data_5GRT # _model_server_result.job_id G-z9t1_kEI_J1p3iZVuUhA _model_server_result.datetime_utc '2024-11-26 16:31:08' _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 5grt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":17}' # _entry.id 5GRT # _exptl.entry_id 5GRT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 867.092 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'GLUTATHIONYLSPERMIDINE DISULFIDE' _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 58.41 _cell.entry_id 5GRT _cell.length_a 120.12 _cell.length_b 84.79 _cell.length_c 63.65 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5GRT _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 _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 1 164.53616 72.22568 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? disulf ? disulf2 A SG CYS 73 A CYS 90 1_555 A SG CYS 73 A CYS 90 2_665 ? ? ? ? ? ? ? ? ? ? ? ? 2.379 ? # _chem_comp.formula 'C34 H66 N12 O10 S2' _chem_comp.formula_weight 867.092 _chem_comp.id TS4 _chem_comp.mon_nstd_flag . _chem_comp.name 'GLUTATHIONYLSPERMIDINE DISULFIDE' _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 N1 CA1 TS4 sing 423 n n N1 HN11 TS4 sing 424 n n N1 HN12 TS4 sing 425 n n CA1 C1 TS4 sing 426 n n CA1 CB1 TS4 sing 427 n n CA1 HA1 TS4 sing 428 n n C1 OE1 TS4 doub 429 n n C1 OE2 TS4 sing 430 n n OE2 HO2 TS4 sing 431 n n CB1 CG1 TS4 sing 432 n n CB1 HB11 TS4 sing 433 n n CB1 HB12 TS4 sing 434 n n CG1 CD1 TS4 sing 435 n n CG1 HG11 TS4 sing 436 n n CG1 HG12 TS4 sing 437 n n CD1 O1 TS4 doub 438 n n CD1 N2 TS4 sing 439 n n N2 CA2 TS4 sing 440 n n N2 HN2 TS4 sing 441 n n CA2 C2 TS4 sing 442 n n CA2 CB2 TS4 sing 443 n n CA2 HA2 TS4 sing 444 n n C2 O2 TS4 doub 445 n n C2 N3 TS4 sing 446 n n CB2 SG2 TS4 sing 447 n n CB2 HB21 TS4 sing 448 n n CB2 HB22 TS4 sing 449 n n SG2 SG5 TS4 sing 450 n n N3 CA3 TS4 sing 451 n n N3 HN3 TS4 sing 452 n n CA3 C3 TS4 sing 453 n n CA3 HA31 TS4 sing 454 n n CA3 HA32 TS4 sing 455 n n C3 O3 TS4 doub 456 n n C3 N1' TS4 sing 457 n n N4 CA4 TS4 sing 458 n n N4 C5 TS4 sing 459 n n N4 HN4 TS4 sing 460 n n CA4 C4 TS4 sing 461 n n CA4 HA41 TS4 sing 462 n n CA4 HA42 TS4 sing 463 n n C4 O4 TS4 doub 464 n n C4 N1T TS4 sing 465 n n C5 O5 TS4 doub 466 n n C5 CA5 TS4 sing 467 n n CA5 N5 TS4 sing 468 n n CA5 CB5 TS4 sing 469 n n CA5 HA5 TS4 sing 470 n n N5 CD6 TS4 sing 471 n n N5 HN5 TS4 sing 472 n n CB5 SG5 TS4 sing 473 n n CB5 HB51 TS4 sing 474 n n CB5 HB52 TS4 sing 475 n n CA6 C6 TS4 sing 476 n n CA6 N6 TS4 sing 477 n n CA6 CB6 TS4 sing 478 n n CA6 HA6 TS4 sing 479 n n C6 OE6 TS4 doub 480 n n C6 OE7 TS4 sing 481 n n OE7 HO7 TS4 sing 482 n n N6 HN61 TS4 sing 483 n n N6 HN62 TS4 sing 484 n n CB6 CG6 TS4 sing 485 n n CB6 HB61 TS4 sing 486 n n CB6 HB62 TS4 sing 487 n n CG6 CD6 TS4 sing 488 n n CG6 HG61 TS4 sing 489 n n CG6 HG62 TS4 sing 490 n n CD6 O6 TS4 doub 491 n n N1' C1' TS4 sing 492 n n N1' HN1' TS4 sing 493 n n C1' C2' TS4 sing 494 n n C1' "H1'1" TS4 sing 495 n n C1' "H1'2" TS4 sing 496 n n C2' C3' TS4 sing 497 n n C2' "H2'1" TS4 sing 498 n n