data_5B6Y # _model_server_result.job_id GmmLZ9cZ_QLe8Ucz0dXwMw _model_server_result.datetime_utc '2024-11-26 16:02:03' _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":"H","auth_seq_id":605}' # _entry.id 5B6Y # _exptl.entry_id 5B6Y _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 114.229 _entity.id 7 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description N-OCTANE _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 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 7 G N N ? 7 H N N ? 7 P N 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 'C8 H18' _chem_comp.formula_weight 114.229 _chem_comp.id OCT _chem_comp.mon_nstd_flag . _chem_comp.name N-OCTANE _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 C1 C2 OCT sing 506 n n C1 H11 OCT sing 507 n n C1 H12 OCT sing 508 n n C1 H13 OCT sing 509 n n C2 C3 OCT sing 510 n n C2 H21 OCT sing 511 n n C2 H22 OCT sing 512 n n C3 C4 OCT sing 513 n n C3 H31 OCT sing 514 n n C3 H32 OCT sing 515 n n C4 C5 OCT sing 516 n n C4 H41 OCT sing 517 n n C4 H42 OCT sing 518 n n C5 C6 OCT sing 519 n n C5 H51 OCT sing 520 n n C5 H52 OCT sing 521 n n C6 C7 OCT sing 522 n n C6 H61 OCT sing 523 n n C6 H62 OCT sing 524 n n C7 C8 OCT sing 525 n n C7 H71 OCT sing 526 n n C7 H72 OCT sing 527 n n C8 H81 OCT sing 528 n n C8 H82 OCT sing 529 n n C8 H83 OCT sing 530 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 OCT . . . H 7 -5.331 -1.987 6.403 1 87.37 ? C1 OCT 605 A 1 HETATM 2 C C2 OCT . . . H 7 -4.283 -2.245 5.323 1 88.29 ? C2 OCT 605 A 1 HETATM 3 C C3 OCT . . . H 7 -4.96 -2.26 3.954 1 83.36 ? C3 OCT 605 A 1 HETATM 4 C C4 OCT . . . H 7 -4.073 -2.987 2.945 1 83.84 ? C4 OCT 605 A 1 HETATM 5 C C5 OCT . . . H 7 -4.695 -2.864 1.556 1 89.1 ? C5 OCT 605 A 1 HETATM 6 C C6 OCT . . . H 7 -3.964 -3.775 0.572 1 71.85 ? C6 OCT 605 A 1 HETATM 7 C C7 OCT . . . H 7 -4.677 -3.726 -0.777 1 67.37 ? C7 OCT 605 A 1 HETATM 8 C C8 OCT . . . H 7 -3.879 -4.519 -1.81 1 78.98 ? C8 OCT 605 A 1 HETATM 9 H H11 OCT . . . H 7 -4.903 -1.978 7.273 1 104.84 ? H11 OCT 605 A 1 HETATM 10 H H12 OCT . . . H 7 -6 -2.689 6.379 1 104.84 ? H12 OCT 605 A 1 HETATM 11 H H13 OCT . . . H 7 -5.756 -1.13 6.243 1 104.84 ? H13 OCT 605 A 1 HETATM 12 H H21 OCT . . . H 7 -3.857 -3.102 5.483 1 105.95 ? H21 OCT 605 A 1 HETATM 13 H H22 OCT . . . H 7 -3.615 -1.542 5.346 1 105.95 ? H22 OCT 605 A 1 HETATM 14 H H31 OCT . . . H 7 -5.813 -2.717 4.021 1 100.03 ? H31 OCT 605 A 1 HETATM 15 H H32 OCT . . . H 7 -5.106 -1.348 3.657 1 100.03 ? H32 OCT 605 A 1 HETATM 16 H H41 OCT . . . H 7 -4.004 -3.923 3.188 1 100.6 ? H41 OCT 605 A 1 HETATM 17 H H42 OCT . . . H 7 -3.189 -2.587 2.942 1 100.6 ? H42 OCT 605 A 1 HETATM 18 H H51 OCT . . . H 7 -5.629 -3.121 1.598 1 106.91 ? H51 OCT 605 A 1 HETATM 19 H H52 OCT . . . H 7 -4.628 -1.945 1.254 1 106.91 ? H52 OCT 605 A 1 HETATM 20 H H61 OCT . . . H 7 -3.049 -3.471 0.467 1 86.22 ? H61 OCT 605 A 1 HETATM 21 H H62 OCT . . . H 7 -3.967 -4.685 0.908 1 86.22 ? H62 OCT 605 A 1 HETATM 22 H H71 OCT . . . H 7 -5.563 -4.112 -0.688 1 80.85 ? H71 OCT 605 A 1 HETATM 23 H H72 OCT . . . H 7 -4.754 -2.804 -1.068 1 80.85 ? H72 OCT 605 A 1 HETATM 24 H H81 OCT . . . H 7 -4.335 -4.486 -2.666 1 94.77 ? H81 OCT 605 A 1 HETATM 25 H H82 OCT . . . H 7 -2.994 -4.133 -1.9 1 94.77 ? H82 OCT 605 A 1 HETATM 26 H H83 OCT . . . H 7 -3.802 -5.441 -1.52 1 94.77 ? H83 OCT 605 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 260 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 26 #