data_5TAD # _model_server_result.job_id 6R5TuHlJrGigkhQQRf01hA _model_server_result.datetime_utc '2025-02-27 01:19:22' _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 5tad # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":1002}' # _entry.id 5TAD # _exptl.entry_id 5TAD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 147.195 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description LYSINE _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 5TAD _cell.length_a 93.779 _cell.length_b 93.779 _cell.length_c 131.076 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5TAD _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 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 _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 5 _struct_asym.id H _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 G C VAL . A VAL 1001 1_555 H N LYS . A LYS 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 sing metalc ? metalc1 A OD1 ASP 57 A ASP 57 1_555 D CA CA . A CA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.422 ? metalc ? metalc2 A OD2 ASP 57 A ASP 57 1_555 D CA CA . A CA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.531 ? metalc ? metalc3 A OD1 ASP 59 A ASP 59 1_555 D CA CA . A CA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.42 ? metalc ? metalc4 A O GLN 61 A GLN 61 1_555 D CA CA . A CA 403 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.257 ? metalc ? metalc5 A O GLN 61 A GLN 61 1_555 D CA CA . A CA 403 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.313 ? metalc ? metalc6 A OD2 ASP 138 A ASP 138 1_555 B CA CA . A CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.523 ? metalc ? metalc7 A NE2 HIS 142 A HIS 142 1_555 F ZN ZN . A ZN 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? metalc ? metalc8 A NE2 HIS 146 A HIS 146 1_555 F ZN ZN . A ZN 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? metalc ? metalc9 A OE2 GLU 166 A GLU 166 1_555 F ZN ZN . A ZN 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? metalc ? metalc10 A OE1 GLU 177 A GLU 177 1_555 B CA CA . A CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.536 ? metalc ? metalc11 A OE2 GLU 177 A GLU 177 1_555 B CA CA . A CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.675 ? metalc ? metalc12 A OE2 GLU 177 A GLU 177 1_555 C CA CA . A CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.761 ? metalc ? metalc13 A O ASN 183 A ASN 183 1_555 C CA CA . A CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.544 ? metalc ? metalc14 A OD1 ASP 185 A ASP 185 1_555 B CA CA . A CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.521 ? metalc ? metalc15 A OD2 ASP 185 A ASP 185 1_555 C CA CA . A CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.723 ? metalc ? metalc16 A O GLU 187 A GLU 187 1_555 B CA CA . A CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.32 ? metalc ? metalc17 A OE1 GLU 190 A GLU 190 1_555 B CA CA . A CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.472 ? metalc ? metalc18 A OE2 GLU 190 A GLU 190 1_555 B CA CA . A CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.492 ? metalc ? metalc19 A OE2 GLU 190 A GLU 190 1_555 C CA CA . A CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.45 ? metalc ? metalc20 A O TYR 193 A TYR 193 1_555 E CA CA . A CA 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.385 ? metalc ? metalc21 A O THR 194 A THR 194 1_555 E CA CA . A CA 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.427 ? metalc ? metalc22 A OG1 THR 194 A THR 194 1_555 E CA CA . A CA 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.429 ? metalc ? metalc23 A O ILE 197 A ILE 197 1_555 E CA CA . A CA 