data_3CBP # _model_server_result.job_id C6BwL6E0YwCZ5Viybt1ExQ _model_server_result.datetime_utc '2024-12-18 04:57:13' _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 3cbp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1501}' # _entry.id 3CBP # _exptl.entry_id 3CBP _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 381.387 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description SINEFUNGIN _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 3CBP _cell.length_a 102.042 _cell.length_b 38.786 _cell.length_c 66.571 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3CBP _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details PISA _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,E,F,G,H,I _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 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 covale ? covale1 A SG CYS 9 A CYS 119 1_555 F S2 BME . A BME 397 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.653 ? covale ? covale2 A SG CYS 90 A CYS 200 1_555 E S2 BME . A BME 396 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.808 ? covale ? covale3 A SG CYS 178 A CYS 288 1_555 D S2 BME . A BME 395 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.039 ? # _chem_comp.formula 'C15 H23 N7 O5' _chem_comp.formula_weight 381.387 _chem_comp.id SFG _chem_comp.mon_nstd_flag . _chem_comp.name SINEFUNGIN _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ADENOSYL-ORNITHINE # 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 SFG sing 312 n n N HN1 SFG sing 313 n n N HN2 SFG sing 314 n n CA C SFG sing 315 n n CA CB SFG sing 316 n n CA HA SFG sing 317 n n C O SFG doub 318 n n C OXT SFG sing 319 n n OXT HXT SFG sing 320 n n CB CG SFG sing 321 n n CB HB1 SFG sing 322 n n CB HB2 SFG sing 323 n n CG CD SFG sing 324 n n CG HG1 SFG sing 325 n n CG HG2 SFG sing 326 n n CD NE SFG sing 327 n n CD C5' SFG sing 328 n n CD HD SFG sing 329 n n NE HNE1 SFG sing 330 n n NE HNE2 SFG sing 331 n n C5' C4' SFG sing 332 n n C5' "H5'1" SFG sing 333 n n C5' "H5'2" SFG sing 334 n n C4' O4' SFG sing 335 n n C4' C3' SFG sing 336 n n C4' H4' SFG sing 337 n n O4' C1' SFG sing 338 n n C3' O3' SFG sing 339 n n C3' C2' SFG sing 340 n n C3' H3' SFG sing 341 n n O3' HO3' SFG sing 342 n n C2' O2' SFG sing 343 n n C2' C1' SFG sing 344 n n C2' H2' SFG sing 345 n n O2' HO2' SFG sing 346 n n C1' N9 SFG sing 347 n n C1' H1' SFG sing 348 n n N9 C8 SFG sing 349 n y N9 C4 SFG sing 350 n y C8 N7 SFG doub 351 n y C8 H8 SFG sing 352 n n N7 C5 SFG sing 353 n y C5 C6 SFG sing 354 n y C5 C4 SFG doub 355 n y C6 N6 SFG sing 356 n n C6 N1 SFG doub 357 n y N6 HN61 SFG sing 358 n n N6 HN62 SFG sing 359 n n N1 C2 SFG sing 360 n y C2 N3 SFG doub 361 n y C2 H2 SFG sing 362 n n N3 C4 SFG sing 363 n y # _atom_sites.entry_id 3CBP _atom_sites.fract_transf_matrix[1][1] 0.0098 _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] 0.025782 _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] 0.015022 _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 