data_3W5A # _model_server_result.job_id fa2uF9ZAMBGggVNIA4qJuA _model_server_result.datetime_utc '2024-11-23 22:06:49' _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 3w5a # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":1001}' # _entry.id 3W5A # _exptl.entry_id 3W5A _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 558.31 _entity.id 3 _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 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 119.02 _cell.angle_gamma 90 _cell.entry_id 3W5A _cell.length_a 352.883 _cell.length_b 55.729 _cell.length_c 187.951 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3W5A _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 ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 J N 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 877 A CYS 876 1_555 A SG CYS 889 A CYS 888 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf2 B SG CYS 877 B CYS 876 1_555 B SG CYS 889 B CYS 888 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? covale ? covale1 A C ACE 1 A ACE 0 1_555 A N MET 2 A MET 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale2 B C ACE 1 B ACE 0 1_555 B N MET 2 B MET 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? metalc ? metalc1 A O ALA 306 A ALA 305 1_555 G MG MG . A MG 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.736 ? metalc ? metalc2 A O LEU 712 A LEU 711 1_555 I NA NA . A NA 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.436 ? metalc ? metalc3 A O LYS 713 A LYS 712 1_555 I NA NA . A NA 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.819 ? metalc ? metalc4 A O ALA 715 A ALA 714 1_555 I NA NA . A NA 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.591 ? metalc ? metalc5 A OE1 GLU 733 A GLU 732 1_555 I NA NA . A NA 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.569 ? metalc ? metalc6 A OE2 GLU 733 A GLU 732 1_555 I NA NA . A NA 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.722 ? metalc ? metalc7 A OE1 GLU 772 A GLU 771 1_555 G MG MG . A MG 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.445 ? metalc ? metalc8 A OD1 ASN 797 A ASN 796 1_555 G MG MG . A MG 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.734 ? metalc ? metalc9 A OD2 ASP 801 A ASP 800 1_555 G MG MG . A MG 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.574 ? metalc ? metalc10 G MG MG . A MG 1004 1_555 Q O HOH . A HOH 4002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.313 ? metalc ? metalc11 H MG MG . A MG 1005 1_555 Q O HOH . A HOH 4003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.995 ? metalc ? metalc12 H MG MG . A MG 1005 1_555 Q O HOH . A HOH 4004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.765 ? metalc ? metalc13 H MG MG . A MG 1005 1_555 Q O HOH . A HOH 4005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.36 ? metalc ? metalc14 H MG MG . A MG 1005 1_555 Q O HOH . A HOH 4006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.23 ? metalc ? metalc15 B O ALA 306 B ALA 305 1_555 N MG MG . B MG 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.157 ? metalc ? metalc16 B O LEU 712 B LEU 711 1_555 P NA NA . B NA 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.03 ? metalc ? metalc17 B O LYS 713 B LYS 712 1_555 P NA NA . B NA 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.835 ? metalc ? metalc18 B O ALA 715 B ALA 714 1_555 P NA NA . B NA 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? metalc ? metalc19 B OE1 GLU 733 B GLU 732 1_555 P NA NA . B NA 