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.345 ? metalc ? metalc24 A OD1 ASP 200 A ASP 200 1_555 E CA CA . A CA 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.41 ? metalc ? metalc25 B CA CA . A CA 401 1_555 J O HOH . A HOH 556 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.568 ? metalc ? metalc26 C CA CA . A CA 402 1_555 J O HOH . A HOH 516 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.559 ? metalc ? metalc27 C CA CA . A CA 402 1_555 J O HOH . A HOH 564 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.479 ? metalc ? metalc28 D CA CA . A CA 403 1_555 J O HOH . A HOH 533 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.521 ? metalc ? metalc29 D CA CA . A CA 403 1_555 J O HOH . A HOH 566 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.428 ? metalc ? metalc30 D CA CA . A CA 403 1_555 J O HOH . A HOH 620 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.271 ? metalc ? metalc31 E CA CA . A CA 404 1_555 J O HOH . A HOH 520 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.476 ? metalc ? metalc32 E CA CA . A CA 404 1_555 J O HOH . A HOH 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? metalc ? metalc33 F ZN ZN . A ZN 405 1_555 I O3 PO4 . A PO4 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.806 ? # _chem_comp.formula 'C6 H15 N2 O2 1' _chem_comp.formula_weight 147.195 _chem_comp.id LYS _chem_comp.mon_nstd_flag y _chem_comp.name LYSINE _chem_comp.type 'l-peptide linking' _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 N CA LYS sing 181 n n N H LYS sing 182 n n N H2 LYS sing 183 n n CA C LYS sing 184 n n CA CB LYS sing 185 n n CA HA LYS sing 186 n n C O LYS doub 187 n n C OXT LYS sing 188 n n CB CG LYS sing 189 n n CB HB2 LYS sing 190 n n CB HB3 LYS sing 191 n n CG CD LYS sing 192 n n CG HG2 LYS sing 193 n n CG HG3 LYS sing 194 n n CD CE LYS sing 195 n n CD HD2 LYS sing 196 n n CD HD3 LYS sing 197 n n CE NZ LYS sing 198 n n CE HE2 LYS sing 199 n n CE HE3 LYS sing 200 n n NZ HZ1 LYS sing 201 n n NZ HZ2 LYS sing 202 n n NZ HZ3 LYS sing 203 n n OXT HXT LYS sing 204 n n # _atom_sites.entry_id 5TAD _atom_sites.fract_transf_matrix[1][1] 0.010663 _atom_sites.fract_transf_matrix[1][2] 0.006156 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012313 _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] 0.007629 _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 CA A 1 401 401 CA CA . C 2 CA A 1 402 402 CA CA . D 2 CA A 1 403 403 CA CA . E 2 CA A 1 404 404 CA CA . F 3 ZN A 1 405 405 ZN ZN . G 4 VAL A 1 1001 1001 VAL VAL . H 5 LYS A 1 1002 1002 LYS LYS . I 6 PO4 A 1 408 1 PO4 PO4 . J 7 HOH A 1 501 52 HOH HOH . J 7 HOH A 2 502 1 HOH HOH . J 7 HOH A 3 503 21 HOH HOH . J 7 HOH A 4 504 39 HOH HOH . J 7 HOH A 5 505 5 HOH HOH . J 7 HOH A 6 506 31 HOH HOH . J 7 HOH A 7 507 38 HOH HOH . J 7 HOH A 8 508 26 HOH HOH . J 7 HOH A 9 509 32 HOH HOH . J 7 HOH A 10 510 6 HOH HOH . J 7 HOH A 11 511 50 HOH HOH . J 7 HOH A 12 512 71 HOH HOH . J 7 HOH A 13 513 70 HOH HOH . J 7 HOH A 14 514 42 HOH HOH . J 7 HOH A 15 515 8 HOH HOH . J 7 HOH A 16 516 39 HOH HOH . J 7 HOH A 17 517 51 HOH HOH . J 7 HOH A 18 518 13 HOH HOH . J 7 HOH A 19 519 87 HOH HOH . J 7 HOH A 20 520 47 HOH HOH . J 7 HOH A 21 521 119 HOH HOH . J 7 HOH A 22 522 14 HOH HOH . J 7 HOH A 23 523 12 HOH HOH . J 7 HOH A 24 524 23 HOH HOH . J 7 HOH A 25 525 120 HOH HOH . J 7 HOH A 26 526 118 HOH HOH . J 7 HOH A 27 527 2 HOH HOH . J 7 HOH A 28 528 8 HOH HOH . J 7 HOH A 29 529 86 HOH HOH . J 7 HOH A 30 530 59 HOH HOH . J 7 HOH A 31 531 16 HOH HOH . J 7 HOH A 32 532 48 HOH HOH . J 7 HOH A 33 533 69 HOH HOH . J 7 HOH A 34 534 36 HOH HOH . J 7 HOH A 35 535 14 HOH HOH . J 7 HOH A 36 536 7 HOH HOH . J 7 HOH A 37 537 18 HOH HOH . J 