data_3BDY
#
_model_server_result.job_id            '_eka2UGbaByrJP51sDzcFQ' 
_model_server_result.datetime_utc      '2024-11-22 17:50:31' 
_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          3bdy 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":215}' 
#
_entry.id    3BDY 
#
_exptl.entry_id    3BDY 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              92.094 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            GLYCEROL 
_entity.pdbx_number_of_molecules    1 
_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            3BDY 
_cell.length_a            100.6 
_cell.length_b            197.978 
_cell.length_c            77.65 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3BDY 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        20 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 2 2 21' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_software_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,D,E,F 1 1 
C 2 1,2 
#
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]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 4_545 x,-y-1,-z 1 0 0 0 -1 0 0 0 -1 0 -197.978 0 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      4 
_struct_asym.id                             D 
_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
disulf ? disulf1 A SG CYS 25 H CYS 22 1_555 A SG CYS 99 H CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.996 ? 
disulf ? disulf2 A SG CYS 150 H CYS 142 1_555 A SG CYS 206 H CYS 198 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? 
disulf ? disulf3 B SG CYS 23 L CYS 23 1_555 B SG CYS 92 L CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? 
disulf ? disulf4 B SG CYS 138 L CYS 134 1_555 B SG CYS 198 L CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? 
disulf ? disulf5 C SG CYS 19 V CYS 26 1_555 C SG CYS 61 V CYS 68 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? 
disulf ? disulf6 C SG CYS 44 V CYS 51 1_555 C SG CYS 53 V CYS 60 4_545 ? ? ? ? ? ? ? ? ? ? ? ? 2.467 ? 
disulf ? disulf7 C SG CYS 50 V CYS 57 1_555 C SG CYS 95 V CYS 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? 
disulf ? disulf8 C SG CYS 54 V CYS 61 1_555 C SG CYS 97 V CYS 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? 
#
_chem_comp.formula           'C3 H8 O3' 
_chem_comp.formula_weight    92.094 
_chem_comp.id                GOL 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              GLYCEROL 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     GLYCERIN;PROPANE-1,2,3-TRIOL 
#
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
C1 O1 GOL sing 129 n n 
C1 C2 GOL sing 130 n n 
C1 H11 GOL sing 131 n n 
C1 H12 GOL sing 132 n n 
O1 HO1 GOL sing 133 n n 
C2 O2 GOL sing 134 n n 
C2 C3 GOL sing 135 n n 
C2 H2 GOL sing 136 n n 
O2 HO2 GOL sing 137 n n 
C3 O3 GOL sing 138 n n 
C3 H31 GOL sing 139 n n 
C3 H32 GOL sing 140 n n 
O3 HO3 GOL sing 141 n n 
#
_atom_sites.entry_id                     3BDY 
_atom_sites.fract_transf_matrix[1][1]    0.00994 
_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]    0.005051 
_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]    0.012878 
_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 GOL L 1 215 1 GOL GOL . 
E 5 HOH H 1 223 1 HOH HOH . 
E 5 HOH H 2 224 2 HOH HOH . 
E 5 HOH H 3 225 3 HOH HOH . 
E 5 HOH H 4 226 4 HOH HOH . 
E 5 HOH H 5 227 5 HOH HOH . 
E 5 HOH H 6 228 7 HOH HOH . 
E 5 HOH H 7 229 10 HOH HOH . 
E 5 HOH H 8 230 11 HOH HOH . 
E 5 HOH H 9 231 13 HOH HOH . 
E 5 HOH H 10 232 14 HOH HOH . 
E 5 HOH H 11 233 16 HOH HOH . 
E 5 HOH H 12 234 17 HOH HOH . 
E 5 HOH H 13 235 19 HOH HOH . 
E 5 HOH H 14 236 23 HOH HOH . 
E 5 HOH H 15 237 24 HOH HOH . 
E 5 HOH H 16 238 27 HOH HOH . 
E 5 HOH H 17 239 28 HOH HOH . 
E 5 HOH H 18 240 30 HOH HOH . 
E 5 HOH H 19 241 32 HOH HOH . 
E 5 HOH H 20 242 34 HOH HOH . 
E 5 HOH H 21 243 37 HOH HOH . 
E 5 HOH H 22 244 38 HOH HOH . 
E 5 HOH H 23 245 39 HOH HOH . 
E 5 HOH H 24 246 46 HOH HOH . 
E 5 HOH H 25 247 48 HOH HOH . 
F 5 HOH L 1 216 6 HOH HOH . 
F 5 HOH L 2 217 8 HOH HOH . 
F 5 HOH L 3 218 9 HOH HOH . 
F 5 HOH L 4 219 12 HOH HOH . 
F 5 HOH L 5 220 15 HOH HOH . 
F 5 HOH L 6 221 18 HOH HOH . 
F 5 HOH L 7 222 20 HOH HOH . 
F 5 HOH L 8 223 21 HOH HOH . 
F 5 HOH L 9 224 22 HOH HOH . 
F 5 HOH L 10 225 25 HOH HOH . 
F 5 HOH L 11 226 26 HOH HOH . 
F 5 HOH L 12 227 29 HOH HOH . 
F 5 HOH L 13 228 31 HOH HOH . 
F 5 HOH L 14 229 33 HOH HOH . 
F 5 HOH L 15 230 35 HOH HOH . 
F 5 HOH L 16 231 36 HOH HOH . 
F 5 HOH L 17 232 40 HOH HOH . 
F 5 HOH L 18 233 41 HOH HOH . 
F 5 HOH L 19 234 44 HOH HOH . 
F 5 HOH L 20 235 45 HOH HOH . 
F 5 HOH L 21 236 47 HOH HOH . 
F 5 HOH L 22 237 49 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 C C1 GOL . . . D 4 -48.801 -55.128 0.14 1 55.1 ? C1 GOL 215 L 1 
HETATM 2 O O1 GOL . . . D 4 -47.843 -56.146 0.32 1 53.95 ? O1 GOL 215 L 1 
HETATM 3 C C2 GOL . . . D 4 -49.771 -55.513 -0.983 1 59.62 ? C2 GOL 215 L 1 
HETATM 4 O O2 GOL . . . D 4 -50.369 -56.747 -0.666 1 58.81 ? O2 GOL 215 L 1 
HETATM 5 C C3 GOL . . . D 4 -50.891 -54.462 -1.173 1 60.37 ? C3 GOL 215 L 1 
HETATM 6 O O3 GOL . . . D 4 -51.137 -54.128 -2.532 1 52.25 ? O3 GOL 215 L 1 
#
_model_server_stats.io_time_ms              31 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           267 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           6 
#