data_5K64 # _model_server_result.job_id 704V6K1cnDhDFO2F3k6KbA _model_server_result.datetime_utc '2025-03-09 03:39:04' _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 5k64 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":508}' # _entry.id 5K64 # _exptl.entry_id 5K64 _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 3 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 94.23 _cell.angle_gamma 90 _cell.entry_id 5K64 _cell.length_a 92.72 _cell.length_b 38.86 _cell.length_c 97.2 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5K64 _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 dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 ? 4 E N N ? 4 G N N ? 4 H N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide 3 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 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 2 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 2 4 3 MAN BMA C1 O1 . O3 HO3 . sing 4 ? 2 5 3 MAN BMA C1 O1 . O6 HO6 . sing 5 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 6 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . sing 7 ? 3 4 3 MAN BMA C1 O1 . O6 HO6 . sing 8 ? 3 5 4 NAG MAN C1 O1 . O2 HO2 . sing 9 ? 3 6 3 MAN BMA C1 O1 . O3 HO3 . 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 2 n C NAG 1 C 1 NAG A 500 NAG 2 n C NAG 2 C 2 NAG A 501 NAG 2 n C BMA 3 C 3 BMA A 502 BMA 2 n C MAN 4 C 4 MAN A 504 MAN 2 n C MAN 5 C 5 MAN A 503 MAN 3 n D NAG 1 D 1 NAG B 500 NAG 3 n D NAG 2 D 2 NAG B 501 NAG 3 n D BMA 3 D 3 BMA B 502 BMA 3 n D MAN 4 D 4 MAN B 503 MAN 3 n D NAG 5 D 5 NAG B 504 NAG 3 n D MAN 6 D 6 MAN B 506 MAN # 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 37 A CYS 261 1_555 A SG CYS 97 A CYS 321 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf2 A SG CYS 143 A CYS 367 1_555 A SG CYS 206 A CYS 425 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? disulf ? disulf3 B SG CYS 37 B CYS 261 1_555 B SG CYS 97 B CYS 321 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf4 B SG CYS 143 B CYS 367 1_555 B SG CYS 206 B CYS 425 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? covale ? covale1 A ND2 ASN 73 A ASN 297 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.428 ? covale ? covale2 B ND2 ASN 73 B ASN 297 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale3 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale4 C O4 NAG . C NAG 2 1_555 C C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale5 C O3 BMA . C BMA 3 1_555 C C1 MAN . C MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale6 C O6 BMA . C BMA 3 1_555 C C1 MAN . C MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale7 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale8 D O4 NAG . D NAG 2 1_555 D C1 BMA . D BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale9 D O6 BMA . D BMA 3 1_555 D C1 MAN . D MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale10 D O3 BMA . D BMA 3 1_555 D C1 MAN . D MAN 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale11 D O2 MAN . D MAN 4 1_555 D C1 NAG . D NAG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? # _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 153 n n C1 C2 GOL sing 154 n n C1 H11 GOL sing 155 n n C1 H12 GOL sing 156 n