C2' "H2'2" TS4 sing 499 n n N2' C3' TS4 sing 500 n n N2' C4' TS4 sing 501 n n N2' HN2' TS4 sing 502 n n C3' "H3'1" TS4 sing 503 n n C3' "H3'2" TS4 sing 504 n n C4' C5' TS4 sing 505 n n C4' "H4'1" TS4 sing 506 n n C4' "H4'2" TS4 sing 507 n n C5' C6' TS4 sing 508 n n C5' "H5'1" TS4 sing 509 n n C5' "H5'2" TS4 sing 510 n n C6' C7' TS4 sing 511 n n C6' "H6'1" TS4 sing 512 n n C6' "H6'2" TS4 sing 513 n n C7' N3' TS4 sing 514 n n C7' "H7'1" TS4 sing 515 n n C7' "H7'2" TS4 sing 516 n n N3' HN31 TS4 sing 517 n n N3' HN32 TS4 sing 518 n n N1T C1T TS4 sing 519 n n N1T HN1 TS4 sing 520 n n C1T C2T TS4 sing 521 n n C1T H1T1 TS4 sing 522 n n C1T H1T2 TS4 sing 523 n n C2T C3T TS4 sing 524 n n C2T H2T1 TS4 sing 525 n n C2T H2T2 TS4 sing 526 n n C3T N2T TS4 sing 527 n n C3T H3T1 TS4 sing 528 n n C3T H3T2 TS4 sing 529 n n N2T C4T TS4 sing 530 n n N2T H2N TS4 sing 531 n n C4T C5T TS4 sing 532 n n C4T H4T1 TS4 sing 533 n n C4T H4T2 TS4 sing 534 n n C5T C6T TS4 sing 535 n n C5T H5T1 TS4 sing 536 n n C5T H5T2 TS4 sing 537 n n C6T C7T TS4 sing 538 n n C6T H6T1 TS4 sing 539 n n C6T H6T2 TS4 sing 540 n n C7T N3T TS4 sing 541 n n C7T H7T1 TS4 sing 542 n n C7T H7T2 TS4 sing 543 n n N3T HNT1 TS4 sing 544 n n N3T HNT2 TS4 sing 545 n n # _atom_sites.entry_id 5GRT _atom_sites.fract_transf_matrix[1][1] 0.008325 _atom_sites.fract_transf_matrix[1][2] -0.00512 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013845 _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] 0.015711 _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 TS4 A 1 17 17 TS4 TS4 . # 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 TS4 . . . C 3 69.708 34.569 18.451 1 48.58 ? N1 TS4 17 A 1 HETATM 2 C CA1 TS4 . . . C 3 69.153 35.702 17.677 1 52.03 ? CA1 TS4 17 A 1 HETATM 3 C C1 TS4 . . . C 3 68.786 35.195 16.295 1 50.85 ? C1 TS4 17 A 1 HETATM 4 O OE1 TS4 . . . C 3 68.058 34.181 16.252 1 52.09 ? OE1 TS4 17 A 1 HETATM 5 O OE2 TS4 . . . C 3 69.217 35.81 15.289 1 47.75 ? OE2 TS4 17 A 1 HETATM 6 C CB1 TS4 . . . C 3 67.913 36.256 18.386 1 56.41 ? CB1 TS4 17 A 1 HETATM 7 C CG1 TS4 . . . C 3 67.388 37.569 17.819 1 60.5 ? CG1 TS4 17 A 1 HETATM 8 C CD1 TS4 . . . C 3 66.505 37.4 16.586 1 62.99 ? CD1 TS4 17 A 1 HETATM 9 O O1 TS4 . . . C 3 66.862 37.869 15.496 1 64.96 ? O1 TS4 17 A 1 HETATM 10 N N2 TS4 . . . C 3 65.513 36.513 16.708 1 63.25 ? N2 TS4 17 A 1 HETATM 11 C CA2 TS4 . . . C 3 64.545 36.243 15.64 1 63.21 ? CA2 TS4 17 A 1 HETATM 12 C C2 TS4 . . . C 3 64.917 35.125 14.64 1 63.98 ? C2 TS4 17 A 1 HETATM 13 O O2 TS4 . . . C 3 64.333 35.043 13.548 1 63.29 ? O2 TS4 17 A 1 HETATM 14 C CB2 TS4 . . . C 3 64.174 37.553 14.93 1 61.14 ? CB2 TS4 17 A 1 HETATM 15 S SG2 TS4 . . . C 3 63.604 38.847 16.087 1 59.54 ? SG2 TS4 17 A 1 HETATM 16 N N3 TS4 . . . C 3 65.515 34.075 15.213 1 62.54 ? N3 TS4 17 A 1 HETATM 17 C CA3 TS4 . . . C 3 65.963 32.859 14.52 1 61.27 ? CA3 TS4 17 A 1 HETATM 18 C C3 TS4 . . . C 3 65.319 31.504 14.934 1 61.27 ? C3 TS4 17 A 1 HETATM 19 O O3 TS4 . . . C 3 64.874 30.747 14.055 1 58.99 ? O3 TS4 17 A 1 HETATM 20 N N4 TS4 . . . C 3 63.551 38.229 