data_3W5A # _model_server_result.job_id dnFZ4b9eXfYu2OQvHuvpDw _model_server_result.datetime_utc '2024-11-23 21:58:27' _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":"D","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 . . . D 3 69.558 24.371 107.035 1 65.37 ? N1 TM1 1001 A 1 HETATM 2 C C2 TM1 . . . D 3 69.107 23.18 107.591 1 64.02 ? C2 TM1 1001 A 1 HETATM 3 N N3 TM1 . . . D 3 69.229 21.989 106.917 1 60.46 ? N3 TM1 1001 A 1 HETATM 4 C C4 TM1 . . . D 3 69.801 21.874 105.651 1 60.73 ? C4 TM1 1001 A 1 HETATM 5 C C5 TM1 . . . D 3 70.269 23.036 105.046 1 61.31 ? C5 TM1 1001 A 1 HETATM 6 C C6 TM1 . . . D 3 70.159 24.33 105.734 1 63.5 ? C6 TM1 1001 A 1 HETATM 7 N N6 TM1 . . . D 3 70.611 25.44 105.149 1 64.15 ? N6 TM1 1001 A 1 HETATM 8 N N7 TM1 . . . D 3 70.776 22.758 103.861 1 62.98 ? N7 TM1 1001 A 1 HETATM 9 C C8 TM1 . . . D 3 70.635 21.438 103.706 1 62.16 ? C8 TM1 1001 A 1 HETATM 10 N N9 TM1 . . . D 3 70.044 20.909 104.79 1 61.51 ? N9 TM1 1001 A 1 HETATM 11 P PA TM1 . . . D 3 73.702 18.637 100.87 1 45.49 ? PA TM1 1001 A 1 HETATM 12 C C1' TM1 . . . D 3 69.696 19.398 105.012 1 63.66 ? C1' TM1 1001 A 1 HETATM 13 O O1A TM1 . . . D 3 74.113 17.863 99.578 1 46.86 ? O1A TM1 1001 A 1 HETATM 14 C C1F TM1 . . . D 3 67.191 17.17 104.154 1 81.83 ? C1F TM1 1001 A 1 HETATM 15 C C2' TM1 . . . D 3 68.62 18.91 103.999 1 68.77 ? C2' TM1 1001 A 1 HETATM 16 O O2' TM1 . . . D 3 67.304 18.607 104.544 1 77.48 ? O2' TM1 1001 A 1 HETATM 17 O O2A TM1 . . . D 3 74.911 19.35 101.395 1 44.97 ? O2A TM1 1001 A 1 HETATM 18 C C2F TM1 . . . D 3 65.916 17.174 103.253 1 86.48 ? C2F TM1 1001 A 1 HETATM 19 N N2F TM1 . . . D 3 65.755 17.988 102.005 1 90.75 ? N2F TM1 1001 A 1 HETATM 20 O O2F TM1 . . . D 3 66.571 18.753 101.49 1 92.65 ? O2F TM1 1001 A 1 HETATM 21 C C3' TM1 . . . D 3 69.254 17.802 103.244 1 68.55 ? C3' TM1 1001 A 1 HETATM 22 O O3' TM1 . . . D 3 68.434 16.618 103.471 1 76.47 ? O3' TM1 1001 A 1 HETATM 23 O O3A TM1 . . . D 3 72.559 19.643 100.493 1 46.74 ? O3A TM1 1001 A 1 HETATM 24 C C3F TM1 . . . D 3 64.809 16.392 103.591 1 88.05 ? C3F TM1 1001 A 1 HETATM 25 O O3F TM1 . . . D 3 64.7 17.942 101.328 1 92.43 ? O3F TM1 1001 A 1 HETATM 26 C C4' TM1 . . . D 3 70.62 17.556 103.655 1 62.57 ? C4' TM1 1001 A 1 HETATM 27 O O4' TM1 . . . D 3 70.768 18.534 104.678 1 59.45 ? O4' TM1 1001 A 1 HETATM 28 C C4F TM1 . . . D 3 64.683 15.546 104.678 1 89.55 ? C4F TM1 1001 A 1 HETATM 29 N N4F TM1 . . . D 3 63.617 14.81 104.974 1 92.5 ? N4F TM1 1001 A 1 HETATM 30 O O4F TM1 . . . D 3 62.952 14.985 105.97 1 93.64 ? O4F TM1 1001 A 1 HETATM 31 C C5' TM1 . . . D 3 71.703 17.672 102.451 1 56.94 ? C5' TM1 1001 A 1 HETATM 32 O O5' TM1 . . . D 3 73.121 17.584 101.999 1 51.07 ? O5' TM1 1001 A 1 HETATM 33 C C5F TM1 . . . D 3 65.79 15.477 105.557 1 86.24 ? C5F TM1 1001 A 1 HETATM 34 O O5F TM1 . . . D 3 63.242 13.913 104.273 1 95.45 ? O5F TM1 1001 A 1 HETATM 35 C C6F TM1 . . . D 3 67.071 16.239 105.371 1 84.02 ? C6F TM1 1001 A 1 HETATM 36 N N6F TM1 . . . D 3 68.035 16.02 106.384 1 85.08 ? N6F TM1 1001 A 1 HETATM 37 O O6F TM1 . . . D 3 67.811 15.257 107.311 1 85.72 ? O6F TM1 1001 A 1 HETATM 38 O O7F TM1 . . . D 3 69.097 16.517 106.445 1 85.95 ? O7F TM1 1001 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 243 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 38 #