data_6BXK # _model_server_result.job_id MqadE49GNJlwlkOTimF1vw _model_server_result.datetime_utc '2024-11-29 16:46:20' _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 6bxk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 6BXK # _exptl.entry_id 6BXK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 297.334 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-DEOXY-5'-METHYLTHIOADENOSINE" _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 90 _cell.angle_gamma 90 _cell.entry_id 6BXK _cell.length_a 55.509 _cell.length_b 80.458 _cell.length_c 161.92 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6BXK _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _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,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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 F 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 metalc ? metalc1 A SG CYS 95 A CYS 59 1_555 E FE1 SF4 . A SF4 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.307 ? metalc ? metalc2 A SG CYS 199 A CYS 163 1_555 E FE2 SF4 . A SF4 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.27 ? metalc ? metalc3 A SG CYS 323 A CYS 287 1_555 E FE3 SF4 . A SF4 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.276 ? metalc ? metalc4 D O4 SO4 . A SO4 402 1_555 E FE4 SF4 . A SF4 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.316 ? metalc ? metalc5 B SG CYS 95 B CYS 59 1_555 H FE1 SF4 . B SF4 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? metalc ? metalc6 B SG CYS 199 B CYS 163 1_555 H FE2 SF4 . B SF4 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.257 ? metalc ? metalc7 B SG CYS 323 B CYS 287 1_555 H FE3 SF4 . B SF4 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.223 ? metalc ? metalc8 G O3 SO4 . B SO4 402 1_555 H FE4 SF4 . B SF4 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.286 ? # _chem_comp.formula 'C11 H15 N5 O3 S' _chem_comp.formula_weight 297.334 _chem_comp.id MTA _chem_comp.mon_nstd_flag . _chem_comp.name "5'-DEOXY-5'-METHYLTHIOADENOSINE" _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 CS S5' MTA sing 237 n n CS HCS1 MTA sing 238 n n CS HCS2 MTA sing 239 n n CS HCS3 MTA sing 240 n n S5' C5' MTA sing 241 n n C5' C4' MTA sing 242 n n C5' "H5'1" MTA sing 243 n n C5' "H5'2" MTA sing 244 n n C4' O4' MTA sing 245 n n C4' C3' MTA sing 246 n n C4' H4' MTA sing 247 n n O4' C1' MTA sing 248 n n C2' O2' MTA sing 249 n n C2' C3' MTA sing 250 n n C2' C1' MTA sing 251 n n C2' H2' MTA sing 252 n n O2' HO2' MTA sing 253 n n C3' O3' MTA sing 254 n n C3' H3' MTA sing 255 n n O3' H3T MTA sing 256 n n C1' N9 MTA sing 257 n n C1' H1' MTA sing 258 n n N9 C8 MTA sing 259 n y N9 C4 MTA sing 260 n y C8 N7 MTA doub 261 n y C8 H8 MTA sing 262 n n N7 C5 MTA sing 263 n y C5 C6 MTA sing 264 n y C5 C4 MTA doub 265 n y C6 N6 MTA sing 266 n n C6 N1 MTA doub 267 n y N6 H61 MTA sing 268 n n N6 H62 MTA sing 269 n n N1 C2 MTA sing 270 n y C2 N3 MTA doub 271 n y C2 H2 MTA sing 272 n n N3 C4 MTA sing 273 n y # _atom_sites.entry_id 6BXK _atom_sites.fract_transf_matrix[1][1] 0.018015 _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] 0.012429 _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] 0.006176 _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 2 MTA A 1 401 1 MTA MTA . D 3 SO4 A 1 402 1 SO4 SO4 . E 4 SF4 A 1 403 1 SF4 SF4 . F 2 MTA B 1 401 2 MTA