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.565 ? metalc ? metalc20 B OE2 GLU 733 B GLU 732 1_555 P NA NA . B NA 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.83 ? metalc ? metalc21 B OD1 ASN 769 B ASN 768 1_555 N MG MG . B MG 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.521 ? metalc ? metalc22 B OE1 GLU 772 B GLU 771 1_555 N MG MG . B MG 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.717 ? metalc ? metalc23 B OD1 ASN 797 B ASN 796 1_555 N MG MG . B MG 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.251 ? metalc ? metalc24 B OD2 ASP 801 B ASP 800 1_555 N MG MG . B MG 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.87 ? metalc ? metalc25 N MG MG . B MG 1005 1_555 R O HOH . B HOH 4002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.986 ? metalc ? metalc26 O MG MG . B MG 1006 1_555 R O HOH . B HOH 4003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.453 ? metalc ? metalc27 O MG MG . B MG 1006 1_555 R O HOH . B HOH 4004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? metalc ? metalc28 O MG MG . B MG 1006 1_555 R O HOH . B HOH 4005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.58 ? metalc ? metalc29 O MG MG . B MG 1006 1_555 R O HOH . B HOH 4006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.99 ? # _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 441 n y N1 C6 TM1 sing 442 n y C2 N3 TM1 sing 443 n y C2 H2 TM1 sing 444 n n N3 C4 TM1 doub 445 n y C4 C5 TM1 sing 446 n y C4 N9 TM1 sing 447 n y C5 C6 TM1 doub 448 n y C5 N7 TM1 sing 449 n y C6 N6 TM1 sing 450 n n N6 HN6 TM1 sing 451 n n N6 HN6A TM1 sing 452 n n N7 C8 TM1 doub 453 n y C8 N9 TM1 sing 454 n y C8 H8 TM1 sing 455 n n N9 C1' TM1 sing 456 n n PA O1A TM1 sing 457 n n PA O2A TM1 doub 458 n n PA O3A TM1 sing 459 n n PA O5' TM1 sing 460 n n C1' C2' TM1 sing 461 n n C1' O4' TM1 sing 462 n n C1' H1' TM1 sing 463 n n O1A HO1A TM1 sing 464 n n C1F O2' TM1 sing 465 n n C1F C2F TM1 sing 466 n n C1F O3' TM1 sing 467 n n C1F C6F TM1 sing 468 n n C2' O2' TM1 sing 469 n n C2' C3' TM1 sing 470 n n C2' H2' TM1 sing 471 n n C2F N2F TM1 sing 472 n n C2F C3F TM1 doub 473 n n N2F O2F TM1 sing 474 n n N2F O3F TM1 doub 475 n n C3' O3' TM1 sing 476 n n C3' C4' TM1 sing 477 n n C3' H3' TM1 sing 478 n n O3A HO3A TM1 sing 479 n n C3F C4F TM1 sing 480 n n C3F H3F TM1 sing 481 n n C4' O4' TM1 sing 482 n n C4' C5' TM1 sing 483 n n C4' H4' TM1 sing 484 n n C4F N4F TM1 sing 485 n n C4F C5F TM1 sing 486 n n C4F H4F TM1 sing 487 n n N4F O4F TM1 sing 488 n n N4F O5F TM1 doub 489 n n C5' O5' TM1 sing 490 n n C5' H5' TM1 sing 491 n n C5' "H5'A" TM1 sing 492 n n C5F C6F TM1 doub 493 n n C5F H5F TM1 sing 494 n n C6F N6F TM1 sing 495 n n N6F O6F TM1 sing 496 n n N6F O7F TM1 doub 497 n n # _atom_sites.entry_id 3W5A _atom_sites.fract_transf_matrix[1][1] 0.002834 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001572 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017944 _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] 0.006084 _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 D 3 TM1 A 1 1001 999 TM1 TM1 . E 4 PTY A 1 1002 1001 PTY PTY . F 4 PTY A 1 1003 1002 PTY PTY . G 5 MG A 1 1004 2001 MG MG . H 5 MG A 1 1005 2002 MG MG . I 6 NA A 1 1006 2003 NA NA . J 3 TM1 B 1 1001 999 TM1 TM1 . K 4 PTY B 1 1002 1001 PTY PTY . L 4 PTY B 1 1003 1002 PTY PTY . M 4 PTY B 1 1004 1003 PTY PTY . N 5 MG B 1 1005 2001 MG MG . O 5 MG B 1 1006 2002 MG MG . P 6 NA B 1 1007 2003 NA NA . Q 7 HOH A 1 4001 4001 HOH HOH . Q 7 HOH A 2 4002 4002 HOH HOH . Q 7 HOH