data_5WRJ # _model_server_result.job_id 5iqLj97ULoyijOf7WSgTvg _model_server_result.datetime_utc '2024-11-15 03:25:47' _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 5wrj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":401}' # _entry.id 5WRJ # _exptl.entry_id 5WRJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 3 _entity.src_method man _entity.type non-polymer _entity.pdbx_description "ADENOSINE-3'-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90.6 _cell.angle_beta 93.39 _cell.angle_gamma 103.39 _cell.entry_id 5WRJ _cell.length_a 51.668 _cell.length_b 93.263 _cell.length_c 93.012 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5WRJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA tetrameric 4 author_and_software_defined_assembly 1 PISA tetrameric 4 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,F,I,J,K,L,Q,R 1 1 C,D,G,H,M,N,O,P,S,T 2 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 I N N ? 3 K N N ? 3 M N N ? 3 O 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 59 A CYS 97 1_555 A SG CYS 119 A CYS 157 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? disulf ? disulf2 A SG CYS 188 A CYS 226 1_555 A SG CYS 196 A CYS 234 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf3 B SG CYS 59 B CYS 97 1_555 B SG CYS 119 B CYS 157 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf4 B SG CYS 188 B CYS 226 1_555 B SG CYS 196 B CYS 234 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf5 C SG CYS 59 C CYS 97 1_555 C SG CYS 119 C CYS 157 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf6 C SG CYS 188 C CYS 226 1_555 C SG CYS 196 C CYS 234 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf7 D SG CYS 59 D CYS 97 1_555 D SG CYS 119 D CYS 157 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf8 D SG CYS 188 D CYS 226 1_555 D SG CYS 196 D CYS 234 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id A3P _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-3'-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _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 P1 O1P A3P doub 1 n n P1 O2P A3P sing 2 n n P1 O3P A3P sing 3 n n P1 O3' A3P sing 4 n n O2P HOP2 A3P sing 5 n n O3P HOP3 A3P sing 6 n n P2 O4P A3P doub 7 n n P2 O5P A3P sing 8 n n P2 O6P A3P sing 9 n n P2 O5' A3P sing 10 n n O5P HOP5 A3P sing 11 n n O6P HOP6 A3P sing 12 n n O5' C5' A3P sing 13 n n C5' C4' A3P sing 14 n n C5' "H5'1" A3P sing 15 n n C5' "H5'2" A3P sing 16 n n C4' O4' A3P sing 17 n n C4' C3' A3P sing 18 n n C4' H4' A3P sing 19 n n O4' C1' A3P sing 20 n n C3' O3' A3P sing 21 n n C3' C2' A3P sing 22 