data_5B6Y # _model_server_result.job_id trglVwaco97-5yj42Gkiqw _model_server_result.datetime_utc '2024-11-23 01:54:00' _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 5b6y # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":601}' # _entry.id 5B6Y # _exptl.entry_id 5B6Y _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 184.361 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description TRIDECANE _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 5B6Y _cell.length_a 62.5 _cell.length_b 62.5 _cell.length_c 112 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5B6Y _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 63' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # 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' 2_455 -y-1,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 -62.5 0 0 3 'crystal symmetry operation' 3_445 -x+y-1,-x-1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -31.25 -54.126588 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 covale ? covale1 A NZ LYS 216 A LYS 216 1_555 B C15 RET . A RET 300 1_555 ? A ? ? A ? ? ? ? ? ? ? 1.311 ? covale ? covale2 A NZ LYS 216 A LYS 216 1_555 B C15 RET . A RET 300 1_555 ? B ? ? B ? ? ? ? ? ? ? 1.31 ? # _chem_comp.formula 'C13 H28' _chem_comp.formula_weight 184.361 _chem_comp.id TRD _chem_comp.mon_nstd_flag . _chem_comp.name TRIDECANE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'LIPID FRAGMENT' # 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 C2 TRD sing 649 n n C1 H11 TRD sing 650 n n C1 H12 TRD sing 651 n n C1 H13 TRD sing 652 n n C2 C3 TRD sing 653 n n C2 H21 TRD sing 654 n n C2 H22 TRD sing 655 n n C3 C4 TRD sing 656 n n C3 H31 TRD sing 657 n n C3 H32 TRD sing 658 n n C4 C5 TRD sing 659 n n C4 H41 TRD sing 660 n n C4 H42 TRD sing 661 n n C5 C6 TRD sing 662 n n C5 H51 TRD sing 663 n n C5 H52 TRD sing 664 n n C6 C7 TRD sing 665 n n C6 H61 TRD sing 666 n n C6 H62 TRD sing 667 n n C7 C8 TRD sing 668 n n C7 H71 TRD sing 669 n n C7 H72 TRD sing 670 n n C8 C9 TRD sing 671 n n C8 H81 TRD sing 672 n n C8 H82 TRD sing 673 n n C9 C10 TRD sing 674 n n C9 H91 TRD sing 675 n n C9 H92 TRD sing 676 n n C10 C11 TRD sing 677 n n C10 H101 TRD sing 678 n n C10 H102 TRD sing 679 n n C11 C12 TRD sing 680 n n C11 H111 TRD sing 681 n n C11 H112 TRD sing 682 n n C12 C13 TRD sing 683 n n C12 H121 TRD sing 684 n n C12 H122 TRD sing 685 n n C13 H131 TRD sing 686 n n C13 H132 TRD sing 687 n n C13 H133 TRD sing 688 n n # _atom_sites.entry_id 5B6Y _atom_sites.fract_transf_matrix[1][1] 0.016 _atom_sites.fract_transf_matrix[1][2] 0.009238 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018475 _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] 0.008929 _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 B 2 RET A 1 300 300 RET RET . C 3 L2P A 1 600 600 L2P L2P . D 4 TRD A 1 601 601 TRD TRD . E 5 D10 A 1 602 602 D10 D10 . F 6 HP6 A 1 603 603 HP6 HP6 . G 7 OCT A 1 604 604 OCT OCT . H 7 OCT A 1 605 605 OCT OCT . I 8 MYS A 1 606 606 MYS MYS . J 9 UND A 1 607 607 UND UND . K 3 L2P A 1 608 608 L2P L2P . L 3 L2P A 1 609 609 L2P L2P . M 8 MYS A 1 610 610 MYS MYS . N 10 DD9 A 1 611 611 DD9 DD9 . O 11 C14 A 1 612 612 C14 C14 . P 7 OCT A 1 613 613 OCT OCT . Q 9 UND A 1 614 614 UND UND . R 12 HOH A 1 400 400 HOH HOH . R 12 HOH A 2 401 401 HOH HOH . R 12 HOH A 3 402 402 HOH HOH . R 12 HOH A 4 403 403 HOH HOH . R 12 HOH A 5 404 404 HOH HOH . R 12 HOH A 6 405 405 HOH HOH . R 12 HOH A 7 406 406 HOH HOH . R 12 HOH A 8 407 407 HOH HOH . R 12 HOH A 9 408 408 HOH HOH . R 12 HOH A 10 414 414 HOH HOH . R 12 HOH A 11 425 425 HOH HOH . R 12 HOH A 12 424 424 HOH