data_3GRT # _model_server_result.job_id q2Oi6Q0lnHaXrIwm0RcvWA _model_server_result.datetime_utc '2024-11-30 02:07:55' _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 3grt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":17}' # _entry.id 3GRT # _exptl.entry_id 3GRT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 721.846 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '2-AMINO-4-[4-(4-AMINO-4-CARBOXY-BUTYRYLAMINO)-5,8,19,22-TETRAOXO-1,2-DITHIA-6,9,13,18,21-PENTAAZA-CYCLOTETRACOS-23-YLCARBAMOYL]-BUTYRIC ACID' _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 58.68 _cell.entry_id 3GRT _cell.length_a 119.66 _cell.length_b 84.69 _cell.length_c 63.67 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3GRT _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'B 1 1 2' # _pdbx_struct_assembly.method_details PISA,PQS _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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_665 -x+1,-y+1,z -1 0 0 0 -1 0 0 0 1 163.683331 72.348756 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _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 disulf ? disulf1 A SG CYS 41 A CYS 58 1_555 A SG CYS 46 A CYS 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf2 A SG CYS 73 A CYS 90 1_555 A SG CYS 73 A CYS 90 2_665 ? ? ? ? ? ? ? ? ? ? ? ? 2.385 ? # _chem_comp.formula 'C27 H47 N9 O10 S2' _chem_comp.formula_weight 721.846 _chem_comp.id TS2 _chem_comp.mon_nstd_flag . _chem_comp.name '2-AMINO-4-[4-(4-AMINO-4-CARBOXY-BUTYRYLAMINO)-5,8,19,22-TETRAOXO-1,2-DITHIA-6,9,13,18,21-PENTAAZA-CYCLOTETRACOS-23-YLCARBAMOYL]-BUTYRIC ACID' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'RING WITH GLUTATHIONE AND SPERMIDINE' # 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 N1 CA1 TS2 sing 425 n n N1 HN11 TS2 sing 426 n n N1 HN12 TS2 sing 427 n n CA1 C1 TS2 sing 428 n n CA1 CB1 TS2 sing 429 n n CA1 HA1 TS2 sing 430 n n C1 OE1 TS2 doub 431 n n C1 OE2 TS2 sing 432 n n OE2 HO2 TS2 sing 433 n n CB1 CG1 TS2 sing 434 n n CB1 HB11 TS2 sing 435 n n CB1 HB12 TS2 sing 436 n n CG1 CD1 TS2 sing 437 n n CG1 HG11 TS2 sing 438 n n CG1 HG12 TS2 sing 439 n n CD1 O1 TS2 doub 440 n n CD1 N2 TS2 sing 441 n n N2 CA2 TS2 sing 442 n n N2 HN2 TS2 sing 443 n n CA2 C2 TS2 sing 444 n n CA2 CB2 TS2 sing 445 n n CA2 HA2 TS2 sing 446 n n C2 O2 TS2 doub 447 n n C2 N3 TS2 sing 448 n n CB2 SG2 TS2 sing 449 n n CB2 HB21 TS2 sing 450 n n CB2 HB22 TS2 sing 451 n n SG2 SG5 TS2 sing 452 n n N3 CA3 TS2 sing 453 n n N3 HN3 TS2 sing 454 n n CA3 C3 TS2 sing 455 n n CA3 HA31 TS2 sing 456 n n CA3 HA32 TS2 sing 457 n n C3 O3 TS2 doub 458 n n C3 N3' TS2 sing 459 n n N4 CA4 TS2 sing 460 n n N4 C5 TS2 sing 461 n n N4 HN4 TS2 sing 462 n n CA4 C4 TS2 sing 463 n n CA4 HA41 TS2 sing 464 n n CA4 