n O1 HO1 GOL sing 157 n n C2 O2 GOL sing 158 n n C2 C3 GOL sing 159 n n C2 H2 GOL sing 160 n n O2 HO2 GOL sing 161 n n C3 O3 GOL sing 162 n n C3 H31 GOL sing 163 n n C3 H32 GOL sing 164 n n O3 HO3 GOL sing 165 n n # _atom_sites.entry_id 5K64 _atom_sites.fract_transf_matrix[1][1] 0.010785 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000798 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.025733 _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] 0.010316 _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 4 GOL A 1 506 5 GOL GOL . F 5 MES A 1 507 1 MES MES . G 4 GOL B 1 507 3 GOL GOL . H 4 GOL B 1 508 4 GOL GOL . I 6 HOH A 1 601 28 HOH HOH . I 6 HOH A 2 602 38 HOH HOH . I 6 HOH A 3 603 4 HOH HOH . I 6 HOH A 4 604 24 HOH HOH . I 6 HOH A 5 605 32 HOH HOH . I 6 HOH A 6 606 14 HOH HOH . I 6 HOH A 7 607 26 HOH HOH . I 6 HOH A 8 608 2 HOH HOH . I 6 HOH A 9 609 6 HOH HOH . I 6 HOH A 10 610 5 HOH HOH . I 6 HOH A 11 611 22 HOH HOH . I 6 HOH A 12 612 33 HOH HOH . I 6 HOH A 13 613 12 HOH HOH . I 6 HOH A 14 614 46 HOH HOH . I 6 HOH A 15 615 48 HOH HOH . I 6 HOH A 16 616 35 HOH HOH . I 6 HOH A 17 617 34 HOH HOH . I 6 HOH A 18 618 13 HOH HOH . J 6 HOH B 1 601 18 HOH HOH . J 6 HOH B 2 602 27 HOH HOH . J 6 HOH B 3 603 36 HOH HOH . J 6 HOH B 4 604 20 HOH HOH . J 6 HOH B 5 605 17 HOH HOH . J 6 HOH B 6 606 1 HOH HOH . J 6 HOH B 7 607 3 HOH HOH . J 6 HOH B 8 608 10 HOH HOH . J 6 HOH B 9 609 29 HOH HOH . J 6 HOH B 10 610 19 HOH HOH . J 6 HOH B 11 611 45 HOH HOH . J 6 HOH B 12 612 7 HOH HOH . J 6 HOH B 13 613 16 HOH HOH . J 6 HOH B 14 614 42 HOH HOH . J 6 HOH B 15 615 9 HOH HOH . J 6 HOH B 16 616 43 HOH HOH . J 6 HOH B 17 617 21 HOH HOH . J 6 HOH B 18 618 40 HOH HOH . J 6 HOH B 19 619 39 HOH HOH . J 6 HOH B 20 620 8 HOH HOH . J 6 HOH B 21 621 25 HOH HOH . J 6 HOH B 22 622 47 HOH HOH . J 6 HOH B 23 623 37 HOH HOH . J 6 HOH B 24 624 41 HOH HOH . J 6 HOH B 25 625 31 HOH HOH . J 6 HOH B 26 626 30 HOH HOH . J 6 HOH B 27 627 11 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 . . . H 4 4.956 15.502 39.759 1 104.96 ? C1 GOL 508 B 1 HETATM 2 O O1 GOL . . . H 4 4.369 16.05 38.601 1 108.7 ? O1 GOL 508 B 1 HETATM 3 C C2 GOL . . . H 4 6.461 15.731 39.703 1 98.59 ? C2 GOL 508 B 1 HETATM 4 O O2 GOL . . . H 4 6.8 16.426 38.524 1 101.45 ? O2 GOL 508 B 1 HETATM 5 C C3 GOL . . . H 4 6.913 16.529 40.918 1 79.92 ? C3 GOL 508 B 1 HETATM 6 O O3 GOL . . . H 4 8.193 17.072 40.686 1 88.92 ? O3 GOL 508 B 1 HETATM 7 H H11 GOL . . . H 4 4.541 15.979 40.646 1 125.96 ? H11 GOL 508 B 1 HETATM 8 H H12 GOL . . . H 4 4.745 14.434 39.812 1 125.96 ? H12 GOL 508 B 1 HETATM 9 H HO1 GOL . . . H 4 3.409 15.85 38.596 1 130.44 ? HO1 GOL 508 B 1 HETATM 10 H H2 GOL . . . H 4 6.961 14.762 39.717 1 118.31 ? H2 GOL 508 B 1 HETATM 11 H HO2 GOL . . . H 4 6.366 17.305 38.527 1 121.74 ? HO2 GOL 508 B 1 HETATM 12 H H31 GOL . . . H 4 6.204 17.333 41.114 1 95.9 ? H31 GOL 508 B 1 HETATM 13 H H32 GOL . . . H 4 6.943 15.881 41.793 1 95.9 ? H32 GOL 508 B 1 HETATM 14 H HO3 GOL . . . H 4 8.373 17.084 39.723 1 106.7 ? HO3 GOL 508 B 1 # _model_server_stats.io_time_ms 57 _model_server_stats.parse_time_ms 26 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 285 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 14 #