data_4DM3 # _model_server_result.job_id Y9H0zD2gq_m13MACzlcsKQ _model_server_result.datetime_utc '2024-11-06 17:45:02' _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 4dm3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":301}' # _entry.id 4DM3 # _exptl.entry_id 4DM3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 384.411 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description S-ADENOSYL-L-HOMOCYSTEINE _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 4DM3 _cell.length_a 93.908 _cell.length_b 93.908 _cell.length_c 188.615 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4DM3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # _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 disulf ? disulf1 A SG CYS 48 A CYS 48 1_555 B SG CYS 139 B CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? disulf ? disulf2 A SG CYS 139 A CYS 139 1_555 B SG CYS 48 B CYS 48 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? # _chem_comp.formula 'C14 H20 N6 O5 S' _chem_comp.formula_weight 384.411 _chem_comp.id SAH _chem_comp.mon_nstd_flag n _chem_comp.name S-ADENOSYL-L-HOMOCYSTEINE _chem_comp.type 'l-peptide linking' _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 4DM3 _atom_sites.fract_transf_matrix[1][1] 0.010649 _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] 0.010649 _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] 0.005302 _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 SAH A 1 2001 2001 SAH SAH . D 3 RCO A 1 2002 1 RCO RCO . E 4 IMD A 1 2003 1 IMD IMD . F 2 SAH B 1 301 2002 SAH SAH . G 3 RCO B 1 302 1 RCO RCO . H 4 IMD B 1 303 1 IMD IMD . I 5 HOH A 1 2101 1 HOH HOH . I 5 HOH A 2 2102 2 HOH HOH . I 5 HOH A 3 2103 3 HOH HOH . I 5 HOH A 4 2104 4 HOH HOH . I 5 HOH A 5 2105 5 HOH HOH . I 5 HOH A 6 2106 6 HOH HOH . I 5 HOH A 7 2107 7 HOH HOH . I 5 HOH A 8 2108 8 HOH HOH . I 5 HOH A 9 2109 9 HOH HOH . I 5 HOH A 10 2110 10 HOH HOH . I 5 HOH A 11 2111 11 HOH HOH . I 5 HOH A 12 2112 12 HOH HOH . I 5 HOH A 13 2113 13 HOH HOH . I 5 HOH A 14 2114 14 HOH HOH . I 5 HOH A 15 2115 15 HOH HOH . I 5 HOH A 16 2116 16 HOH HOH . I 5 HOH A 17 2117 17 HOH HOH . I 5 HOH A 18 2118 18 HOH HOH . I 5 HOH A 19 2119 19 HOH HOH . I 5 HOH A 20 2120 20 HOH HOH . I 5 HOH A 21 2121 21 HOH HOH . I 5 HOH A 22 2122 22 HOH HOH . I 5 HOH A 23 2123 23 HOH HOH . I 5 HOH A 24 2124 24 HOH HOH . I 5 HOH A 25 2125 25 HOH HOH . I 5 HOH A 26 2126 26 HOH HOH . I 5 HOH A 27 2127 27 HOH HOH . I 5 HOH A 28 2128 28 HOH HOH . I 5 HOH A 29 