HA42 TS2 sing 465 n n C4 O4 TS2 doub 466 n n C4 N1' TS2 sing 467 n n C5 O5 TS2 doub 468 n n C5 CA5 TS2 sing 469 n n CA5 N5 TS2 sing 470 n n CA5 CB5 TS2 sing 471 n n CA5 HA5 TS2 sing 472 n n N5 CD6 TS2 sing 473 n n N5 HN5 TS2 sing 474 n n CB5 SG5 TS2 sing 475 n n CB5 HB51 TS2 sing 476 n n CB5 HB52 TS2 sing 477 n n CA6 C6 TS2 sing 478 n n CA6 N6 TS2 sing 479 n n CA6 CB6 TS2 sing 480 n n CA6 HA6 TS2 sing 481 n n C6 OE6 TS2 doub 482 n n C6 OE7 TS2 sing 483 n n OE7 HO7 TS2 sing 484 n n N6 HN61 TS2 sing 485 n n N6 HN62 TS2 sing 486 n n CB6 CG6 TS2 sing 487 n n CB6 HB61 TS2 sing 488 n n CB6 HB62 TS2 sing 489 n n CG6 CD6 TS2 sing 490 n n CG6 HG61 TS2 sing 491 n n CG6 HG62 TS2 sing 492 n n CD6 O6 TS2 doub 493 n n N1' C1' TS2 sing 494 n n N1' HN1' TS2 sing 495 n n C1' C2' TS2 sing 496 n n C1' "H1'1" TS2 sing 497 n n C1' "H1'2" TS2 sing 498 n n C2' C3' TS2 sing 499 n n C2' "H2'1" TS2 sing 500 n n C2' "H2'2" TS2 sing 501 n n N2' C3' TS2 sing 502 n n N2' C4' TS2 sing 503 n n N2' HN2' TS2 sing 504 n n C3' "H3'1" TS2 sing 505 n n C3' "H3'2" TS2 sing 506 n n C4' C5' TS2 sing 507 n n C4' "H4'1" TS2 sing 508 n n C4' "H4'2" TS2 sing 509 n n C5' C6' TS2 sing 510 n n C5' "H5'1" TS2 sing 511 n n C5' "H5'2" TS2 sing 512 n n C6' C7' TS2 sing 513 n n C6' "H6'1" TS2 sing 514 n n C6' "H6'2" TS2 sing 515 n n C7' N3' TS2 sing 516 n n C7' "H7'1" TS2 sing 517 n n C7' "H7'2" TS2 sing 518 n n N3' HN3' TS2 sing 519 n n # _atom_sites.entry_id 3GRT _atom_sites.fract_transf_matrix[1][1] 0.008357 _atom_sites.fract_transf_matrix[1][2] -0.005085 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013822 _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] 0.015706 _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 FAD A 1 479 479 FAD FAD . C 3 TS2 A 1 17 17 TS2 TS2 . D 4 HOH A 1 480 480 HOH HOH . D 4 HOH A 2 484 484 HOH HOH . D 4 HOH A 3 485 485 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 N1 TS2 . . . C 3 69.163 36.142 18.753 1 15 ? N1 TS2 17 A 1 HETATM 2 C CA1 TS2 . . . C 3 69.396 35.426 17.471 1 15 ? CA1 TS2 17 A 1 HETATM 3 C C1 TS2 . . . C 3 69.744 36.39 16.315 1 15 ? C1 TS2 17 A 1 HETATM 4 O OE1 TS2 . . . C 3 69.886 37.604 16.593 1 15 ? OE1 TS2 17 A 1 HETATM 5 O OE2 TS2 . . . C 3 69.913 35.932 15.154 1 15 ? OE2 TS2 17 A 1 HETATM 6 C CB1 TS2 . . . C 3 68.181 34.578 17.138 1 15 ? CB1 TS2 17 A 1 HETATM 7 C CG1 TS2 . . . C 3 67.096 35.285 16.349 1 15 ? CG1 TS2 17 A 1 HETATM 8 C CD1 TS2 . . . C 3 66.428 36.458 17.073 1 15 ? CD1 TS2 17 A 1 HETATM 9 O O1 TS2 . . . C 3 67.053 37.284 17.754 1 15 ? O1 TS2 17 A 1 HETATM 10 N N2 TS2 . . . C 3 65.116 36.516 16.91 1 15 ? N2 TS2 17 A 1 HETATM 11 C CA2 TS2 . . . C 3 64.309 37.575 17.48 1 15 ? CA2 TS2 17 A 1 HETATM 12 C C2 TS2 . . . C 3 62.9 37.006 17.658 1 15 ? C2 TS2 17 A 1 