A 3 4003 5001 HOH HOH . Q 7 HOH A 4 4004 5002 HOH HOH . Q 7 HOH A 5 4005 5003 HOH HOH . Q 7 HOH A 6 4006 5004 HOH HOH . R 7 HOH B 1 4001 4001 HOH HOH . R 7 HOH B 2 4002 4002 HOH HOH . R 7 HOH B 3 4003 5001 HOH HOH . R 7 HOH B 4 4004 5002 HOH HOH . R 7 HOH B 5 4005 5003 HOH HOH . R 7 HOH B 6 4006 5004 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 . . . J 3 150.652 52.136 -22.264 1 71.4 ? N1 TM1 1001 B 1 HETATM 2 C C2 TM1 . . . J 3 151.248 50.935 -22.617 1 70.46 ? C2 TM1 1001 B 1 HETATM 3 N N3 TM1 . . . J 3 150.92 49.762 -21.98 1 69.15 ? N3 TM1 1001 B 1 HETATM 4 C C4 TM1 . . . J 3 149.98 49.675 -20.947 1 70.22 ? C4 TM1 1001 B 1 HETATM 5 C C5 TM1 . . . J 3 149.348 50.853 -20.554 1 70.83 ? C5 TM1 1001 B 1 HETATM 6 C C6 TM1 . . . J 3 149.677 52.123 -21.213 1 72.18 ? C6 TM1 1001 B 1 HETATM 7 N N6 TM1 . . . J 3 149.064 53.256 -20.825 1 73.33 ? N6 TM1 1001 B 1 HETATM 8 N N7 TM1 . . . J 3 148.497 50.599 -19.578 1 71.16 ? N7 TM1 1001 B 1 HETATM 9 C C8 TM1 . . . J 3 148.58 49.29 -19.347 1 71.41 ? C8 TM1 1001 B 1 HETATM 10 N N9 TM1 . . . J 3 149.48 48.727 -20.176 1 71.7 ? N9 TM1 1001 B 1 HETATM 11 P PA TM1 . . . J 3 145.476 46.577 -16.615 1 65.34 ? PA TM1 1001 B 1 HETATM 12 C C1' TM1 . . . J 3 149.873 47.204 -20.226 1 75.62 ? C1' TM1 1001 B 1 HETATM 13 O O1A TM1 . . . J 3 145.062 46.216 -15.128 1 64.19 ? O1A TM1 1001 B 1 HETATM 14 C C1F TM1 . . . J 3 152.347 45.043 -19.056 1 91.95 ? C1F TM1 1001 B 1 HETATM 15 C C2' TM1 . . . J 3 150.937 46.82 -19.143 1 80.03 ? C2' TM1 1001 B 1 HETATM 16 O O2' TM1 . . . J 3 152.274 46.461 -19.588 1 88.11 ? O2' TM1 1001 B 1 HETATM 17 O O2A TM1 . . . J 3 144.282 46.507 -17.536 1 65.48 ? O2A TM1 1001 B 1 HETATM 18 C C2F TM1 . . . J 3 153.507 45.086 -17.997 1 94.94 ? C2F TM1 1001 B 1 HETATM 19 N N2F TM1 . . . J 3 153.556 45.997 -16.813 1 96.69 ? N2F TM1 1001 B 1 HETATM 20 O O2F TM1 . . . J 3 152.737 46.839 -16.484 1 98.86 ? O2F TM1 1001 B 1 HETATM 21 C C3' TM1 . . . J 3 150.296 45.774 -18.308 1 79.57 ? C3' TM1 1001 B 1 HETATM 22 O O3' TM1 . . . J 3 151.068 44.569 -18.434 1 86.72 ? O3' TM1 1001 B 1 HETATM 23 O O3A TM1 . . . J 3 146.073 48.023 -16.628 1 68.23 ? O3A TM1 1001 B 1 HETATM 24 C C3F TM1 . . . J 3 154.595 44.222 -18.097 1 96.16 ? C3F TM1 1001 B 1 HETATM 25 O O3F TM1 . . . J 3 154.508 45.963 -16.011 1 96.56 ? O3F TM1 1001 B 1 HETATM 26 C C4' TM1 . . . J 3 148.982 45.473 -18.696 1 74.91 ? C4' TM1 1001 B 1 HETATM 27 O O4' TM1 . . . J 3 148.812 46.352 -19.814 1 72.85 ? O4' TM1 1001 B 1 HETATM 28 C C4F TM1 . . . J 3 154.812 43.275 -19.072 1 98.32 ? C4F TM1 1001 B 1 HETATM 29 N N4F TM1 . . . J 3 155.867 42.476 -19.114 1 100.61 ? N4F TM1 1001 B 1 HETATM 30 O O4F TM1 . . . J 3 156.904 42.771 -19.656 1 101.52 ? O4F TM1 1001 B 1 HETATM 31 C C5' TM1 . . . J 3 147.976 45.642 -17.471 1 71.41 ? C5' TM1 1001 B 1 HETATM 32 O O5' TM1 . . . J 3 146.58 45.504 -17.083 1 67.39 ? O5' TM1 1001 B 1 HETATM 33 C C5F TM1 . . . J 3 153.819 43.154 -20.095 1 96.66 ? C5F TM1 1001 B 1 HETATM 34 O O5F TM1 . . . J 3 155.846 41.396 -18.601 1 103.69 ? O5F TM1 1001 B 1 HETATM 35 C C6F TM1 . . . J 3 152.559 43.998 -20.17 1 95.6 ? C6F TM1 1001 B 1 HETATM 36 N N6F TM1 . . . J 3 151.694 43.723 -21.294 1 98.81 ? N6F TM1 1001 B 1 HETATM 37 O O6F TM1 . . . J 3 151.976 42.858 -22.127 1 99.88 ? O6F TM1 1001 B 1 HETATM 38 O O7F TM1 . . . J 3 150.668 44.271 -21.546 1 100.8 ? O7F TM1 1001 B 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 33 _model_server_stats.query_time_ms 279 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 38 #