2129 29 HOH HOH . I 5 HOH A 30 2130 30 HOH HOH . I 5 HOH A 31 2131 31 HOH HOH . I 5 HOH A 32 2132 32 HOH HOH . I 5 HOH A 33 2133 33 HOH HOH . I 5 HOH A 34 2134 34 HOH HOH . I 5 HOH A 35 2135 35 HOH HOH . I 5 HOH A 36 2136 36 HOH HOH . I 5 HOH A 37 2137 37 HOH HOH . I 5 HOH A 38 2138 38 HOH HOH . I 5 HOH A 39 2139 39 HOH HOH . I 5 HOH A 40 2140 40 HOH HOH . I 5 HOH A 41 2141 41 HOH HOH . I 5 HOH A 42 2142 43 HOH HOH . I 5 HOH A 43 2143 44 HOH HOH . I 5 HOH A 44 2144 45 HOH HOH . I 5 HOH A 45 2145 46 HOH HOH . I 5 HOH A 46 2146 47 HOH HOH . I 5 HOH A 47 2147 48 HOH HOH . I 5 HOH A 48 2148 49 HOH HOH . I 5 HOH A 49 2149 50 HOH HOH . I 5 HOH A 50 2150 51 HOH HOH . I 5 HOH A 51 2151 52 HOH HOH . I 5 HOH A 52 2152 144 HOH HOH . I 5 HOH A 53 2153 148 HOH HOH . I 5 HOH A 54 2154 150 HOH HOH . I 5 HOH A 55 2155 151 HOH HOH . I 5 HOH A 56 2156 153 HOH HOH . I 5 HOH A 57 2157 154 HOH HOH . I 5 HOH A 58 2158 155 HOH HOH . I 5 HOH A 59 2159 157 HOH HOH . I 5 HOH A 60 2160 159 HOH HOH . I 5 HOH A 61 2161 163 HOH HOH . I 5 HOH A 62 2162 165 HOH HOH . I 5 HOH A 63 2163 166 HOH HOH . I 5 HOH A 64 2164 167 HOH HOH . I 5 HOH A 65 2165 169 HOH HOH . I 5 HOH A 66 2166 174 HOH HOH . I 5 HOH A 67 2167 176 HOH HOH . I 5 HOH A 68 2168 178 HOH HOH . I 5 HOH A 69 2169 179 HOH HOH . I 5 HOH A 70 2170 181 HOH HOH . I 5 HOH A 71 2171 183 HOH HOH . I 5 HOH A 72 2172 184 HOH HOH . I 5 HOH A 73 2173 185 HOH HOH . I 5 HOH A 74 2174 187 HOH HOH . I 5 HOH A 75 2175 188 HOH HOH . I 5 HOH A 76 2176 193 HOH HOH . I 5 HOH A 77 2177 194 HOH HOH . I 5 HOH A 78 2178 195 HOH HOH . I 5 HOH A 79 2179 196 HOH HOH . I 5 HOH A 80 2180 197 HOH HOH . I 5 HOH A 81 2181 203 HOH HOH . I 5 HOH A 82 2182 205 HOH HOH . I 5 HOH A 83 2183 208 HOH HOH . J 5 HOH B 1 401 53 HOH HOH . J 5 HOH B 2 402 54 HOH HOH . J 5 HOH B 3 403 55 HOH HOH . J 5 HOH B 4 404 56 HOH HOH . J 5 HOH B 5 405 57 HOH HOH . J 5 HOH B 6 406 58 HOH HOH . J 5 HOH B 7 407 59 HOH HOH . J 5 HOH B 8 408 60 HOH HOH . J 5 HOH B 9 409 61 HOH HOH . J 5 HOH B 10 410 62 HOH HOH . J 5 HOH B 11 411 63 HOH HOH . J 5 HOH B 12 412 64 HOH HOH . J 5 HOH B 13 413 65 HOH HOH . J 5 HOH B 14 414 66 HOH HOH . J 5 HOH B 15 415 67 HOH HOH . J 5 HOH B 16 416 68 HOH HOH . J 5 HOH B 17 417 69 HOH HOH . J 5 HOH B 18 418 70 HOH HOH . J 5 HOH B 19 419 71 HOH HOH . J 5 HOH B 20 420 72 HOH HOH . J 5 HOH B 21 421 73 HOH HOH . J 5 HOH B 22 422 74 HOH HOH . J 5 HOH B 23 423 75 HOH HOH . J 5 HOH B 24 424 76 HOH HOH . J 5 HOH B 25 425 77 HOH HOH . J 5 HOH B 26 426 78 