HOH . R 12 HOH A 13 433 433 HOH HOH . R 12 HOH A 14 438 438 HOH HOH . R 12 HOH A 15 441 441 HOH HOH . R 12 HOH A 16 442 442 HOH HOH . R 12 HOH A 17 443 443 HOH HOH . R 12 HOH A 18 451 451 HOH HOH . R 12 HOH A 19 453 453 HOH HOH . R 12 HOH A 20 454 454 HOH HOH . R 12 HOH A 21 456 456 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 TRD . . . D 4 -13.119 3.22 6.774 1 78.2 ? C1 TRD 601 A 1 HETATM 2 C C2 TRD . . . D 4 -12.959 2.131 7.833 1 75.94 ? C2 TRD 601 A 1 HETATM 3 C C3 TRD . . . D 4 -11.481 2.018 8.211 1 88.43 ? C3 TRD 601 A 1 HETATM 4 C C4 TRD . . . D 4 -10.925 0.622 7.921 1 76.14 ? C4 TRD 601 A 1 HETATM 5 C C5 TRD . . . D 4 -11.086 0.259 6.443 1 92.41 ? C5 TRD 601 A 1 HETATM 6 C C6 TRD . . . D 4 -9.74 0.219 5.723 1 98.96 ? C6 TRD 601 A 1 HETATM 7 C C7 TRD . . . D 4 -9.953 0.679 4.282 1 97.83 ? C7 TRD 601 A 1 HETATM 8 C C8 TRD . . . D 4 -9.068 -0.117 3.328 1 100.97 ? C8 TRD 601 A 1 HETATM 9 C C9 TRD . . . D 4 -9.25 0.445 1.919 1 89.74 ? C9 TRD 601 A 1 HETATM 10 C C10 TRD . . . D 4 -9.664 -0.666 0.958 1 81.53 ? C10 TRD 601 A 1 HETATM 11 C C11 TRD . . . D 4 -9.511 -0.164 -0.476 1 75.78 ? C11 TRD 601 A 1 HETATM 12 C C12 TRD . . . D 4 -10.55 -0.826 -1.379 1 71.61 ? C12 TRD 601 A 1 HETATM 13 C C13 TRD . . . D 4 -10.579 -0.099 -2.721 1 73.87 ? C13 TRD 601 A 1 HETATM 14 H H11 TRD . . . D 4 -12.81 4.067 7.132 1 93.84 ? H11 TRD 601 A 1 HETATM 15 H H12 TRD . . . D 4 -12.595 2.989 5.991 1 93.84 ? H12 TRD 601 A 1 HETATM 16 H H13 TRD . . . D 4 -14.054 3.296 6.527 1 93.84 ? H13 TRD 601 A 1 HETATM 17 H H21 TRD . . . D 4 -13.478 2.363 8.619 1 91.12 ? H21 TRD 601 A 1 HETATM 18 H H22 TRD . . . D 4 -13.269 1.284 7.477 1 91.12 ? H22 TRD 601 A 1 HETATM 19 H H31 TRD . . . D 4 -10.974 2.671 7.703 1 106.11 ? H31 TRD 601 A 1 HETATM 20 H H32 TRD . . . D 4 -11.382 2.207 9.157 1 106.11 ? H32 TRD 601 A 1 HETATM 21 H H41 TRD . . . D 4 -9.983 0.6 8.153 1 91.37 ? H41 TRD 601 A 1 HETATM 22 H H42 TRD . . . D 4 -11.4 -0.028 8.462 1 91.37 ? H42 TRD 601 A 1 HETATM 23 H H51 TRD . . . D 4 -11.507 -0.612 6.375 1 110.89 ? H51 TRD 601 A 1 HETATM 24 H H52 TRD . . . D 4 -11.654 0.919 6.015 1 110.89 ? H52 TRD 601 A 1 HETATM 25 H H61 TRD . . . D 4 -9.114 0.813 6.167 1 118.75 ? H61 TRD 601 A 1 HETATM 26 H H62 TRD . . . D 4 -9.393 -0.687 5.729 1 118.75 ? H62 TRD 601 A 1 HETATM 27 H H71 TRD . . . D 4 -9.733 1.621 4.211 1 117.39 ? H71 TRD 601 A 1 HETATM 28 H H72 TRD . . . D 4 -10.883 0.549 4.039 1 117.39 ? H72 TRD 601 A 1 HETATM 29 H H81 TRD . . . D 4 -8.14 -0.032 3.596 1 121.16 ? H81 TRD 601 A 1 HETATM 30 H H82 TRD . . . D 4 -9.329 -1.051 3.343 1 121.16 ? H82 TRD 601 A 1 HETATM 31 H H91 TRD . . . D 4 -9.937 1.13 1.933 1 107.69 ? H91 TRD 601 A 1 HETATM 32 H H92 TRD . . . D 4 -8.414 0.835 1.618 1 107.69 ? H92 TRD 601 A 1 HETATM 33 H H101 TRD . . . D 4 -9.096 -1.441 1.093 1 97.84 ? H101 TRD 601 A 1 HETATM 34 H H102 TRD . . . D 4 -10.589 -0.908 1.121 1 97.84 ? H102 TRD 601 A 1 HETATM 35 H H111 TRD . . . D 4 -9.636 0.798 -0.495 1 90.94 ? H111 TRD 601 A 1 HETATM 36 H H112 TRD . . . D 4 -8.622 -0.379 -0.798 1 90.94 ? H112 TRD 601 A 1 HETATM 37 H H121 TRD . . . D 4 -10.313 -1.756 -1.519 1 85.93 ? H121 TRD 601 A 1 HETATM 38 H H122 TRD . . . D 4 -11.424 -0.773 -0.962 1 85.93 ? H122 TRD 601 A 1 HETATM 39 H H131 TRD . . . D 4 -11.236 -0.516 -3.3 1 88.64 ? H131 TRD 601 A 1 HETATM 40 H H132 TRD . . . D 4 -9.703 -0.15 -3.135 1 88.64 ? H132 TRD 601 A 1 HETATM 41 H H133 TRD . . . D 4 -10.816 0.831 -2.58 1 88.64 ? H133 TRD 601 A 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 40 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 398 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 41 #