data_6XTA # _model_server_result.job_id bYaCsw3fetD1B_NNQ6r-6w _model_server_result.datetime_utc '2024-12-21 18:23:52' _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 6xta # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":612}' # _entry.id 6XTA # _exptl.entry_id 6XTA _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 474.681 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (2~{S})-2-(butylamino)-3-(1~{H}-indol-3-yl)-~{N}-[2-[(4~{R})-1-(phenylmethyl)azepan-4-yl]ethyl]propanamide _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 6XTA _cell.length_a 154.04 _cell.length_b 154.04 _cell.length_c 127.97 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6XTA _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 _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 4 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 FUC NAG C1 O1 . O6 HO6 . sing 2 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 4 ? 4 3 1 TGY NAG C2 O2 . 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 530 NAG 2 n B FUC 2 B 2 FUC A 532 FUC 3 n C NAG 1 C 1 NAG A 533 NAG 3 n C NAG 2 C 2 NAG A 534 NAG 2 n D NAG 1 D 1 NAG A 535 NAG 2 n D FUC 2 D 2 FUC A 540 FUC 4 n E NAG 1 E 1 NAG A 536 NAG 4 n E NAG 2 E 2 NAG A 537 NAG 4 n E TGY 3 E 3 TGY A 538 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? disulf ? disulf2 A SG CYS 252 A CYS 252 1_555 A SG CYS 263 A CYS 263 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? disulf ? disulf3 A SG CYS 400 A CYS 400 1_555 A SG CYS 519 A CYS 519 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.95 ? covale ? covale1 A ND2 ASN 57 A ASN 57 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale2 A ND2 ASN 106 A ASN 106 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale3 A ND2 ASN 241 A ASN 241 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.473 ? covale ? covale4 A ND2 ASN 256 A ASN 256 1_555 G C1 NAG . A NAG 611 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale5 A ND2 ASN 341 A ASN 341 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale6 A ND2 ASN 485 A ASN 485 1_555 F C1 NAG . A NAG 610 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale7 B O6 NAG . B NAG 1 1_555 B C1 FUC . B FUC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale8 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.426 ? covale ? covale9 D O6 NAG . D NAG 1 1_555 D C1 FUC . D FUC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale10 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale11 E O6 NAG . E NAG 1 1_555 E C2 TGY . E TGY 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.377 ? # _chem_comp.formula 'C30 H42 N4 O' _chem_comp.formula_weight 474.681 _chem_comp.id O0Z _chem_comp.mon_nstd_flag . _chem_comp.name (2~{S})-2-(butylamino)-3-(1~{H}-indol-3-yl)-~{N}-[2-[(4~{R})-1-(phenylmethyl)azepan-4-yl]ethyl]propanamide _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 C07 C08 O0Z sing 290 n n C07 C06 O0Z sing 291 n n O18 C17 O0Z doub 292 n n N05 C06 O0Z sing 293 n n N05 C04 O0Z sing 294 n n C30 C29 O0Z doub 295 n y C30 C31 O0Z sing 296 n y C03 C04 O0Z sing 297 n n C03 C02 O0Z sing 298 n n C09 C08 O0Z doub 299 n y C09 N10 O0Z sing 300 n y C01 C02 O0Z sing 301 n n C29 C28 O0Z sing 302 n y C08 C16 O0Z sing 303 n y C31 C32 O0Z doub 304 n y C06 C17 O0Z sing 305 n n C17 N19 O0Z sing 306 