HOH HOH . J 5 HOH B 27 427 79 HOH HOH . J 5 HOH B 28 428 80 HOH HOH . J 5 HOH B 29 429 81 HOH HOH . J 5 HOH B 30 430 82 HOH HOH . J 5 HOH B 31 431 83 HOH HOH . J 5 HOH B 32 432 84 HOH HOH . J 5 HOH B 33 433 85 HOH HOH . J 5 HOH B 34 434 86 HOH HOH . J 5 HOH B 35 435 87 HOH HOH . J 5 HOH B 36 436 88 HOH HOH . J 5 HOH B 37 437 89 HOH HOH . J 5 HOH B 38 438 90 HOH HOH . J 5 HOH B 39 439 91 HOH HOH . J 5 HOH B 40 440 92 HOH HOH . J 5 HOH B 41 441 93 HOH HOH . J 5 HOH B 42 442 94 HOH HOH . J 5 HOH B 43 443 95 HOH HOH . J 5 HOH B 44 444 96 HOH HOH . J 5 HOH B 45 445 97 HOH HOH . J 5 HOH B 46 446 98 HOH HOH . J 5 HOH B 47 447 99 HOH HOH . J 5 HOH B 48 448 100 HOH HOH . J 5 HOH B 49 449 101 HOH HOH . J 5 HOH B 50 450 102 HOH HOH . J 5 HOH B 51 451 103 HOH HOH . J 5 HOH B 52 452 104 HOH HOH . J 5 HOH B 53 453 105 HOH HOH . J 5 HOH B 54 454 106 HOH HOH . J 5 HOH B 55 455 107 HOH HOH . J 5 HOH B 56 456 108 HOH HOH . J 5 HOH B 57 457 109 HOH HOH . J 5 HOH B 58 458 110 HOH HOH . J 5 HOH B 59 459 111 HOH HOH . J 5 HOH B 60 460 112 HOH HOH . J 5 HOH B 61 461 113 HOH HOH . J 5 HOH B 62 462 114 HOH HOH . J 5 HOH B 63 463 115 HOH HOH . J 5 HOH B 64 464 116 HOH HOH . J 5 HOH B 65 465 117 HOH HOH . J 5 HOH B 66 466 118 HOH HOH . J 5 HOH B 67 467 119 HOH HOH . J 5 HOH B 68 468 120 HOH HOH . J 5 HOH B 69 469 121 HOH HOH . J 5 HOH B 70 470 122 HOH HOH . J 5 HOH B 71 471 123 HOH HOH . J 5 HOH B 72 472 124 HOH HOH . J 5 HOH B 73 473 125 HOH HOH . J 5 HOH B 74 474 126 HOH HOH . J 5 HOH B 75 475 127 HOH HOH . J 5 HOH B 76 476 128 HOH HOH . J 5 HOH B 77 477 129 HOH HOH . J 5 HOH B 78 478 130 HOH HOH . J 5 HOH B 79 479 131 HOH HOH . J 5 HOH B 80 480 132 HOH HOH . J 5 HOH B 81 481 133 HOH HOH . J 5 HOH B 82 482 134 HOH HOH . J 5 HOH B 83 483 135 HOH HOH . J 5 HOH B 84 484 136 HOH HOH . J 5 HOH B 85 485 137 HOH HOH . J 5 HOH B 86 486 138 HOH HOH . J 5 HOH B 87 487 139 HOH HOH . J 5 HOH B 88 488 140 HOH HOH . J 5 HOH B 89 489 143 HOH HOH . J 5 HOH B 90 490 146 HOH HOH . J 5 HOH B 91 491 149 HOH HOH . J 5 HOH B 92 492 156 HOH HOH . J 5 HOH B 93 493 158 HOH HOH . J 5 HOH B 94 494 160 HOH HOH . J 5 HOH B 95 495 161 HOH HOH . J 5 HOH B 96 496 164 HOH HOH . J 5 HOH B 97 497 168 HOH HOH . J 5 HOH B 98 498 170 HOH HOH . J 5 HOH B 99 499 171 HOH HOH . J 5 HOH B 100 500 172 HOH HOH . J 5 HOH B 101 501 173 HOH HOH . J 5 HOH B 102 502 175 HOH HOH . J 5 HOH B 103 503 177 HOH HOH . J 5 HOH B 104 504 180 HOH HOH . J 5 HOH B 105 505 182 HOH HOH . J 5 HOH B 106 506 186 HOH HOH . J 5 HOH B 