C 3 SFG A 1 1501 1501 SFG SFG . D 4 BME A 1 395 395 BME BME . E 4 BME A 1 396 396 BME BME . F 4 BME A 1 397 397 BME BME . G 5 GOL A 1 1502 397 GOL GOL . H 6 HOH A 1 1503 1 HOH TIP . H 6 HOH A 2 1504 2 HOH TIP . H 6 HOH A 3 1505 3 HOH TIP . H 6 HOH A 4 1506 4 HOH TIP . H 6 HOH A 5 1507 5 HOH TIP . H 6 HOH A 6 1508 6 HOH TIP . H 6 HOH A 7 1509 7 HOH TIP . H 6 HOH A 8 1510 8 HOH TIP . H 6 HOH A 9 1511 9 HOH TIP . H 6 HOH A 10 1512 10 HOH TIP . H 6 HOH A 11 1513 11 HOH TIP . H 6 HOH A 12 1514 12 HOH TIP . H 6 HOH A 13 1515 13 HOH TIP . H 6 HOH A 14 1516 14 HOH TIP . H 6 HOH A 15 1517 15 HOH TIP . H 6 HOH A 16 1518 16 HOH TIP . H 6 HOH A 17 1519 17 HOH TIP . H 6 HOH A 18 1520 18 HOH TIP . H 6 HOH A 19 1521 19 HOH TIP . H 6 HOH A 20 1522 20 HOH TIP . H 6 HOH A 21 1523 21 HOH TIP . H 6 HOH A 22 1524 22 HOH TIP . H 6 HOH A 23 1525 23 HOH TIP . H 6 HOH A 24 1526 24 HOH TIP . H 6 HOH A 25 1527 25 HOH TIP . H 6 HOH A 26 1528 26 HOH TIP . H 6 HOH A 27 1529 27 HOH TIP . H 6 HOH A 28 1530 28 HOH TIP . H 6 HOH A 29 1531 29 HOH TIP . H 6 HOH A 30 1532 30 HOH TIP . H 6 HOH A 31 1533 31 HOH TIP . H 6 HOH A 32 1534 32 HOH TIP . H 6 HOH A 33 1535 33 HOH TIP . H 6 HOH A 34 1536 34 HOH TIP . H 6 HOH A 35 1537 35 HOH TIP . H 6 HOH A 36 1538 36 HOH TIP . H 6 HOH A 37 1539 37 HOH TIP . H 6 HOH A 38 1540 38 HOH TIP . H 6 HOH A 39 1541 39 HOH TIP . H 6 HOH A 40 1542 40 HOH TIP . H 6 HOH A 41 1543 41 HOH TIP . H 6 HOH A 42 1544 42 HOH TIP . H 6 HOH A 43 1545 43 HOH TIP . H 6 HOH A 44 1546 44 HOH TIP . H 6 HOH A 45 1547 45 HOH TIP . H 6 HOH A 46 1548 46 HOH TIP . H 6 HOH A 47 1549 47 HOH TIP . H 6 HOH A 48 1550 48 HOH TIP . H 6 HOH A 49 1551 49 HOH TIP . H 6 HOH A 50 1552 50 HOH TIP . H 6 HOH A 51 1553 51 HOH TIP . H 6 HOH A 52 1554 52 HOH TIP . H 6 HOH A 53 1555 54 HOH TIP . H 6 HOH A 54 1556 57 HOH TIP . H 6 HOH A 55 1557 58 HOH TIP . H 6 HOH A 56 1558 59 HOH TIP . H 6 HOH A 57 1559 60 HOH TIP . H 6 HOH A 58 1560 61 HOH TIP . H 6 HOH A 59 1561 62 HOH TIP . H 6 HOH A 60 1562 63 HOH TIP . H 6 HOH A 61 1563 64 HOH TIP . H 6 HOH A 62 1564 65 HOH TIP . H 6 HOH A 63 1565 66 HOH TIP . H 6 HOH A 64 1566 67 HOH TIP . H 6 HOH A 65 1567 68 HOH TIP . H 6 HOH A 66 1568 69 HOH TIP . H 6 HOH A 67 1569 70 HOH TIP . H 6 HOH A 68 1570 71 HOH TIP . H 6 HOH A 69 1571 72 HOH TIP . H 6 HOH A 70 1572 73 HOH TIP . H 6 HOH A 71 1573 74 HOH TIP . H 6 HOH A 72 1574 75 HOH TIP . H 6 HOH A 73 1575 76 HOH TIP . H 6 HOH A 74 1576 77 HOH TIP . H 6 HOH A 75 1577 78 HOH TIP . H 6 HOH A 76 1578 79 HOH TIP . H 6 HOH A 77 1579 80 HOH TIP . H 6 HOH A 78 1580 81 HOH TIP . H 6 HOH A 79 1581 84 HOH TIP . H 6 HOH A 80 1582 85 HOH TIP . H 6 HOH A 81 1583 86 HOH TIP . H 6 HOH A 82 1584 87 HOH TIP . H 6 HOH A 83 1585 88 HOH TIP . H 6 HOH A 84 1586 89 HOH TIP . H 6 HOH A 85 1587 90 HOH TIP . H 6 HOH A 86 1588 91 HOH TIP . H 6 HOH A 87 1589 92 HOH TIP . H 6 HOH A 88 1590 93 HOH TIP . H 6 HOH A 89 1591 94 HOH TIP . H 6 HOH A 90 1592 95 HOH TIP . H 6 HOH A 91 1593 96 HOH TIP . H 6 HOH A 92 1594 97 