n n C3' H3' A3P sing 23 n n C2' O2' A3P sing 24 n n C2' C1' A3P sing 25 n n C2' H2' A3P sing 26 n n O2' HO2' A3P sing 27 n n C1' N9 A3P sing 28 n n C1' H1' A3P sing 29 n n N9 C8 A3P sing 30 n y N9 C4 A3P sing 31 n y C8 N7 A3P doub 32 n y C8 H8 A3P sing 33 n n N7 C5 A3P sing 34 n y C5 C6 A3P sing 35 n y C5 C4 A3P doub 36 n y C6 N6 A3P sing 37 n n C6 N1 A3P doub 38 n y N6 HN61 A3P sing 39 n n N6 HN62 A3P sing 40 n n N1 C2 A3P sing 41 n y C2 N3 A3P doub 42 n y C2 H2 A3P sing 43 n n N3 C4 A3P sing 44 n y # _atom_sites.entry_id 5WRJ _atom_sites.fract_transf_matrix[1][1] 0.019354 _atom_sites.fract_transf_matrix[1][2] 0.004608 _atom_sites.fract_transf_matrix[1][3] 0.001259 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011022 _atom_sites.fract_transf_matrix[2][3] 0.000273 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.010773 _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 I 3 A3P A 1 401 4 A3P A3P . J 4 MG A 1 402 4 MG MG . K 3 A3P B 1 401 1 A3P A3P . L 4 MG B 1 402 2 MG MG . M 3 A3P C 1 401 2 A3P A3P . N 4 MG C 1 402 1 MG MG . O 3 A3P D 1 401 3 A3P A3P . P 4 MG D 1 402 3 MG MG . Q 5 HOH A 1 501 246 HOH HOH . Q 5 HOH A 2 502 110 HOH HOH . Q 5 HOH A 3 503 21 HOH HOH . Q 5 HOH A 4 504 23 HOH HOH . Q 5 HOH A 5 505 194 HOH HOH . Q 5 HOH A 6 506 89 HOH HOH . Q 5 HOH A 7 507 43 HOH HOH . Q 5 HOH A 8 508 218 HOH HOH . Q 5 HOH A 9 509 8 HOH HOH . Q 5 HOH A 10 510 39 HOH HOH . Q 5 HOH A 11 511 30 HOH HOH . Q 5 HOH A 12 512 25 HOH HOH . Q 5 HOH A 13 513 90 HOH HOH . Q 5 HOH A 14 514 118 HOH HOH . Q 5 HOH A 15 515 6 HOH HOH . Q 5 HOH A 16 516 78 HOH HOH . Q 5 HOH A 17 517 200 HOH HOH . Q 5 HOH A 18 518 86 HOH HOH . Q 5 HOH A 19 519 131 HOH HOH . Q 5 HOH A 20 520 109 HOH HOH . Q 5 HOH A 21 521 62 HOH HOH . Q 5 HOH A 22 522 55 HOH HOH . Q 5 HOH A 23 523 32 HOH HOH . Q 5 HOH A 24 524 203 HOH HOH . Q 5 HOH A 25 525 143 HOH HOH . Q 5 HOH A 26 526 91 HOH HOH . Q 5 HOH A 27 527 123 HOH HOH . Q 5 HOH A 28 528 58 HOH HOH . Q 5 HOH A 29 529 83 HOH HOH . Q 5 HOH A 30 530 103 HOH HOH . Q 5 HOH A 31 531 74 HOH HOH . Q 5 HOH A 32 532 172 HOH HOH . Q 5 HOH A 33 533 36 HOH HOH . Q 5 HOH A 34 534 185 HOH HOH . Q 5 HOH A 35 535 245 HOH HOH . Q 5 HOH A 36 536 33 HOH HOH . Q 5 HOH A 37 537 2 HOH HOH . Q 5 HOH A 38 538 59 HOH HOH . Q 5 HOH A 39 539 129 HOH HOH . Q 5 HOH A 40 540 235 HOH HOH . Q 5 HOH A 41 541 95 HOH HOH . Q 5 HOH A 42 542 160 HOH HOH . Q 5 HOH A 43 543 217 HOH HOH . Q 5 HOH A 44 544 175 HOH HOH . Q 5 HOH A 45 545 165 HOH HOH . R 5 HOH B 1 501 101 HOH HOH . R 5 HOH B 2 502 247 HOH HOH . R 5 HOH B 3 503 3 HOH HOH . R 5 HOH B 4 504 61 HOH