107 507 189 HOH HOH . J 5 HOH B 108 508 190 HOH HOH . J 5 HOH B 109 509 191 HOH HOH . J 5 HOH B 110 510 192 HOH HOH . J 5 HOH B 111 511 198 HOH HOH . J 5 HOH B 112 512 199 HOH HOH . J 5 HOH B 113 513 200 HOH HOH . J 5 HOH B 114 514 201 HOH HOH . J 5 HOH B 115 515 202 HOH HOH . J 5 HOH B 116 516 204 HOH HOH . J 5 HOH B 117 517 206 HOH HOH . J 5 HOH B 118 518 207 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 N SAH . . . F 2 27.909 50.689 -27.648 1 23.67 ? N SAH 301 B 1 HETATM 2 C CA SAH . . . F 2 28.751 51.679 -26.976 1 25.62 ? CA SAH 301 B 1 HETATM 3 C CB SAH . . . F 2 29.702 52.412 -27.935 1 31.23 ? CB SAH 301 B 1 HETATM 4 C CG SAH . . . F 2 29.102 53.207 -29.112 1 30.13 ? CG SAH 301 B 1 HETATM 5 S SD SAH . . . F 2 30.381 54.236 -29.904 1 34.73 ? SD SAH 301 B 1 HETATM 6 C C SAH . . . F 2 27.916 52.641 -26.14 1 28.88 ? C SAH 301 B 1 HETATM 7 O O SAH . . . F 2 26.738 52.38 -25.86 1 27.64 ? O SAH 301 B 1 HETATM 8 O OXT SAH . . . F 2 28.41 53.688 -25.701 1 33.44 ? OXT SAH 301 B 1 HETATM 9 C C5' SAH . . . F 2 30.245 53.52 -31.578 1 24.97 ? C5' SAH 301 B 1 HETATM 10 C C4' SAH . . . F 2 31.097 52.254 -31.782 1 33.34 ? C4' SAH 301 B 1 HETATM 11 O O4' SAH . . . F 2 30.965 51.734 -33.095 1 34.15 ? O4' SAH 301 B 1 HETATM 12 C C3' SAH . . . F 2 32.601 52.412 -31.571 1 33.87 ? C3' SAH 301 B 1 HETATM 13 O O3' SAH . . . F 2 32.977 51.477 -30.59 1 27.28 ? O3' SAH 301 B 1 HETATM 14 C C2' SAH . . . F 2 33.204 52.012 -32.911 1 31.95 ? C2' SAH 301 B 1 HETATM 15 O O2' SAH . . . F 2 34.461 51.372 -32.847 1 31.18 ? O2' SAH 301 B 1 HETATM 16 C C1' SAH . . . F 2 32.152 51.059 -33.44 1 29.5 ? C1' SAH 301 B 1 HETATM 17 N N9 SAH . . . F 2 32.254 50.881 -34.888 1 35.54 ? N9 SAH 301 B 1 HETATM 18 C C8 SAH . . . F 2 32.923 51.715 -35.748 1 33.27 ? C8 SAH 301 B 1 HETATM 19 N N7 SAH . . . F 2 32.788 51.218 -36.988 1 33.19 ? N7 SAH 301 B 1 HETATM 20 C C5 SAH . . . F 2 32.058 50.084 -36.951 1 31.6 ? C5 SAH 301 B 1 HETATM 21 C C6 SAH . . . F 2 31.634 49.207 -37.949 1 32.14 ? C6 SAH 301 B 1 HETATM 22 N N6 SAH . . . F 2 31.948 49.419 -39.234 1 35.14 ? N6 SAH 301 B 1 HETATM 23 N N1 SAH . . . F 2 30.874 48.109 -37.599 1 35.4 ? N1 SAH 301 B 1 HETATM 24 C C2 SAH . . . F 2 30.54 47.891 -36.266 1 31.53 ? C2 SAH 301 B 1 HETATM 25 N N3 SAH . . . F 2 30.965 48.772 -35.29 1 33.34 ? N3 SAH 301 B 1 HETATM 26 C C4 SAH . . . F 2 31.709 49.858 -35.624 1 36.52 ? C4 SAH 301 B 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 301 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 26 #