HOH TIP . H 6 HOH A 93 1595 98 HOH TIP . H 6 HOH A 94 1596 99 HOH TIP . H 6 HOH A 95 1597 100 HOH TIP . H 6 HOH A 96 1598 101 HOH TIP . H 6 HOH A 97 1599 102 HOH TIP . H 6 HOH A 98 1600 103 HOH TIP . H 6 HOH A 99 1601 105 HOH TIP . H 6 HOH A 100 1602 106 HOH TIP . H 6 HOH A 101 1603 107 HOH TIP . H 6 HOH A 102 1604 108 HOH TIP . H 6 HOH A 103 1605 109 HOH TIP . H 6 HOH A 104 1606 110 HOH TIP . H 6 HOH A 105 1607 111 HOH TIP . H 6 HOH A 106 1608 112 HOH TIP . H 6 HOH A 107 1609 113 HOH TIP . H 6 HOH A 108 1610 114 HOH TIP . H 6 HOH A 109 1611 115 HOH TIP . H 6 HOH A 110 1612 116 HOH TIP . H 6 HOH A 111 1613 117 HOH TIP . H 6 HOH A 112 1614 118 HOH TIP . H 6 HOH A 113 1615 120 HOH TIP . H 6 HOH A 114 1616 121 HOH TIP . H 6 HOH A 115 1617 122 HOH TIP . H 6 HOH A 116 1618 123 HOH TIP . I 6 HOH B 1 119 119 HOH TIP . # 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 SFG . . . C 3 12.357 3.316 10.458 1 19.59 ? N SFG 1501 A 1 HETATM 2 C CA SFG . . . C 3 12.946 3.959 11.642 1 20.3 ? CA SFG 1501 A 1 HETATM 3 C C SFG . . . C 3 12.794 5.49 11.672 1 20.53 ? C SFG 1501 A 1 HETATM 4 O O SFG . . . C 3 12.176 6.038 10.723 1 21.51 ? O SFG 1501 A 1 HETATM 5 O OXT SFG . . . C 3 13.237 6.112 12.67 1 20.21 ? OXT SFG 1501 A 1 HETATM 6 C CB SFG . . . C 3 14.394 3.448 11.967 1 19.21 ? CB SFG 1501 A 1 HETATM 7 C CG SFG . . . C 3 14.241 1.985 12.503 1 19.48 ? CG SFG 1501 A 1 HETATM 8 C CD SFG . . . C 3 13.864 1.9 14.003 1 19.71 ? CD SFG 1501 A 1 HETATM 9 N NE SFG . . . C 3 15.037 1.568 14.878 1 17.83 ? NE SFG 1501 A 1 HETATM 10 C C5' SFG . . . C 3 12.927 0.689 14.146 1 20.15 ? C5' SFG 1501 A 1 HETATM 11 C C4' SFG . . . C 3 11.473 1.039 13.706 1 21.33 ? C4' SFG 1501 A 1 HETATM 12 O O4' SFG . . . C 3 11.375 1.09 12.276 1 20.99 ? O4' SFG 1501 A 1 HETATM 13 C C3' SFG . . . C 3 10.35 0.084 14.156 1 22.31 ? C3' SFG 1501 A 1 HETATM 14 O O3' SFG . . . C 3 9.822 0.5 15.404 1 22.21 ? O3' SFG 1501 A 1 HETATM 15 C C2' SFG . . . C 3 9.392 0.127 12.966 1 22.09 ? C2' SFG 1501 A 1 HETATM 16 O O2' SFG . . . C 3 8.477 1.24 13.031 1 23.54 ? O2' SFG 1501 A 1 HETATM 17 C C1' SFG . . . C 3 10.3 0.308 11.741 1 22.22 ? C1' SFG 1501 A 1 HETATM 18 N N9 SFG . . . C 3 10.874 -0.874 11.044 1 21.94 ? N9 SFG 1501 A 1 HETATM 19 C C8 SFG . . . C 3 12.113 -1.455 11.04 1 21.41 ? C8 SFG 1501 A 1 HETATM 20 N N7 SFG . . . C 3 12.285 -2.503 10.222 1 22.18 ? N7 SFG 1501 A 1 HETATM 21 C C5 SFG . . . C 3 11.034 -2.653 9.638 1 22.94 ? C5 SFG 1501 A 1 HETATM 22 C C6 SFG . . . C 3 10.437 -3.521 8.701 1 23.26 ? C6 SFG 1501 A 1 HETATM 23 N N6 SFG . . . C 3 11.186 -4.51 8.15 1 23.46 ? N6 SFG 1501 A 1 HETATM 24 N N1 SFG . . . C 3 9.1 -3.389 8.339 1 23.72 ? N1 SFG 1501 A 1 HETATM 25 C C2 SFG . . . C 3 8.307 -2.397 8.865 1 23.74 ? C2 SFG 1501 A 1 HETATM 26 N N3 SFG . . . C 3 8.829 -1.506 9.769 1 23.09 ? N3 SFG 1501 A 1 HETATM 27 C C4 SFG . . . C 3 10.156 -1.647 10.145 1 22.75 ? C4 SFG 1501 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 442 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 27 #