data_6SAM # _model_server_result.job_id FFbnMVn6UDIZz-NJ8Gp_Ug _model_server_result.datetime_utc '2024-12-21 18:28:14' _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 6sam # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":603}' # _entry.id 6SAM # _exptl.entry_id 6SAM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 337.435 _entity.id 6 _entity.src_method man _entity.type non-polymer _entity.pdbx_description '[(3~{S})-1-(2,3-dihydro-1~{H}-inden-2-yl)piperidin-1-ium-3-yl] ~{N}-phenylcarbamate' _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 6SAM _cell.length_a 154.28 _cell.length_b 154.28 _cell.length_c 127.9 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6SAM _symmetry.cell_setting ? _symmetry.Int_Tables_number 97 _symmetry.space_group_name_Hall 'I 4 2' _symmetry.space_group_name_H-M 'I 4 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 6 _struct_asym.id H _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 1 FUC NAG C1 O1 . O6 HO6 . sing 3 ? 3 2 1 FUC NAG C1 O1 . O6 HO6 . 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 B NAG 1 B 1 NAG A 902 NAG 2 n B NAG 2 B 2 NAG A 903 NAG 2 n B FUC 3 B 3 FUC A 907 FUC 2 n C NAG 1 C 1 NAG A 908 NAG 2 n C NAG 2 C 2 NAG A 909 NAG 2 n C FUC 3 C 3 FUC A 910 FUC 2 n D NAG 1 D 1 NAG A 911 NAG 2 n D NAG 2 D 2 NAG A 912 NAG 2 n D FUC 3 D 3 FUC A 1002 FUC 3 n E NAG 1 E 1 NAG A 1003 NAG 3 n E FUC 2 E 2 FUC A 1004 FUC # 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 65 A CYS 65 1_555 A SG CYS 92 A CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf2 A SG CYS 252 A CYS 252 1_555 A SG CYS 263 A CYS 263 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf3 A SG CYS 400 A CYS 400 1_555 A SG CYS 519 A CYS 519 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? covale ? covale1 A ND2 ASN 57 A ASN 57 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.46 ? covale ? covale2 A ND2 ASN 106 A ASN 106 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale3 A ND2 ASN 241 A ASN 241 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale4 A ND2 ASN 256 A ASN 256 1_555 J C1 NAG . A NAG 616 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale5 A ND2 ASN 341 A ASN 341 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale6 A ND2 ASN 485 A ASN 485 1_555 K C1 NAG . A NAG 617 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale7 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.376 ? covale ? covale8 B O6 NAG . B NAG 1 1_555 B C1 FUC . B FUC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.376 ? covale ? covale9 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.381 ? covale ? covale10 C O6 NAG . C NAG 1 1_555 C C1 FUC . C FUC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.374 ? covale ? covale11 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.375 ? covale ? covale12 D O6 NAG . D NAG 1 1_555 D C1 FUC . D FUC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.374 ? covale ? covale13 E O6 NAG . E NAG 1 1_555 E C1 FUC . E FUC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.376 ? # _chem_comp.formula 'C21 H25 N2 O2 1' _chem_comp.formula_weight 337.435 _chem_comp.id L3H _chem_comp.mon_nstd_flag . _chem_comp.name '[(3~{S})-1-(2,3-dihydro-1~{H}-inden-2-yl)piperidin-1-ium-3-yl] ~{N}-phenylcarbamate' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 