data_6XPX # _model_server_result.job_id D8difppsy5YMrLDy0H60yA _model_server_result.datetime_utc '2024-10-17 09:24:15' _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 6xpx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"P","auth_seq_id":501}' # _entry.id 6XPX # _exptl.entry_id 6XPX _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 7 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description GLYCEROL _entity.pdbx_number_of_molecules 7 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 108.01 _cell.angle_gamma 90 _cell.entry_id 6XPX _cell.length_a 68.42 _cell.length_b 101.56 _cell.length_c 77.41 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6XPX _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_and_software_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 _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 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 H N N ? 7 I N N ? 7 K N N ? 7 M N N ? 7 N N N ? 7 O N N ? 7 P N N # _pdbx_entity_branch.entity_id 4 _pdbx_entity_branch.type oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 4 3 2 BMA NAG C1 O1 . O4 HO4 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 4 n D NAG 1 D 1 NAG A 802 NAG 4 n D NAG 2 D 2 NAG A 803 NAG 4 n D BMA 3 D 3 BMA A 804 BMA # 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 16 A CYS 52 1_555 A SG CYS 241 A CYS 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.111 ? disulf ? disulf2 A SG CYS 28 A CYS 64 1_555 A SG CYS 40 A CYS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? disulf ? disulf3 A SG CYS 61 A CYS 97 1_555 A SG CYS 103 A CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? disulf ? disulf4 A SG CYS 245 A CYS 281 1_555 A SG CYS 269 A CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? disulf ? disulf5 B SG CYS 23 C CYS 23 1_555 B SG CYS 94 C CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.094 ? disulf ? disulf6 B SG CYS 140 C CYS 140 1_555 B SG CYS 200 C CYS 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? disulf ? disulf7 C SG CYS 22 B CYS 22 1_555 C SG CYS 96 B CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.988 ? disulf ? disulf8 C SG CYS 143 B CYS 143 1_555 C SG CYS 199 B CYS 199 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? covale ? covale1 A ND2 ASN 45 A ASN 81 1_555 F C1 NAG . A NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? covale ? covale2 A ND2 ASN 129 A ASN 165 1_555 E C1 NAG . A NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.467 ? covale ? covale3 A ND2 ASN 249 A ASN 285 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale4 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale5 D O4 NAG . D NAG 2 1_555 D C1 BMA . D BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? # _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 213 n n C1 C2 GOL sing 214 n n C1 H11 GOL sing 215 n n C1 H12 GOL sing 216 n n O1 HO1 GOL sing 217 n n C2 O2 GOL sing 218 n n C2 C3 GOL sing 219 n n C2 H2 GOL sing 220 n n O2 HO2 GOL sing 221 n n C3 O3 GOL sing 222 n n C3 H31 GOL sing 223 n n C3 H32 GOL sing 224 n n O3 HO3 GOL sing 225 n n # _atom_sites.entry_id 6XPX _atom_sites.fract_transf_matrix[1][1] 0.014616 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004753 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009846 _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] 0.013584 _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 E 5 NAG A 1 401 312 NAG NAG . F 5 NAG A 1 402 313 NAG NAG . G 6 BCN A 1 403 401 BCN BCN . H 7 GOL A 1 404 501 GOL GOL . I 7 GOL A 1 405 601 GOL GOL . J 6 BCN A 1 406 701 BCN BCN . K 7 GOL A 1 407 801 GOL GOL . L 8 1PE C 1 301 301 1PE 1PE . M 7 GOL C 1 302 401 GOL GOL . N 7 GOL C 1 303 601 GOL GOL . O 7 GOL C 1 304 701 GOL GOL . P 7 GOL B 1 501 501 GOL GOL . Q 9 HOH A 1 501 3 HOH HOH . Q 9 HOH A 2 502 2 HOH HOH . Q 9 HOH A 3 503 13 HOH HOH . Q 9 HOH A 4 504 4 HOH HOH . Q 9 HOH A 5 505 8 HOH HOH . Q 9 HOH A 6 506 9 HOH HOH . Q 9 HOH A 7 507 12 HOH HOH . R 9 HOH C 1 401 5 HOH HOH . R 9 HOH C 2 402 11 HOH HOH . R 9 HOH C 3 403 10 HOH HOH . R 9 HOH C 4 404 6 HOH HOH . R 9 HOH C 5 405 16 HOH HOH . R 9 HOH C 6 406 1 HOH HOH . R 9 HOH C 7 407 15 HOH HOH . S 9 HOH B 1 601 14 HOH HOH . S 9 HOH B 2 602 7 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 . . . P 7 20.963 -58.686 -21.78 1 92.07 ? C1 GOL 501 B 1 HETATM 2 O O1 GOL . . . P 7 21.662 -58.661 -22.998 1 91.22 ? O1 GOL 501 B 1 HETATM 3 C C2 GOL . . . P 7 19.978 -59.89 -21.746 1 93.41 ? C2 GOL 501 B 1 HETATM 4 O O2 GOL . . . P 7 19.989 -60.554 -20.506 1 94.13 ? O2 GOL 501 B 1 HETATM 5 C C3 GOL . . . P 7 18.578 -59.268 -22.038 1 97.11 ? C3 GOL 501 B 1 HETATM 6 O O3 GOL . . . P 7 17.632 -60.331 -22.026 1 100.83 ? O3 GOL 501 B 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 36 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 308 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 6 #