137.634 121.444 1 8.88 ? N1 GDD 501 A 1 
HETATM 4 N N3 GDD . . . M 3 148.947 136.953 119.186 1 8.88 ? N3 GDD 501 A 1 
HETATM 5 C C4 GDD . . . M 3 148.481 138.131 118.778 1 8.88 ? C4 GDD 501 A 1 
HETATM 6 C C5 GDD . . . M 3 148.076 139.106 119.667 1 8.88 ? C5 GDD 501 A 1 
HETATM 7 C C6 GDD . . . M 3 148.164 138.824 121.03 1 8.88 ? C6 GDD 501 A 1 
HETATM 8 O O6 GDD . . . M 3 147.808 139.664 121.832 1 8.88 ? O6 GDD 501 A 1 
HETATM 9 N N7 GDD . . . M 3 147.65 140.18 118.969 1 8.88 ? N7 GDD 501 A 1 
HETATM 10 C C8 GDD . . . M 3 147.772 139.911 117.671 1 8.88 ? C8 GDD 501 A 1 
HETATM 11 N N9 GDD . . . M 3 148.283 138.659 117.561 1 8.88 ? N9 GDD 501 A 1 
HETATM 12 C C1' GDD . . . M 3 148.524 138.102 116.247 1 8.88 ? C1' GDD 501 A 1 
HETATM 13 C C2' GDD . . . M 3 147.53 138.689 115.245 1 8.88 ? C2' GDD 501 A 1 
HETATM 14 O O2' GDD . . . M 3 146.434 137.812 115.047 1 8.88 ? O2' GDD 501 A 1 
HETATM 15 C C3' GDD . . . M 3 148.365 138.697 113.973 1 8.88 ? C3' GDD 501 A 1 
HETATM 16 O O3' GDD . . . M 3 148.331 137.386 113.445 1 8.88 ? O3' GDD 501 A 1 
HETATM 17 C C4' GDD . . . M 3 149.776 138.985 114.493 1 8.88 ? C4' GDD 501 A 1 
HETATM 18 O O4' GDD . . . M 3 149.797 138.546 115.862 1 8.88 ? O4' GDD 501 A 1 
HETATM 19 C C5' GDD . . . M 3 150.08 140.477 114.46 1 8.88 ? C5' GDD 501 A 1 
HETATM 20 O O5' GDD . . . M 3 148.919 141.203 114.072 1 8.88 ? O5' GDD 501 A 1 
HETATM 21 P PA GDD . . . M 3 148.711 142.671 114.668 1 8.88 ? PA GDD 501 A 1 
HETATM 22 O O1A GDD . . . M 3 149.358 142.774 115.989 1 8.88 ? O1A GDD 501 A 1 
HETATM 23 O O2A GDD . . . M 3 147.134 142.952 114.784 1 8.88 ? O2A GDD 501 A 1 
HETATM 24 O O3A GDD . . . M 3 149.383 143.737 113.669 1 8.88 ? O3A GDD 501 A 1 
HETATM 25 P PB GDD . . . M 3 149.385 143.847 112.068 1 8.88 ? PB GDD 501 A 1 
HETATM 26 O O2B GDD . . . M 3 148.376 144.983 111.563 1 8.88 ? O2B GDD 501 A 1 
HETATM 27 O O3B GDD . . . M 3 149.075 142.541 111.466 1 8.88 ? O3B GDD 501 A 1 
HETATM 28 O O1B GDD . . . M 3 150.882 144.251 111.701 1 8.88 ? O1B GDD 501 A 1 
HETATM 29 C C11 GDD . . . M 3 151.926 143.295 111.82 1 8.88 ? C11 GDD 501 A 1 
HETATM 30 O O51 GDD . . . M 3 152.002 142.493 110.655 1 8.88 ? O51 GDD 501 A 1 
HETATM 31 C C51 GDD . . . M 3 152.043 143.256 109.45 1 8.88 ? C51 GDD 501 A 1 
HETATM 32 C C61 GDD . . . M 3 152.062 142.279 108.282 1 8.88 ? C61 GDD 501 A 1 
HETATM 33 O O6A GDD . . . M 3 150.716 142.02 107.88 1 8.88 ? O6A GDD 501 A 1 
HETATM 34 C C21 GDD . . . M 3 153.229 144.053 111.953 1 8.88 ? C21 GDD 501 A 1 
HETATM 35 O O21 GDD . . . M 3 154.272 143.089 111.954 1 8.88 ? O21 GDD 501 A 1 
HETATM 36 C C31 GDD . . . M 3 153.462 144.915 110.72 1 8.88 ? C31 GDD 501 A 1 
HETATM 37 O O31 GDD . . . M 3 154.812 145.355 110.822 1 8.88 ? O31 GDD 501 A 1 
HETATM 38 C C41 GDD . . . M 3 153.273 144.156 109.403 1 8.88 ? C41 GDD 501 A 1 
HETATM 39 O O41 GDD . . . M 3 153.12 145.083 108.342 1 8.88 ? O41 GDD 501 A 1 
#
_model_server_stats.io_time_ms              17 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    57 
_model_server_stats.query_time_ms           269 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           39 
#