C12 C11 L3H sing 218 n n C12 C13 L3H sing 219 n n C11 O10 L3H sing 220 n n C11 C16 L3H sing 221 n n C13 C14 L3H sing 222 n n O10 C02 L3H sing 223 n n O01 C02 L3H doub 224 n n C02 N03 L3H sing 225 n n C16 N15 L3H sing 226 n n C14 N15 L3H sing 227 n n N03 C04 L3H sing 228 n n N15 C17 L3H sing 229 n n C04 C09 L3H doub 230 n y C04 C05 L3H sing 231 n y C09 C08 L3H sing 232 n y C21 C17 L3H sing 233 n n C21 C20 L3H sing 234 n n C05 C06 L3H doub 235 n y C17 C18 L3H sing 236 n n C22 C20 L3H doub 237 n y C22 C23 L3H sing 238 n y C20 C19 L3H sing 239 n y C08 C07 L3H doub 240 n y C06 C07 L3H sing 241 n y C23 C24 L3H doub 242 n y C18 C19 L3H sing 243 n n C19 C25 L3H doub 244 n y C24 C25 L3H sing 245 n y C05 H1 L3H sing 246 n n C06 H2 L3H sing 247 n n C07 H3 L3H sing 248 n n C08 H4 L3H sing 249 n n C09 H5 L3H sing 250 n n C11 H6 L3H sing 251 n n C12 H7 L3H sing 252 n n C12 H8 L3H sing 253 n n C13 H9 L3H sing 254 n n C13 H10 L3H sing 255 n n C14 H11 L3H sing 256 n n C14 H12 L3H sing 257 n n C16 H13 L3H sing 258 n n C16 H14 L3H sing 259 n n C17 H15 L3H sing 260 n n C18 H16 L3H sing 261 n n C18 H17 L3H sing 262 n n C21 H18 L3H sing 263 n n C21 H19 L3H sing 264 n n C22 H20 L3H sing 265 n n C23 H21 L3H sing 266 n n C24 H22 L3H sing 267 n n C25 H23 L3H sing 268 n n N03 H24 L3H sing 269 n n N15 H25 L3H sing 270 n n # _atom_sites.entry_id 6SAM _atom_sites.fract_transf_matrix[1][1] 0.006482 _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] 0.006482 _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] 0.007819 _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 4 DMS A 1 601 601 DMS DMS . G 5 GOL A 1 602 801 GOL GOL . H 6 L3H A 1 603 901 L3H GNS . I 5 GOL A 1 613 1001 GOL GOL . J 7 NAG A 1 616 1005 NAG NAG . K 7 NAG A 1 617 1006 NAG NAG . L 8 SO4 A 1 618 1 SO4 SO4 . M 8 SO4 A 1 619 2 SO4 SO4 . N 9 HOH A 1 701 4 HOH HOH . N 9 HOH A 2 702 82 HOH HOH . N 9 HOH A 3 703 23 HOH HOH . N 9 HOH A 4 704 50 HOH HOH . N 9 HOH A 5 705 71 HOH HOH . N 9 HOH A 6 706 85 HOH HOH . N 9 HOH A 7 707 6 HOH HOH . N 9 HOH A 8 708 24 HOH HOH . N 9 HOH A 9 709 66 HOH HOH . N 9 HOH A 10 710 73 HOH HOH . N 9 HOH A 11 711 46 HOH HOH . N 9 HOH A 12 712 19 HOH HOH . N 9 HOH A 13 713 42 HOH HOH . N 9 HOH A 14 714 36 HOH HOH . N 9 HOH A 15 715 79 HOH HOH . N 9 HOH A 16 716 32 HOH HOH . N 9 HOH A 17 717 39 HOH HOH . N 9 HOH A 18 718 29 HOH HOH . N 9 HOH A 19 719 60 HOH HOH . N 9 HOH A 20 720 78 HOH HOH . N 9 HOH A 21 721 35 HOH HOH . N 9 HOH A 22 722 7 HOH HOH . N 9 HOH A 23 723 22 HOH HOH . N 9 HOH A 24 724 5 HOH HOH . N 9 HOH A 25 725 86 HOH HOH . N 9 HOH A 26 726 61 HOH HOH . N 9 HOH A 27 727 43 HOH HOH . N 9 HOH A 28 728 49 HOH HOH . N 9 HOH A 29 729 14 HOH HOH . N 9 HOH A 30 730 54 HOH HOH . N 9 HOH A 31 731 2 HOH HOH . N 9 HOH A 32 732 25 HOH HOH . N 9 HOH A 33 733 74 HOH HOH . N 9 HOH A 34 734 10 HOH HOH . N 9 HOH A 35 735 31 HOH HOH . N 9 HOH A 36 736 34 HOH HOH . N 9 HOH A 37 737 41 HOH HOH . N 9 HOH A 38 738 58 HOH HOH . N 9 HOH A 39 739 45 HOH HOH . N 9 HOH A 40 740 51 HOH HOH . N 9 HOH A 41 741 18 HOH HOH . N 9 HOH A 42 742 13 HOH HOH . N 9 HOH A 43 743 77 HOH HOH . N 9 HOH A 44 744 37 HOH HOH . N 9 HOH A 45 745 28 HOH HOH . N 9 HOH A 46 746 48 HOH HOH . N 9 HOH A 47 747 30 HOH HOH . N 