n n C24 C25 O0Z sing 307 n n C24 C23 O0Z sing 308 n n N10 C11 O0Z sing 309 n y C25 N26 O0Z sing 310 n n C23 C22 O0Z sing 311 n n C16 C11 O0Z doub 312 n y C16 C15 O0Z sing 313 n y C28 C33 O0Z doub 314 n y C28 C27 O0Z sing 315 n n C32 C33 O0Z sing 316 n y C11 C12 O0Z sing 317 n y N19 C20 O0Z sing 318 n n C15 C14 O0Z doub 319 n y C20 C21 O0Z sing 320 n n C27 N26 O0Z sing 321 n n C22 C21 O0Z sing 322 n n C22 C35 O0Z sing 323 n n N26 C34 O0Z sing 324 n n C12 C13 O0Z doub 325 n y C14 C13 O0Z sing 326 n y C34 C35 O0Z sing 327 n n C12 H1 O0Z sing 328 n n C13 H2 O0Z sing 329 n n C14 H3 O0Z sing 330 n n C01 H4 O0Z sing 331 n n C01 H5 O0Z sing 332 n n C01 H6 O0Z sing 333 n n C02 H7 O0Z sing 334 n n C02 H8 O0Z sing 335 n n C03 H9 O0Z sing 336 n n C03 H10 O0Z sing 337 n n C04 H11 O0Z sing 338 n n C04 H12 O0Z sing 339 n n C06 H13 O0Z sing 340 n n C07 H14 O0Z sing 341 n n C07 H15 O0Z sing 342 n n C09 H16 O0Z sing 343 n n C15 H17 O0Z sing 344 n n C20 H18 O0Z sing 345 n n C20 H19 O0Z sing 346 n n C21 H20 O0Z sing 347 n n C21 H21 O0Z sing 348 n n C22 H22 O0Z sing 349 n n C23 H23 O0Z sing 350 n n C23 H24 O0Z sing 351 n n C24 H25 O0Z sing 352 n n C24 H26 O0Z sing 353 n n C25 H27 O0Z sing 354 n n C25 H28 O0Z sing 355 n n C27 H29 O0Z sing 356 n n C27 H30 O0Z sing 357 n n C29 H31 O0Z sing 358 n n C30 H32 O0Z sing 359 n n C31 H33 O0Z sing 360 n n C32 H34 O0Z sing 361 n n C33 H35 O0Z sing 362 n n C34 H36 O0Z sing 363 n n C34 H37 O0Z sing 364 n n C35 H38 O0Z sing 365 n n C35 H39 O0Z sing 366 n n N05 H40 O0Z sing 367 n n N10 H42 O0Z sing 368 n n N19 H43 O0Z sing 369 n n # _atom_sites.entry_id 6XTA _atom_sites.fract_transf_matrix[1][1] 0.006492 _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] 0.006492 _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] 0.007814 _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 5 NAG A 1 610 539 NAG NAG . G 5 NAG A 1 611 541 NAG NAG . H 6 O0Z A 1 612 601 O0Z 445 . I 7 SO4 A 1 613 1 SO4 SO4 . J 7 SO4 A 1 614 2 SO4 SO4 . K 8 CL A 1 615 1 CL CL . L 9 HOH A 1 701 6 HOH HOH . L 9 HOH A 2 702 28 HOH HOH . L 9 HOH A 3 703 43 HOH HOH . L 9 HOH A 4 704 45 HOH HOH . L 9 HOH A 5 705 54 HOH HOH . L 9 HOH A 6 706 15 HOH HOH . L 9 HOH A 7 707 52 HOH HOH . L 9 HOH A 8 708 49 HOH HOH . L 9 HOH A 9 709 2 HOH HOH . L 9 HOH A 10 710 24 HOH HOH . L 9 HOH A 11 711 14 HOH HOH . L 9 HOH A 12 712 30 HOH HOH . L 9 HOH A 13 713 23 HOH HOH . L 9 HOH A 14 714 17 HOH HOH . L 9 HOH A 15 715 26 HOH HOH . L 9 HOH A 16 716 36 HOH HOH . L 9 HOH A 17 717 18 HOH HOH . L 9 HOH A 18 718 51 HOH HOH . L 9 HOH A 19 719 37 HOH HOH . L 9 HOH A 20 720 40 HOH HOH . L 9 HOH A 21 721 55 HOH HOH . L 9 HOH A 22 722 1 HOH HOH . L 9 HOH A 23 723 32 HOH HOH . L 9 HOH A 24 724 31 HOH HOH . L 9 HOH A 25 725 21 HOH HOH . L 9 HOH A 26 726 38 HOH HOH . L 9 HOH A 27 727 8 HOH HOH . L 9 HOH A 28 728 3 HOH HOH . L 9 HOH A 29 729 7 HOH HOH . L 9 HOH A 30 730 44 HOH HOH . L 9 HOH A 31 731 20 HOH HOH . L 9 HOH A 32 732 9 HOH HOH . L 9 HOH A 33 733 19 HOH HOH . L 9 HOH A 34 734 25 HOH HOH . L 9 HOH A 35 735 10 HOH HOH . L 9 HOH A 36 736 11 HOH HOH . L 9 HOH A 37 737 35 HOH HOH . L 9 HOH A 38 738 47 HOH HOH . L 9 HOH A 39 739 27 HOH HOH . L 9 HOH A 40 740 34 HOH HOH . L 9 HOH A 41 741 48 HOH HOH . L 9 HOH A 42 742 4 HOH HOH . L 9 HOH A 43 743 5 HOH HOH . L 9 HOH A 44 744 13 HOH HOH . L 