HOH . R 5 HOH B 5 505 34 HOH HOH . R 5 HOH B 6 506 178 HOH HOH . R 5 HOH B 7 507 198 HOH HOH . R 5 HOH B 8 508 99 HOH HOH . R 5 HOH B 9 509 12 HOH HOH . R 5 HOH B 10 510 104 HOH HOH . R 5 HOH B 11 511 13 HOH HOH . R 5 HOH B 12 512 29 HOH HOH . R 5 HOH B 13 513 49 HOH HOH . R 5 HOH B 14 514 125 HOH HOH . R 5 HOH B 15 515 26 HOH HOH . R 5 HOH B 16 516 14 HOH HOH . R 5 HOH B 17 517 121 HOH HOH . R 5 HOH B 18 518 154 HOH HOH . R 5 HOH B 19 519 65 HOH HOH . R 5 HOH B 20 520 244 HOH HOH . R 5 HOH B 21 521 82 HOH HOH . R 5 HOH B 22 522 44 HOH HOH . R 5 HOH B 23 523 114 HOH HOH . R 5 HOH B 24 524 176 HOH HOH . R 5 HOH B 25 525 17 HOH HOH . R 5 HOH B 26 526 67 HOH HOH . R 5 HOH B 27 527 20 HOH HOH . R 5 HOH B 28 528 135 HOH HOH . R 5 HOH B 29 529 161 HOH HOH . R 5 HOH B 30 530 162 HOH HOH . R 5 HOH B 31 531 132 HOH HOH . R 5 HOH B 32 532 10 HOH HOH . R 5 HOH B 33 533 73 HOH HOH . R 5 HOH B 34 534 202 HOH HOH . S 5 HOH C 1 501 251 HOH HOH . S 5 HOH C 2 502 72 HOH HOH . S 5 HOH C 3 503 182 HOH HOH . S 5 HOH C 4 504 70 HOH HOH . S 5 HOH C 5 505 24 HOH HOH . S 5 HOH C 6 506 147 HOH HOH . S 5 HOH C 7 507 81 HOH HOH . S 5 HOH C 8 508 145 HOH HOH . S 5 HOH C 9 509 41 HOH HOH . S 5 HOH C 10 510 144 HOH HOH . S 5 HOH C 11 511 243 HOH HOH . S 5 HOH C 12 512 146 HOH HOH . S 5 HOH C 13 513 115 HOH HOH . S 5 HOH C 14 514 225 HOH HOH . S 5 HOH C 15 515 249 HOH HOH . S 5 HOH C 16 516 106 HOH HOH . S 5 HOH C 17 517 19 HOH HOH . S 5 HOH C 18 518 116 HOH HOH . S 5 HOH C 19 519 16 HOH HOH . S 5 HOH C 20 520 230 HOH HOH . S 5 HOH C 21 521 229 HOH HOH . S 5 HOH C 22 522 68 HOH HOH . S 5 HOH C 23 523 18 HOH HOH . S 5 HOH C 24 524 15 HOH HOH . S 5 HOH C 25 525 163 HOH HOH . S 5 HOH C 26 526 150 HOH HOH . S 5 HOH C 27 527 191 HOH HOH . S 5 HOH C 28 528 193 HOH HOH . S 5 HOH C 29 529 228 HOH HOH . S 5 HOH C 30 530 37 HOH HOH . S 5 HOH C 31 531 45 HOH HOH . S 5 HOH C 32 532 142 HOH HOH . S 5 HOH C 33 533 207 HOH HOH . T 5 HOH D 1 501 250 HOH HOH . T 5 HOH D 2 502 108 HOH HOH . T 5 HOH D 3 503 64 HOH HOH . T 5 HOH D 4 504 128 HOH HOH . T 5 HOH D 5 505 22 HOH HOH . T 5 HOH D 6 506 126 HOH HOH . T 5 HOH D 7 507 183 HOH HOH . T 5 HOH D 8 508 1 HOH HOH . T 5 HOH D 9 509 50 HOH HOH . T 5 HOH D 10 510 138 HOH HOH . T 5 HOH D 11 511 7 HOH HOH . T 5 HOH D 12 512 92 HOH HOH . T 5 HOH D 13 513 111 HOH HOH . T 5 HOH D 14 514 155 HOH HOH . T 5 HOH D 15 515 51 HOH HOH . T 5 HOH D 16 516 105 HOH HOH . T 5 HOH D 17 517 5 HOH HOH . T 5 HOH D 18 518 119 HOH HOH . T 5 HOH D 19 519 71 HOH HOH . T 5 HOH D 20 520 80 HOH HOH . T 5 HOH D 21 521 48 HOH HOH . T 5 HOH D 22 522 240 HOH HOH . T 5 