7 HOH A 38 538 85 HOH HOH . J 7 HOH A 39 539 33 HOH HOH . J 7 HOH A 40 540 52 HOH HOH . J 7 HOH A 41 541 15 HOH HOH . J 7 HOH A 42 542 97 HOH HOH . J 7 HOH A 43 543 29 HOH HOH . J 7 HOH A 44 544 28 HOH HOH . J 7 HOH A 45 545 89 HOH HOH . J 7 HOH A 46 546 65 HOH HOH . J 7 HOH A 47 547 45 HOH HOH . J 7 HOH A 48 548 44 HOH HOH . J 7 HOH A 49 549 109 HOH HOH . J 7 HOH A 50 550 19 HOH HOH . J 7 HOH A 51 551 54 HOH HOH . J 7 HOH A 52 552 25 HOH HOH . J 7 HOH A 53 553 95 HOH HOH . J 7 HOH A 54 554 88 HOH HOH . J 7 HOH A 55 555 49 HOH HOH . J 7 HOH A 56 556 24 HOH HOH . J 7 HOH A 57 557 57 HOH HOH . J 7 HOH A 58 558 68 HOH HOH . J 7 HOH A 59 559 34 HOH HOH . J 7 HOH A 60 560 40 HOH HOH . J 7 HOH A 61 561 10 HOH HOH . J 7 HOH A 62 562 74 HOH HOH . J 7 HOH A 63 563 41 HOH HOH . J 7 HOH A 64 564 79 HOH HOH . J 7 HOH A 65 565 9 HOH HOH . J 7 HOH A 66 566 75 HOH HOH . J 7 HOH A 67 567 111 HOH HOH . J 7 HOH A 68 568 17 HOH HOH . J 7 HOH A 69 569 27 HOH HOH . J 7 HOH A 70 570 82 HOH HOH . J 7 HOH A 71 571 58 HOH HOH . J 7 HOH A 72 572 105 HOH HOH . J 7 HOH A 73 573 90 HOH HOH . J 7 HOH A 74 574 104 HOH HOH . J 7 HOH A 75 575 53 HOH HOH . J 7 HOH A 76 576 20 HOH HOH . J 7 HOH A 77 577 6 HOH HOH . J 7 HOH A 78 578 12 HOH HOH . J 7 HOH A 79 579 46 HOH HOH . J 7 HOH A 80 580 3 HOH HOH . J 7 HOH A 81 581 99 HOH HOH . J 7 HOH A 82 582 102 HOH HOH . J 7 HOH A 83 583 60 HOH HOH . J 7 HOH A 84 584 73 HOH HOH . J 7 HOH A 85 585 4 HOH HOH . J 7 HOH A 86 586 106 HOH HOH . J 7 HOH A 87 587 66 HOH HOH . J 7 HOH A 88 588 92 HOH HOH . J 7 HOH A 89 589 81 HOH HOH . J 7 HOH A 90 590 30 HOH HOH . J 7 HOH A 91 591 112 HOH HOH . J 7 HOH A 92 592 18 HOH HOH . J 7 HOH A 93 593 96 HOH HOH . J 7 HOH A 94 594 77 HOH HOH . J 7 HOH A 95 595 22 HOH HOH . J 7 HOH A 96 596 11 HOH HOH . J 7 HOH A 97 597 43 HOH HOH . J 7 HOH A 98 598 84 HOH HOH . J 7 HOH A 99 599 62 HOH HOH . J 7 HOH A 100 600 103 HOH HOH . J 7 HOH A 101 601 28 HOH HOH . J 7 HOH A 102 602 15 HOH HOH . J 7 HOH A 103 603 49 HOH HOH . J 7 HOH A 104 604 107 HOH HOH . J 7 HOH A 105 605 25 HOH HOH . J 7 HOH A 106 606 37 HOH HOH . J 7 HOH A 107 607 55 HOH HOH . J 7 HOH A 108 608 83 HOH HOH . J 7 HOH A 109 609 20 HOH HOH . J 7 HOH A 110 610 93 HOH HOH . J 7 HOH A 111 611 11 HOH HOH . J 7 HOH A 112 612 22 HOH HOH . J 7 HOH A 113 613 32 HOH HOH . J 7 HOH A 114 614 98 HOH HOH . J 7 HOH A 115 615 56 HOH HOH . J 7 HOH A 116 616 5 HOH HOH . J 7 HOH A 117 617 60 HOH HOH . J 7 HOH A 118 618 76 HOH HOH . J 7 HOH A 119 619 91 HOH HOH . J 7 HOH A 120 620 121 HOH HOH . J 7 HOH A 121 621 16 HOH HOH . J 7 HOH A 122 622 35 HOH HOH . J 7 HOH A 123 623 61 HOH HOH . J 7 HOH A 124 624 64 HOH HOH . J 7 HOH A 125 625 46 HOH HOH . J 7 HOH A 126 626 27 HOH HOH . J 7 HOH A 127 627 2 HOH HOH . J 7 HOH A 128 628 50 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 N N LYS . . . H 5 -9.135 -41.166 -3.955 1 28.38 ? N LYS 1002 A 1 HETATM 2 C CA LYS . . . H 5 -7.987 -42.034 -4.287 1 29.78 ? CA LYS 1002 A 1 HETATM 3 C C LYS . . . H 5 -8.372 -43.162 -5.248 1 40.88 ? C LYS 1002 A 1 HETATM 4 O O LYS . . . H 5 -7.471 -43.832 -5.794 1 36.98 ? O LYS 1002 A 1 HETATM 5 C CB LYS . . . H 5 -7.363 -42.648 -3.031 1 31.15 ? CB LYS 1002 A 1 HETATM 6 C CG LYS . . . H 5 -8.339 -43.477 -2.171 1 34.94 ? CG LYS 1002 A 1 HETATM 7 C CD LYS . . . H 5 -7.581 -44.169 -1.086 1 54.4 ? CD LYS 1002 A 1 HETATM 8 C CE LYS . . . H 5 -6.578 -45.194 -1.651 1 58.63 ? CE LYS 1002 A 1 HETATM 9 N NZ LYS . . . H 5 -5.688 -45.769 -0.583 1 58.21 ? NZ LYS 1002 A 1 HETATM 10 O OXT LYS . . . H 5 -9.566 -43.424 -5.492 1 35.37 ? OXT LYS 1002 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 244 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 10 #