22.535 1 55.76 ? N4 TS4 17 A 1 HETATM 21 C CA4 TS4 . . . C 3 63.689 37.842 23.929 1 55.92 ? CA4 TS4 17 A 1 HETATM 22 C C4 TS4 . . . C 3 62.171 37.978 24.077 1 56.82 ? C4 TS4 17 A 1 HETATM 23 O O4 TS4 . . . C 3 61.66 39.104 24.219 1 57.27 ? O4 TS4 17 A 1 HETATM 24 C C5 TS4 . . . C 3 64.35 37.894 21.523 1 55.26 ? C5 TS4 17 A 1 HETATM 25 O O5 TS4 . . . C 3 65.027 36.852 21.492 1 52.11 ? O5 TS4 17 A 1 HETATM 26 C CA5 TS4 . . . C 3 63.791 38.522 20.253 1 53.97 ? CA5 TS4 17 A 1 HETATM 27 N N5 TS4 . . . C 3 63.743 39.971 20.275 1 50.87 ? N5 TS4 17 A 1 HETATM 28 C CB5 TS4 . . . C 3 64.37 37.986 18.959 1 55.2 ? CB5 TS4 17 A 1 HETATM 29 S SG5 TS4 . . . C 3 63.022 37.803 17.736 1 60.84 ? SG5 TS4 17 A 1 HETATM 30 C CA6 TS4 . . . C 3 61.847 42.432 20.084 1 48.46 ? CA6 TS4 17 A 1 HETATM 31 C C6 TS4 . . . C 3 62.185 43.622 19.179 1 47.24 ? C6 TS4 17 A 1 HETATM 32 O OE6 TS4 . . . C 3 61.626 44.715 19.415 1 47.06 ? OE6 TS4 17 A 1 HETATM 33 O OE7 TS4 . . . C 3 63.021 43.442 18.259 1 45.23 ? OE7 TS4 17 A 1 HETATM 34 N N6 TS4 . . . C 3 60.409 42.333 20.486 1 46.91 ? N6 TS4 17 A 1 HETATM 35 C CB6 TS4 . . . C 3 62.751 42.47 21.306 1 47.23 ? CB6 TS4 17 A 1 HETATM 36 C CG6 TS4 . . . C 3 64.199 42.157 20.981 1 48.36 ? CG6 TS4 17 A 1 HETATM 37 C CD6 TS4 . . . C 3 64.484 40.707 21.097 1 48.51 ? CD6 TS4 17 A 1 HETATM 38 O O6 TS4 . . . C 3 65.603 40.361 21.482 1 52.74 ? O6 TS4 17 A 1 HETATM 39 N N1' TS4 . . . C 3 65.069 31.288 16.232 1 59.48 ? N1' TS4 17 A 1 HETATM 40 C C1' TS4 . . . C 3 65.561 32.104 17.354 1 53.93 ? C1' TS4 17 A 1 HETATM 41 C C2' TS4 . . . C 3 65.191 31.497 18.704 1 49.55 ? C2' TS4 17 A 1 HETATM 42 N N2' TS4 . . . C 3 64.375 33.423 20.061 1 51 ? N2' TS4 17 A 1 HETATM 43 C C3' TS4 . . . C 3 64.01 32.222 19.309 1 50.98 ? C3' TS4 17 A 1 HETATM 44 C C4' TS4 . . . C 3 64.236 32.991 21.452 1 51.84 ? C4' TS4 17 A 1 HETATM 45 C C5' TS4 . . . C 3 65.217 33.548 22.489 1 49.99 ? C5' TS4 17 A 1 HETATM 46 C C6' TS4 . . . C 3 65.085 32.828 23.834 1 46.9 ? C6' TS4 17 A 1 HETATM 47 C C7' TS4 . . . C 3 65.867 31.52 23.841 1 46.13 ? C7' TS4 17 A 1 HETATM 48 N N3' TS4 . . . C 3 67.349 31.75 23.802 1 42.44 ? N3' TS4 17 A 1 HETATM 49 N N1T TS4 . . . C 3 61.467 36.939 23.618 1 55.04 ? N1T TS4 17 A 1 HETATM 50 C C1T TS4 . . . C 3 62.006 35.591 23.42 1 53.05 ? C1T TS4 17 A 1 HETATM 51 C C2T TS4 . . . C 3 61.581 34.972 22.076 1 52.58 ? C2T TS4 17 A 1 HETATM 52 C C3T TS4 . . . C 3 61.901 35.889 20.893 1 51.05 ? C3T TS4 17 A 1 HETATM 53 N N2T TS4 . . . C 3 60.75 36.391 20.127 1 49.52 ? N2T TS4 17 A 1 HETATM 54 C C4T TS4 . . . C 3 60.615 35.741 18.813 1 47.95 ? C4T TS4 17 A 1 HETATM 55 C C5T TS4 . . . C 3 61.395 34.446 18.565 1 46.28 ? C5T TS4 17 A 1 HETATM 56 C C6T TS4 . . . C 3 61.203 33.888 17.156 1 43.54 ? C6T TS4 17 A 1 HETATM 57 C C7T TS4 . . . C 3 61.439 34.922 16.062 1 42.93 ? C7T TS4 17 A 1 HETATM 58 N N3T TS4 . . . C 3 60.221 35.741 15.788 1 41.64 ? N3T TS4 17 A 1 # _model_server_stats.io_time_ms 52 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 281 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 58 #