data_5KVM # _model_server_result.job_id EuILo7KpdQoLT7aUGHLEqg _model_server_result.datetime_utc '2025-01-09 02:14:17' _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 5kvm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":907}' # _entry.id 5KVM # _exptl.entry_id 5KVM _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 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 120 _cell.entry_id 5KVM _cell.length_a 120.336 _cell.length_b 120.336 _cell.length_c 72.85 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5KVM _symmetry.cell_setting ? _symmetry.Int_Tables_number 170 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65' # _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 _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 # _struct_asym.details ? _struct_asym.entity_id 7 _struct_asym.id G _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 4 oligosaccharide 5 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 3 ? 4 4 3 BMA BMA C1 O1 . O6 HO6 . sing 4 ? 5 2 1 NAG 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 901 NAG 4 n D NAG 2 D 2 NAG A 902 NAG 4 n D BMA 3 D 3 BMA A 903 BMA 4 n D BMA 4 D 4 BMA A 904 BMA 5 n E NAG 1 E 1 NAG A 905 NAG 5 n E NAG 2 E 2 NAG A 906 NAG # 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 8 A CYS 35 1_555 A SG CYS 64 A CYS 91 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf2 A SG CYS 94 A CYS 121 1_555 A SG CYS 150 A CYS 177 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf3 A SG CYS 319 A CYS 346 1_555 A SG CYS 350 A CYS 377 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? disulf ? disulf4 A SG CYS 339 A CYS 366 1_555 A SG CYS 352 A CYS 379 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? covale ? covale1 A ND2 ASN 12 A ASN 39 1_555 F C1 NAG . A NAG 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale2 A ND2 ASN 121 A ASN 148 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale3 A ND2 ASN 207 A ASN 234 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale4 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale5 D O4 NAG . D NAG 2 1_555 D C1 BMA . D BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale6 D O6 BMA . D BMA 3 1_555 D C1 BMA . D BMA 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale7 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? # _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 5KVM _atom_sites.fract_transf_matrix[1][1] 0.00831 _atom_sites.fract_transf_matrix[1][2] 0.004798 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009596 _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] 0.013727 _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 F 6 NAG A 1 900 900 NAG NAG . G 7 GOL A 1 907 907 GOL GOL . H 8 HOH A 1 1001 10 HOH HOH . H 8 HOH A 2 1002 6 HOH HOH . H 8 HOH A 3 1003 13 HOH HOH . H 8 HOH A 4 1004 16 HOH HOH . H 8 HOH A 5 1005 18 HOH HOH . H 8 HOH A 6 1006 11 HOH HOH . H 8 HOH A 7 1007 2 HOH HOH . H 8 HOH A 8 1008 20 HOH HOH . H 8 HOH A 9 1009 5 HOH HOH . H 8 HOH A 10 1010 23 HOH HOH . H 8 HOH A 11 1011 12 HOH HOH . H 8 HOH A 12 1012 8 HOH HOH . I 8 HOH B 1 401 17 HOH HOH . J 8 HOH C 1 101 14 HOH HOH . J 8 HOH C 2 102 3 HOH HOH . J 8 HOH C 3 103 7 HOH HOH . J 8 HOH C 4 104 19 HOH HOH . J 8 HOH C 5 105 4 HOH HOH . J 8 HOH C 6 106 1 HOH HOH . J 8 HOH C 7 107 22 HOH HOH . J 8 HOH C 8 108 9 HOH HOH . J 8 HOH C 9 109 24 HOH HOH . J 8 HOH C 10 110 15 HOH HOH . J 8 HOH C 11 111 21 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 . . . G 7 63.737 8.11 -15.813 1 69.65 ? C1 GOL 907 A 1 HETATM 2 O O1 GOL . . . G 7 65.073 8.171 -16.26 1 66.57 ? O1 GOL 907 A 1 HETATM 3 C C2 GOL . . . G 7 63.521 9.127 -14.699 1 71.93 ? C2 GOL 907 A 1 HETATM 4 O O2 GOL . . . G 7 64.349 10.246 -14.925 1 73.65 ? O2 GOL 907 A 1 HETATM 5 C C3 GOL . . . G 7 62.062 9.571 -14.683 1 75.33 ? C3 GOL 907 A 1 HETATM 6 O O3 GOL . . . G 7 61.227 8.442 -14.55 1 65.04 ? O3 GOL 907 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 250 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 6 #