9 HOH A 48 748 3 HOH HOH . N 9 HOH A 49 749 33 HOH HOH . N 9 HOH A 50 750 53 HOH HOH . N 9 HOH A 51 751 12 HOH HOH . N 9 HOH A 52 752 1 HOH HOH . N 9 HOH A 53 753 16 HOH HOH . N 9 HOH A 54 754 59 HOH HOH . N 9 HOH A 55 755 44 HOH HOH . N 9 HOH A 56 756 8 HOH HOH . N 9 HOH A 57 757 47 HOH HOH . N 9 HOH A 58 758 70 HOH HOH . N 9 HOH A 59 759 65 HOH HOH . N 9 HOH A 60 760 17 HOH HOH . N 9 HOH A 61 761 84 HOH HOH . N 9 HOH A 62 762 52 HOH HOH . N 9 HOH A 63 763 21 HOH HOH . N 9 HOH A 64 764 9 HOH HOH . N 9 HOH A 65 765 15 HOH HOH . N 9 HOH A 66 766 72 HOH HOH . N 9 HOH A 67 767 38 HOH HOH . N 9 HOH A 68 768 64 HOH HOH . N 9 HOH A 69 769 69 HOH HOH . N 9 HOH A 70 770 67 HOH HOH . N 9 HOH A 71 771 11 HOH HOH . N 9 HOH A 72 772 20 HOH HOH . N 9 HOH A 73 773 40 HOH HOH . N 9 HOH A 74 774 76 HOH HOH . N 9 HOH A 75 775 56 HOH HOH . N 9 HOH A 76 776 68 HOH HOH . N 9 HOH A 77 777 75 HOH HOH . N 9 HOH A 78 778 80 HOH HOH . N 9 HOH A 79 779 63 HOH HOH . N 9 HOH A 80 780 55 HOH HOH . N 9 HOH A 81 781 81 HOH HOH . N 9 HOH A 82 782 26 HOH HOH . N 9 HOH A 83 783 57 HOH HOH . N 9 HOH A 84 784 62 HOH HOH . N 9 HOH A 85 785 83 HOH HOH . N 9 HOH A 86 786 27 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 C02 L3H . . . H 6 137.515 112.47 39.637 1 67.24 ? C02 L3H 603 A 1 HETATM 2 C C04 L3H . . . H 6 139.294 113.508 41.136 1 58.48 ? C04 L3H 603 A 1 HETATM 3 C C05 L3H . . . H 6 138.521 114.618 41.594 1 57.75 ? C05 L3H 603 A 1 HETATM 4 C C06 L3H . . . H 6 139.115 115.653 42.343 1 55.41 ? C06 L3H 603 A 1 HETATM 5 C C07 L3H . . . H 6 140.469 115.628 42.678 1 54.31 ? C07 L3H 603 A 1 HETATM 6 C C08 L3H . . . H 6 141.214 114.536 42.254 1 57.07 ? C08 L3H 603 A 1 HETATM 7 C C09 L3H . . . H 6 140.645 113.503 41.494 1 52.79 ? C09 L3H 603 A 1 HETATM 8 C C11 L3H . . . H 6 135.571 111.337 38.596 1 73 ? C11 L3H 603 A 1 HETATM 9 C C12 L3H . . . H 6 135.238 109.969 37.92 1 71.08 ? C12 L3H 603 A 1 HETATM 10 C C13 L3H . . . H 6 135.183 108.816 38.92 1 60.92 ? C13 L3H 603 A 1 HETATM 11 C C14 L3H . . . H 6 134.178 109.118 40.031 1 63.22 ? C14 L3H 603 A 1 HETATM 12 C C16 L3H . . . H 6 134.508 111.581 39.737 1 65.74 ? C16 L3H 603 A 1 HETATM 13 C C17 L3H . . . H 6 133.63 110.666 41.954 1 64.4 ? C17 L3H 603 A 1 HETATM 14 C C18 L3H . . . H 6 134.16 111.82 42.84 1 57.27 ? C18 L3H 603 A 1 HETATM 15 C C19 L3H . . . H 6 133.046 112.829 42.927 1 64.61 ? C19 L3H 603 A 1 HETATM 16 C C20 L3H . . . H 6 131.921 112.393 42.19 1 61.87 ? C20 L3H 603 A 1 HETATM 17 C C21 L3H . . . H 6 132.193 111.063 41.554 1 63.24 ? C21 L3H 603 A 1 HETATM 18 C C22 L3H . . . H 6 130.781 113.185 42.133 1 62.08 ? C22 L3H 603 A 1 HETATM 19 C C23 L3H . . . H 6 130.739 114.42 42.81 1 58.11 ? C23 L3H 603 A 1 HETATM 20 C C24 L3H . . . H 6 131.837 114.858 43.537 1 60.31 ? C24 L3H 603 A 1 HETATM 21 C C25 L3H . . . H 6 133.003 114.056 43.597 1 60.28 ? C25 L3H 603 A 1 HETATM 22 N N03 L3H . . . H 6 138.712 112.412 40.362 1 65.44 ? N03 L3H 603 A 1 HETATM 23 N N15 L3H . . . H 6 134.55 110.448 40.741 1 65.72 ? N15 L3H 603 A 1 HETATM 24 O O01 L3H . . . H 6 136.857 113.495 39.439 1 65.03 ? O01 L3H 603 A 1 HETATM 25 O O10 L3H . . . H 6 136.943 111.31 39.042 1 69.43 ? O10 L3H 603 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 297 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 25 #