data_3W5B # _model_server_result.job_id tIX2mqoR2rIoRfLPkTo0ng _model_server_result.datetime_utc '2025-02-17 14:27:48' _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 3w5b # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1004}' # _entry.id 3W5B # _exptl.entry_id 3W5B _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 558.31 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2',3'-O-[(1r)-2,4,6-trinitrocyclohexa-2,5-diene-1,1-diyl]adenosine 5'-(dihydrogen phosphate)" _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 118.18 _cell.angle_gamma 90 _cell.entry_id 3W5B _cell.length_a 186.787 _cell.length_b 55.293 _cell.length_c 178.278 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3W5B _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _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 4 _struct_asym.id E _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 882 A CYS 876 1_555 A SG CYS 894 A CYS 888 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? metalc ? metalc1 A O ALA 311 A ALA 305 1_555 C MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.631 ? metalc ? metalc2 A O LEU 717 A LEU 711 1_555 B NA NA . A NA 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.8 ? metalc ? metalc3 A O LYS 718 A LYS 712 1_555 B NA NA . A NA 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.617 ? metalc ? metalc4 A O ALA 720 A ALA 714 1_555 B NA NA . A NA 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.073 ? metalc ? metalc5 A OE2 GLU 738 A GLU 732 1_555 B NA NA . A NA 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.724 ? metalc ? metalc6 A OE1 GLU 738 A GLU 732 1_555 B NA NA . A NA 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.737 ? metalc ? metalc7 A OD1 ASN 774 A ASN 768 1_555 C MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.306 ? metalc ? metalc8 A OE1 GLU 777 A GLU 771 1_555 C MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.498 ? metalc ? metalc9 A OD1 ASN 802 A ASN 796 1_555 C MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.619 ? metalc ? metalc10 C MG MG . A MG 1002 1_555 J O HOH . A HOH 1107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.538 ? metalc ? metalc11 D MG MG . A MG 1003 1_555 J O HOH . A HOH 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.686 ? metalc ? metalc12 D MG MG . A MG 1003 1_555 J O HOH . A HOH 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.226 ? metalc ? metalc13 D MG MG . A MG 1003 1_555 J O HOH . A HOH 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.676 ? metalc ? metalc14 D MG MG . A MG 1003 1_555 J O HOH . A HOH 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.429 ? # _chem_comp.formula 'C16 H15 N8 O13 P' _chem_comp.formula_weight 558.31 _chem_comp.id TM1 _chem_comp.mon_nstd_flag . _chem_comp.name "2',3'-O-[(1r)-2,4,6-trinitrocyclohexa-2,5-diene-1,1-diyl]adenosine 5'-(dihydrogen phosphate)" _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 C2 TM1 doub 435 n y N1 C6 TM1 sing 436 n y C2 N3 TM1 sing 437 n y C2 H2 TM1 sing 438 n n N3 C4 TM1 doub 439 n y C4 C5 TM1 sing 440 n y C4 N9 TM1 sing 441 n y C5 C6 TM1 doub 442 n y C5 N7 TM1 sing 443 n y C6 N6 TM1 sing 444 n n N6 HN6 TM1 sing 445 n n N6 HN6A TM1 sing 446 n n N7 C8 TM1 doub 447 n y C8 N9 TM1 sing 448 n y C8 H8 TM1 sing 449 n n N9 C1' TM1 sing 450 n n PA O1A TM1 sing 451 n n PA O2A TM1 doub 452 n n PA O3A TM1 sing 453 n n PA O5' TM1 sing 454 n n C1' C2' TM1 sing 455 n n C1' O4' TM1 sing 456 n n C1' H1' TM1 sing 457 n n O1A HO1A TM1 sing 458 n n C1F O2' TM1 sing 459 n n C1F C2F TM1 sing 460 n n C1F O3' TM1 sing 461 n n C1F C6F TM1 sing 462 n n C2' O2' TM1 sing 463 n n C2' C3' TM1 sing 464 n n C2' H2' TM1 sing 465 n n C2F N2F TM1 sing 466 n n C2F C3F TM1 doub 467 n n N2F O2F TM1 sing 468 n n N2F O3F TM1 doub 469 n n C3' O3' TM1 sing 470 n n C3' C4' TM1 sing 471 n n C3' H3' TM1 sing 472 n n O3A HO3A TM1 sing 473 n n C3F C4F TM1 sing 474 n n C3F H3F TM1 sing 475 n n C4' O4' TM1 sing 476 n n C4' C5' TM1 sing 477 n n C4' H4' TM1 sing 478 n n C4F N4F TM1 sing 479 n n C4F C5F TM1 sing 480 n n C4F H4F TM1 sing 481 n n N4F O4F TM1 sing 482 n n N4F O5F TM1 doub 483 n n C5' O5' TM1 sing 484 n n C5' H5' TM1 sing 485 n n C5' "H5'A" TM1 sing 486 n n C5F C6F TM1 doub 487 n n C5F H5F TM1 sing 488 n n C6F N6F TM1 sing 489 n n N6F O6F TM1 sing 490 n n N6F O7F TM1 doub 491 n n # _atom_sites.entry_id 3W5B _atom_sites.fract_transf_matrix[1][1] 0.005354 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002869 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018085 _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] 0.006364 _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 NA A 1 1001 998 NA NA . C 3 MG A 1 1002 999 MG MG . D 3 MG A 1 1003 1000 MG MG . E 4 TM1 A 1 1004 1001 TM1 TM1 . F 5 PTY A 1 1005 1002 PTY PTY . G 5 PTY A 1 1006 1003 PTY PTY . H 5 PTY A 1 1007 1004 PTY PTY . I 5 PTY A 1 1008 1005 PTY PTY . J 6 HOH A 1 1101 1006 HOH HOH . J 6 HOH A 2 1102 1007 HOH HOH . J 6 HOH A 3 1103 1008 HOH HOH . J 6 HOH A 4 1104 1009 HOH HOH . J 6 HOH A 5 1105 1010 HOH HOH . J 6 HOH A 6 1106 4001 HOH HOH . J 6 HOH A 7 1107 4002 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 TM1 . . . E 4 83.566 -11.691 64.696 1 100.33 ? N1 TM1 1004 A 1 HETATM 2 C C2 TM1 . . . E 4 83.947 -12.882 65.3 1 101.8 ? C2 TM1 1004 A 1 HETATM 3 N N3 TM1 . . . E 4 83.301 -14.06 65.026 1 102.3 ? N3 TM1 1004 A 1 HETATM 4 C C4 TM1 . . . E 4 82.227 -14.17 64.138 1 102.05 ? C4 TM1 1004 A 1 HETATM 5 C C5 TM1 . . . E 4 81.79 -12.998 63.498 1 100.56 ? C5 TM1 1004 A 1 HETATM 6 C C6 TM1 . . . E 4 82.473 -11.714 63.77 1 98.87 ? C6 TM1 1004 A 1 HETATM 7 N N6 TM1 . . . E 4 82.065 -10.588 63.155 1 103.46 ? N6 TM1 1004 A 1 HETATM 8 N N7 TM1 . . . E 4 80.768 -13.27 62.693 1 101.9 ? N7 TM1 1004 A 1 HETATM 9 C C8 TM1 . . . E 4 80.556 -14.581 62.817 1 103.28 ? C8 TM1 1004 A 1 HETATM 10 N N9 TM1 . . . E 4 81.443 -15.128 63.695 1 102.92 ? N9 TM1 1004 A 1 HETATM 11 P PA TM1 . . . E 4 80.133 -17.085 58.715 1 105.03 ? PA TM1 1004 A 1 HETATM 12 C C1' TM1 . . . E 4 81.516 -16.641 64.108 1 106.85 ? C1' TM1 1004 A 1 HETATM 13 O O1A TM1 . . . E 4 79.016 -17.557 57.717 1 108.53 ? O1A TM1 1004 A 1 HETATM 14 C C1F TM1 . . . E 4 79.559 -19.078 65.617 1 115.11 ? C1F TM1 1004 A 1 HETATM 15 C C2' TM1 . . . E 4 80.109 -17.217 64.479 1 108.45 ? C2' TM1 1004 A 1 HETATM 16 O O2' TM1 . . . E 4 79.882 -17.627 65.852 1 112.7 ? O2' TM1 1004 A 1 HETATM 17 O O2A TM1 . . . E 4 81.309 -16.535 57.948 1 102.83 ? O2A TM1 1004 A 1 HETATM 18 C C2F TM1 . . . E 4 78.101 -19.197 66.167 1 118.31 ? C2F TM1 1004 A 1 HETATM 19 N N2F TM1 . . . E 4 76.929 -18.412 65.642 1 120.68 ? N2F TM1 1004 A 1 HETATM 20 O O2F TM1 . . . E 4 76.922 -17.582 64.749 1 122.76 ? O2F TM1 1004 A 1 HETATM 21 C C3' TM1 . . . E 4 79.839 -18.288 63.485 1 109.23 ? C3' TM1 1004 A 1 HETATM 22 O O3' TM1 . . . E 4 79.693 -19.519 64.201 1 112.01 ? O3' TM1 1004 A 1 HETATM 23 O O3A TM1 . . . E 4 79.51 -15.986 59.661 1 103.27 ? O3A TM1 1004 A 1 HETATM 24 C C3F TM1 . . . E 4 77.805 -20.093 67.2 1 120.09 ? C3F TM1 1004 A 1 HETATM 25 O O3F TM1 . . . E 4 75.776 -18.545 66.101 1 121.87 ? O3F TM1 1004 A 1 HETATM 26 C C4' TM1 . . . E 4 80.87 -18.449 62.531 1 108.67 ? C4' TM1 1004 A 1 HETATM 27 O O4' TM1 . . . E 4 81.801 -17.449 62.969 1 108.34 ? O4' TM1 1004 A 1 HETATM 28 C C4F TM1 . . . E 4 78.694 -20.938 67.853 1 122.21 ? C4F TM1 1004 A 1 HETATM 29 N N4F TM1 . . . E 4 78.367 -21.785 68.847 1 125.11 ? N4F TM1 1004 A 1 HETATM 30 O O4F TM1 . . . E 4 78.628 -21.608 70.018 1 125.21 ? O4F TM1 1004 A 1 HETATM 31 C C5' TM1 . . . E 4 80.318 -18.345 61.025 1 107.68 ? C5' TM1 1004 A 1 HETATM 32 O O5' TM1 . . . E 4 80.587 -18.383 59.588 1 105.94 ? O5' TM1 1004 A 1 HETATM 33 C C5F TM1 . . . E 4 80.063 -20.891 67.404 1 119.49 ? C5F TM1 1004 A 1 HETATM 34 O O5F TM1 . . . E 4 77.777 -22.799 68.643 1 128.63 ? O5F TM1 1004 A 1 HETATM 35 C C6F TM1 . . . E 4 80.573 -19.982 66.295 1 116.62 ? C6F TM1 1004 A 1 HETATM 36 N N6F TM1 . . . E 4 81.973 -20.069 65.982 1 117.01 ? N6F TM1 1004 A 1 HETATM 37 O O6F TM1 . . . E 4 82.714 -20.82 66.573 1 115.17 ? O6F TM1 1004 A 1 HETATM 38 O O7F TM1 . . . E 4 82.571 -19.458 65.166 1 119.05 ? O7F TM1 1004 A 1 # _model_server_stats.io_time_ms 22 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 324 _model_server_stats.encode_time_ms 14 _model_server_stats.element_count 38 #