MTA . G 3 SO4 B 1 402 2 SO4 SO4 . H 4 SF4 B 1 403 2 SF4 SF4 . I 5 HOH A 1 501 26 HOH HOH . I 5 HOH A 2 502 44 HOH HOH . I 5 HOH A 3 503 32 HOH HOH . I 5 HOH A 4 504 2 HOH HOH . I 5 HOH A 5 505 9 HOH HOH . I 5 HOH A 6 506 15 HOH HOH . I 5 HOH A 7 507 14 HOH HOH . I 5 HOH A 8 508 23 HOH HOH . I 5 HOH A 9 509 39 HOH HOH . I 5 HOH A 10 510 12 HOH HOH . I 5 HOH A 11 511 30 HOH HOH . I 5 HOH A 12 512 29 HOH HOH . I 5 HOH A 13 513 3 HOH HOH . I 5 HOH A 14 514 47 HOH HOH . I 5 HOH A 15 515 25 HOH HOH . I 5 HOH A 16 516 42 HOH HOH . I 5 HOH A 17 517 33 HOH HOH . I 5 HOH A 18 518 53 HOH HOH . I 5 HOH A 19 519 19 HOH HOH . I 5 HOH A 20 520 43 HOH HOH . I 5 HOH A 21 521 48 HOH HOH . I 5 HOH A 22 522 45 HOH HOH . I 5 HOH A 23 523 40 HOH HOH . I 5 HOH A 24 524 50 HOH HOH . I 5 HOH A 25 525 49 HOH HOH . I 5 HOH A 26 526 46 HOH HOH . J 5 HOH B 1 501 4 HOH HOH . J 5 HOH B 2 502 18 HOH HOH . J 5 HOH B 3 503 5 HOH HOH . J 5 HOH B 4 504 13 HOH HOH . J 5 HOH B 5 505 16 HOH HOH . J 5 HOH B 6 506 11 HOH HOH . J 5 HOH B 7 507 17 HOH HOH . J 5 HOH B 8 508 1 HOH HOH . J 5 HOH B 9 509 51 HOH HOH . J 5 HOH B 10 510 36 HOH HOH . J 5 HOH B 11 511 7 HOH HOH . J 5 HOH B 12 512 38 HOH HOH . J 5 HOH B 13 513 35 HOH HOH . J 5 HOH B 14 514 10 HOH HOH . J 5 HOH B 15 515 37 HOH HOH . J 5 HOH B 16 516 8 HOH HOH . J 5 HOH B 17 517 6 HOH HOH . J 5 HOH B 18 518 41 HOH HOH . J 5 HOH B 19 519 28 HOH HOH . J 5 HOH B 20 520 21 HOH HOH . J 5 HOH B 21 521 27 HOH HOH . J 5 HOH B 22 522 20 HOH HOH . J 5 HOH B 23 523 24 HOH HOH . J 5 HOH B 24 524 34 HOH HOH . J 5 HOH B 25 525 22 HOH HOH . J 5 HOH B 26 526 31 HOH HOH . J 5 HOH B 27 527 52 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 C CS MTA . . . C 2 26.646 28.014 23.45 0.6 94.97 ? CS MTA 401 A 1 HETATM 2 S S5' MTA . . . C 2 25.593 29.425 23.451 0.6 95.4 ? S5' MTA 401 A 1 HETATM 3 C C5' MTA . . . C 2 26.61 30.612 22.624 0.6 90.91 ? C5' MTA 401 A 1 HETATM 4 C C4' MTA . . . C 2 26.834 30.294 21.144 0.6 84.38 ? C4' MTA 401 A 1 HETATM 5 O O4' MTA . . . C 2 25.599 30.322 20.426 0.6 81.94 ? O4' MTA 401 A 1 HETATM 6 C C2' MTA . . . C 2 27.004 31.878 19.302 0.6 77.74 ? C2' MTA 401 A 1 HETATM 7 O O2' MTA . . . C 2 27.661 31.473 18.098 0.6 74.64 ? O2' MTA 401 A 1 HETATM 8 C C3' MTA . . . C 2 27.744 31.33 20.502 0.6 79.44 ? C3' MTA 401 A 1 HETATM 9 O O3' MTA . . . C 2 28.975 30.72 20.1 0.6 81.85 ? O3' MTA 401 A 1 HETATM 10 C C1' MTA . . . C 2 25.614 31.274 19.366 0.6 79.24 ? C1' MTA 401 A 1 HETATM 11 N N9 MTA . . . C 2 24.66 32.348 19.722 0.6 82.46 ? N9 MTA 401 A 1 HETATM 12 C C8 MTA . . . C 2 24.169 32.596 20.952 0.6 77.96 ? C8 MTA 401 A 1 HETATM 13 N N7 MTA . . . C 2 23.322 33.655 20.929 0.6 77.09 ? N7 MTA 401 A 1 HETATM 14 C C5 MTA . . . C 2 23.269 34.108 19.66 0.6 76.77 ? C5 MTA 401 A 1 HETATM 15 C C6 MTA . . . C 2 22.571 35.192 18.929 0.6 72.46 ? C6 MTA 401 A 1 HETATM 16 N N6 MTA . . . C 2 21.729 36.048 19.555 0.6 70.72 ? N6 MTA 401 A 1 HETATM 17 N N1 MTA . . . C 2 22.798 35.301 17.603 0.6 69.93 ? N1 MTA 401 A 1 HETATM 18 C C2 MTA . . . C 2 23.622 34.469 16.949 0.6 72.24 ? C2 MTA 401 A 1 HETATM 19 N N3 MTA . . . C 2 24.286 33.467 17.543 0.6 77.23 ? N3 MTA 401 A 1 HETATM 20 C C4 MTA . . . C 2 24.154 33.24 18.871 0.6 80.01 ? C4 MTA 401 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 32 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 295 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 20 #