HETATM 13 O O2 TS2 . . . C 3 62.27 37.165 18.729 1 15 ? O2 TS2 17 A 1 HETATM 14 C CB2 TS2 . . . C 3 64.283 38.717 16.473 1 15 ? CB2 TS2 17 A 1 HETATM 15 S SG2 TS2 . . . C 3 62.687 39.576 16.375 1 15 ? SG2 TS2 17 A 1 HETATM 16 N N3 TS2 . . . C 3 62.445 36.34 16.584 1 15 ? N3 TS2 17 A 1 HETATM 17 C CA3 TS2 . . . C 3 61.141 35.692 16.448 1 15 ? CA3 TS2 17 A 1 HETATM 18 C C3 TS2 . . . C 3 60.281 35.544 17.673 1 15 ? C3 TS2 17 A 1 HETATM 19 O O3 TS2 . . . C 3 59.308 36.288 17.867 1 15 ? O3 TS2 17 A 1 HETATM 20 N N4 TS2 . . . C 3 61.574 41.476 21.764 1 15 ? N4 TS2 17 A 1 HETATM 21 C CA4 TS2 . . . C 3 60.706 41.887 22.864 1 15 ? CA4 TS2 17 A 1 HETATM 22 C C4 TS2 . . . C 3 59.593 40.981 23.406 1 15 ? C4 TS2 17 A 1 HETATM 23 O O4 TS2 . . . C 3 58.446 41.421 23.405 1 15 ? O4 TS2 17 A 1 HETATM 24 C C5 TS2 . . . C 3 62.019 42.294 20.806 1 15 ? C5 TS2 17 A 1 HETATM 25 O O5 TS2 . . . C 3 61.725 43.497 20.728 1 15 ? O5 TS2 17 A 1 HETATM 26 C CA5 TS2 . . . C 3 62.917 41.666 19.734 1 15 ? CA5 TS2 17 A 1 HETATM 27 N N5 TS2 . . . C 3 63.28 40.237 19.915 1 15 ? N5 TS2 17 A 1 HETATM 28 C CB5 TS2 . . . C 3 62.213 41.882 18.392 1 15 ? CB5 TS2 17 A 1 HETATM 29 S SG5 TS2 . . . C 3 63.182 41.491 16.901 1 15 ? SG5 TS2 17 A 1 HETATM 30 C CA6 TS2 . . . C 3 64.572 37.028 23.097 1 15 ? CA6 TS2 17 A 1 HETATM 31 C C6 TS2 . . . C 3 63.367 37.739 23.779 1 15 ? C6 TS2 17 A 1 HETATM 32 O OE6 TS2 . . . C 3 62.852 37.119 24.746 1 15 ? OE6 TS2 17 A 1 HETATM 33 O OE7 TS2 . . . C 3 62.922 38.853 23.373 1 15 ? OE7 TS2 17 A 1 HETATM 34 N N6 TS2 . . . C 3 64.195 35.684 22.534 1 15 ? N6 TS2 17 A 1 HETATM 35 C CB6 TS2 . . . C 3 65.289 37.905 22.052 1 15 ? CB6 TS2 17 A 1 HETATM 36 C CG6 TS2 . . . C 3 64.442 38.315 20.843 1 15 ? CG6 TS2 17 A 1 HETATM 37 C CD6 TS2 . . . C 3 64.169 39.819 20.819 1 15 ? CD6 TS2 17 A 1 HETATM 38 O O6 TS2 . . . C 3 64.744 40.581 21.608 1 15 ? O6 TS2 17 A 1 HETATM 39 N N1' TS2 . . . C 3 59.958 39.75 23.821 1 15 ? N1' TS2 17 A 1 HETATM 40 C C1' TS2 . . . C 3 59.125 38.68 24.387 1 15 ? C1' TS2 17 A 1 HETATM 41 C C2' TS2 . . . C 3 59.867 37.317 24.728 1 15 ? C2' TS2 17 A 1 HETATM 42 N N2' TS2 . . . C 3 59.634 35.923 22.427 1 15 ? N2' TS2 17 A 1 HETATM 43 C C3' TS2 . . . C 3 60.431 36.563 23.486 1 15 ? C3' TS2 17 A 1 HETATM 44 C C4' TS2 . . . C 3 59.74 34.48 22.737 1 15 ? C4' TS2 17 A 1 HETATM 45 C C5' TS2 . . . C 3 60.857 33.667 22.009 1 15 ? C5' TS2 17 A 1 HETATM 46 C C6' TS2 . . . C 3 60.456 33.179 20.587 1 15 ? C6' TS2 17 A 1 HETATM 47 C C7' TS2 . . . C 3 59.888 34.319 19.758 1 15 ? C7' TS2 17 A 1 HETATM 48 N N3' TS2 . . . C 3 60.63 34.586 18.525 1 15 ? N3' TS2 17 A 1 # _model_server_stats.io_time_ms 60 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 297 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 48 #