9 HOH A 45 745 12 HOH HOH . L 9 HOH A 46 746 42 HOH HOH . L 9 HOH A 47 747 22 HOH HOH . L 9 HOH A 48 748 39 HOH HOH . L 9 HOH A 49 749 56 HOH HOH . L 9 HOH A 50 750 33 HOH HOH . L 9 HOH A 51 751 53 HOH HOH . L 9 HOH A 52 752 50 HOH HOH . L 9 HOH A 53 753 41 HOH HOH . L 9 HOH A 54 754 29 HOH HOH . L 9 HOH A 55 755 57 HOH HOH . L 9 HOH A 56 756 46 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 C11 O0Z . . . H 6 138.076 113.677 40.965 1 65.82 ? C11 O0Z 612 A 1 HETATM 2 C C12 O0Z . . . H 6 138.192 114.655 41.986 1 69.2 ? C12 O0Z 612 A 1 HETATM 3 C C13 O0Z . . . H 6 139.443 114.767 42.646 1 81.03 ? C13 O0Z 612 A 1 HETATM 4 C C14 O0Z . . . H 6 140.548 113.922 42.311 1 70.47 ? C14 O0Z 612 A 1 HETATM 5 C C01 O0Z . . . H 6 142.896 104.126 39.338 1 75.64 ? C01 O0Z 612 A 1 HETATM 6 C C02 O0Z . . . H 6 141.714 104.999 39.842 1 76.47 ? C02 O0Z 612 A 1 HETATM 7 C C03 O0Z . . . H 6 141.534 106.334 39.074 1 72.11 ? C03 O0Z 612 A 1 HETATM 8 C C04 O0Z . . . H 6 140.584 107.329 39.742 1 72.09 ? C04 O0Z 612 A 1 HETATM 9 C C06 O0Z . . . H 6 139.39 109.492 39.568 1 73.7 ? C06 O0Z 612 A 1 HETATM 10 C C07 O0Z . . . H 6 139.395 110.84 38.791 1 61.98 ? C07 O0Z 612 A 1 HETATM 11 C C08 O0Z . . . H 6 138.654 111.943 39.519 1 74.29 ? C08 O0Z 612 A 1 HETATM 12 C C09 O0Z . . . H 6 137.318 112.318 39.283 1 69.52 ? C09 O0Z 612 A 1 HETATM 13 C C15 O0Z . . . H 6 140.381 112.946 41.292 1 73.07 ? C15 O0Z 612 A 1 HETATM 14 C C16 O0Z . . . H 6 139.133 112.814 40.592 1 73.14 ? C16 O0Z 612 A 1 HETATM 15 C C17 O0Z . . . H 6 137.921 108.967 39.759 1 76.67 ? C17 O0Z 612 A 1 HETATM 16 C C20 O0Z . . . H 6 135.991 108.541 41.331 1 67.56 ? C20 O0Z 612 A 1 HETATM 17 C C21 O0Z . . . H 6 135.299 109.556 42.34 1 81.73 ? C21 O0Z 612 A 1 HETATM 18 C C22 O0Z . . . H 6 134.737 110.902 41.724 1 68.04 ? C22 O0Z 612 A 1 HETATM 19 C C23 O0Z . . . H 6 133.902 110.603 40.465 1 73.44 ? C23 O0Z 612 A 1 HETATM 20 C C24 O0Z . . . H 6 133.23 111.82 39.816 1 68.95 ? C24 O0Z 612 A 1 HETATM 21 C C25 O0Z . . . H 6 131.869 112.161 40.4 1 80.19 ? C25 O0Z 612 A 1 HETATM 22 C C27 O0Z . . . H 6 131.18 114.386 41.623 1 68.06 ? C27 O0Z 612 A 1 HETATM 23 C C28 O0Z . . . H 6 131.971 115.497 40.881 1 72.62 ? C28 O0Z 612 A 1 HETATM 24 C C29 O0Z . . . H 6 132.274 115.439 39.499 1 72.1 ? C29 O0Z 612 A 1 HETATM 25 C C30 O0Z . . . H 6 132.979 116.468 38.85 1 67.66 ? C30 O0Z 612 A 1 HETATM 26 C C31 O0Z . . . H 6 133.416 117.599 39.568 1 66.7 ? C31 O0Z 612 A 1 HETATM 27 C C32 O0Z . . . H 6 133.118 117.664 40.943 1 63.61 ? C32 O0Z 612 A 1 HETATM 28 C C33 O0Z . . . H 6 132.403 116.637 41.584 1 64.82 ? C33 O0Z 612 A 1 HETATM 29 C C34 O0Z . . . H 6 133.327 113.016 42.322 1 71.95 ? C34 O0Z 612 A 1 HETATM 30 C C35 O0Z . . . H 6 133.864 111.641 42.766 1 69.56 ? C35 O0Z 612 A 1 HETATM 31 N N05 O0Z . . . H 6 140.154 108.431 38.799 1 73.02 ? N05 O0Z 612 A 1 HETATM 32 N N10 O0Z . . . H 6 136.97 113.35 40.133 1 70.24 ? N10 O0Z 612 A 1 HETATM 33 N N19 O0Z . . . H 6 137.34 108.998 41.072 1 72.09 ? N19 O0Z 612 A 1 HETATM 34 N N26 O0Z . . . H 6 131.889 112.957 41.743 1 85.48 ? N26 O0Z 612 A 1 HETATM 35 O O18 O0Z . . . H 6 137.284 108.542 38.794 1 74.33 ? O18 O0Z 612 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 28 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 317 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 35 #