HOH D 23 523 184 HOH HOH . T 5 HOH D 24 524 9 HOH HOH . T 5 HOH D 25 525 205 HOH HOH . T 5 HOH D 26 526 100 HOH HOH . T 5 HOH D 27 527 206 HOH HOH . T 5 HOH D 28 528 216 HOH HOH . T 5 HOH D 29 529 97 HOH HOH . T 5 HOH D 30 530 177 HOH HOH . T 5 HOH D 31 531 223 HOH HOH . T 5 HOH D 32 532 134 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 P P1 A3P . . . O 3 24.796 -57.558 -18.257 1 37.22 ? P1 A3P 401 D 1 HETATM 2 O O1P A3P . . . O 3 25.395 -56.634 -17.22 1 38.04 ? O1P A3P 401 D 1 HETATM 3 O O2P A3P . . . O 3 24.488 -58.932 -17.732 1 36.62 ? O2P A3P 401 D 1 HETATM 4 O O3P A3P . . . O 3 25.468 -57.549 -19.597 1 36.3 ? O3P A3P 401 D 1 HETATM 5 P P2 A3P . . . O 3 20.675 -54.515 -23.415 1 34.68 ? P2 A3P 401 D 1 HETATM 6 O O4P A3P . . . O 3 19.567 -55.391 -23.922 1 34.62 ? O4P A3P 401 D 1 HETATM 7 O O5P A3P . . . O 3 20.27 -53.061 -23.287 1 34.19 ? O5P A3P 401 D 1 HETATM 8 O O6P A3P . . . O 3 22.01 -54.771 -24.071 1 33.74 ? O6P A3P 401 D 1 HETATM 9 O O5' A3P . . . O 3 20.875 -54.958 -21.885 1 34.93 ? O5' A3P 401 D 1 HETATM 10 C C5' A3P . . . O 3 21.709 -56.047 -21.516 1 35.91 ? C5' A3P 401 D 1 HETATM 11 C C4' A3P . . . O 3 21.541 -56.275 -20.028 1 36.56 ? C4' A3P 401 D 1 HETATM 12 O O4' A3P . . . O 3 20.186 -56.654 -19.791 1 37.35 ? O4' A3P 401 D 1 HETATM 13 C C3' A3P . . . O 3 22.447 -57.381 -19.488 1 37.05 ? C3' A3P 401 D 1 HETATM 14 O O3' A3P . . . O 3 23.372 -56.868 -18.537 1 36.64 ? O3' A3P 401 D 1 HETATM 15 C C2' A3P . . . O 3 21.507 -58.366 -18.832 1 37.39 ? C2' A3P 401 D 1 HETATM 16 O O2' A3P . . . O 3 21.921 -58.805 -17.534 1 37.78 ? O2' A3P 401 D 1 HETATM 17 C C1' A3P . . . O 3 20.198 -57.596 -18.731 1 37.94 ? C1' A3P 401 D 1 HETATM 18 N N9 A3P . . . O 3 19.129 -58.588 -18.832 1 38.37 ? N9 A3P 401 D 1 HETATM 19 C C8 A3P . . . O 3 18.728 -59.22 -19.951 1 39.47 ? C8 A3P 401 D 1 HETATM 20 N N7 A3P . . . O 3 17.744 -60.102 -19.654 1 39.43 ? N7 A3P 401 D 1 HETATM 21 C C5 A3P . . . O 3 17.524 -60.035 -18.333 1 38.62 ? C5 A3P 401 D 1 HETATM 22 C C6 A3P . . . O 3 16.623 -60.691 -17.369 1 39.29 ? C6 A3P 401 D 1 HETATM 23 N N6 A3P . . . O 3 15.74 -61.619 -17.807 1 40.25 ? N6 A3P 401 D 1 HETATM 24 N N1 A3P . . . O 3 16.718 -60.32 -16.068 1 38.27 ? N1 A3P 401 D 1 HETATM 25 C C2 A3P . . . O 3 17.6 -59.388 -15.651 1 37.59 ? C2 A3P 401 D 1 HETATM 26 N N3 A3P . . . O 3 18.447 -58.759 -16.476 1 37.93 ? N3 A3P 401 D 1 HETATM 27 C C4 A3P . . . O 3 18.451 -59.037 -17.795 1 38.17 ? C4 A3P 401 D 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 38 _model_server_stats.query_time_ms 262 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 27 #