data_6DCC # _model_server_result.job_id XPHwMh-30mTL6tB50Fnn3Q _model_server_result.datetime_utc '2024-11-08 07:30:07' _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 6dcc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":701}' # _entry.id 6DCC # _exptl.entry_id 6DCC _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 384.411 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description S-ADENOSYL-L-HOMOCYSTEINE _entity.pdbx_number_of_molecules 1 _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 120 _cell.entry_id 6DCC _cell.length_a 119.69 _cell.length_b 119.69 _cell.length_c 77.82 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6DCC _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 63' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? dimeric 2 author_defined_assembly 1 PISA hexameric 6 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,C,D,E,F 1 1 A,B,C,D,E,F 2 1,2,3 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_565 -y,x-y+1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 -59.845 103.654581 0 3 'crystal symmetry operation' 3_455 -x+y-1,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -119.69 0 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 covale ? covale1 B O3' G5J 1 B G5J 1 1_555 B P G 2 B G 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.618 ? hydrog WATSON-CRICK hydrog1 B N1 G 2 B G 2 1_555 B N3 C 27 B C 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N2 G 2 B G 2 1_555 B O2 C 27 B C 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B O6 G 2 B G 2 1_555 B N4 C 27 B C 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N1 A 3 B A 3 1_555 B N3 U 26 B U 106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B N6 A 3 B A 3 1_555 B O4 U 26 B U 106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'U-G MISPAIR' hydrog6 B O4 U 4 B U 4 1_555 B N2 G 24 B G 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B N1 G 5 B G 5 1_555 B N3 C 22 B C 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B N2 G 5 B G 5 1_555 B O2 C 22 B C 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B O6 G 5 B G 5 1_555 B N4 C 22 B C 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B N3 U 6 B U 6 1_555 B N1 A 21 B A 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B O4 U 6 B U 6 1_555 B N6 A 21 B A 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B N1 G 7 B G 7 1_555 B N3 C 20 B C 100 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B N2 G 7 B G 7 1_555 B O2 C 20 B C 100 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B O6 G 7 B G 7 1_555 B N4 C 20 B C 100 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B N1 A 8 B A 8 1_555 B N3 U 19 B U 99 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B N6 A 8 B A 8 1_555 B O4 U 19 B U 99 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B N1 G 9 B G 9 1_555 B N3 C 18 B C 98 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B N2 G 9 B G 9 1_555 B O2 C 18 B C 98 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 B O6 G 9 B G 9 1_555 B N4 C 18 B C 98 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 B N1 G 10 B G 10 1_555 B N3 C 17 B C 97 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 B N2 G 10 B G 10 1_555 B O2 C 17 B C 97 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 B O6 G 10 B G 10 1_555 B N4 C 17 B C 97 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 B N3 C 11 B C 11 1_555 B N1 G 16 B G 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 B N4 C 11 B C 11 1_555 B O6 G 16 B G 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 B O2 C 11 B C 11 1_555 B N2 G 16 B G 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'U-G MISPAIR' hydrog26 B O2 U 12 B U 12 1_555 B N1 G 15 B G 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _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 ? # 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 N CA SAH sing 445 n n N HN1 SAH sing 446 n n N HN2 SAH sing 447 n n CA CB SAH sing 448 n n CA C SAH sing 449 n n CA HA SAH sing 450 n n CB CG SAH sing 451 n n CB HB1 SAH sing 452 n n CB HB2 SAH sing 453 n n CG SD SAH sing 454 n n CG HG1 SAH sing 455 n n CG HG2 SAH sing 456 n n SD C5' SAH sing 457 n n C O SAH doub 458 n n C OXT SAH sing 459 n n OXT HXT SAH sing 460 n n C5' C4' SAH sing 461 n n C5' "H5'1" SAH sing 462 n n C5' "H5'2" SAH sing 463 n n C4' O4' SAH sing 464 n n C4' C3' SAH sing 465 n n C4' H4' SAH sing 466 n n O4' C1' SAH sing 467 n n C3' O3' SAH sing 468 n n C3' C2' SAH sing 469 n n C3' H3' SAH sing 470 n n O3' HO3' SAH sing 471 n n C2' O2' SAH sing 472 n n C2' C1' SAH sing 473 n n C2' H2' SAH sing 474 n n O2' HO2' SAH sing 475 n n C1' N9 SAH sing 476 n n C1' H1' SAH sing 477 n n N9 C8 SAH sing 478 n y N9 C4 SAH sing 479 n y C8 N7 SAH doub 480 n y C8 H8 SAH sing 481 n n N7 C5 SAH sing 482 n y C5 C6 SAH sing 483 n y C5 C4 SAH doub 484 n y C6 N6 SAH sing 485 n n C6 N1 SAH doub 486 n y N6 HN61 SAH sing 487 n n N6 HN62 SAH sing 488 n n N1 C2 SAH sing 489 n y C2 N3 SAH doub 490 n y C2 H2 SAH sing 491 n n N3 C4 SAH sing 492 n y # _atom_sites.entry_id 6DCC _atom_sites.fract_transf_matrix[1][1] 0.008355 _atom_sites.fract_transf_matrix[1][2] 0.004824 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009647 _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] 0.01285 _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 3 SAH A 1 701 1 SAH SAH . D 4 SO4 A 1 702 1 SO4 SO4 . E 5 HOH A 1 801 89 HOH HOH . E 5 HOH A 2 802 52 HOH HOH . E 5 HOH A 3 803 16 HOH HOH . E 5 HOH A 4 804 39 HOH HOH . E 5 HOH A 5 805 67 HOH HOH . E 5 HOH A 6 806 45 HOH HOH . E 5 HOH A 7 807 47 HOH HOH . E 5 HOH A 8 808 71 HOH HOH . E 5 HOH A 9 809 35 HOH HOH . E 5 HOH A 10 810 64 HOH HOH . E 5 HOH A 11 811 56 HOH HOH . E 5 HOH A 12 812 4 HOH HOH . E 5 HOH A 13 813 57 HOH HOH . E 5 HOH A 14 814 42 HOH HOH . E 5 HOH A 15 815 3 HOH HOH . E 5 HOH A 16 816 41 HOH HOH . E 5 HOH A 17 817 43 HOH HOH . E 5 HOH A 18 818 7 HOH HOH . E 5 HOH A 19 819 18 HOH HOH . E 5 HOH A 20 820 70 HOH HOH . E 5 HOH A 21 821 8 HOH HOH . E 5 HOH A 22 822 12 HOH HOH . E 5 HOH A 23 823 22 HOH HOH . E 5 HOH A 24 824 85 HOH HOH . E 5 HOH A 25 825 24 HOH HOH . E 5 HOH A 26 826 50 HOH HOH . E 5 HOH A 27 827 11 HOH HOH . E 5 HOH A 28 828 49 HOH HOH . E 5 HOH A 29 829 54 HOH HOH . E 5 HOH A 30 830 1 HOH HOH . E 5 HOH A 31 831 32 HOH HOH . E 5 HOH A 32 832 78 HOH HOH . E 5 HOH A 33 833 48 HOH HOH . E 5 HOH A 34 834 59 HOH HOH . E 5 HOH A 35 835 23 HOH HOH . E 5 HOH A 36 836 84 HOH HOH . E 5 HOH A 37 837 81 HOH HOH . E 5 HOH A 38 838 13 HOH HOH . E 5 HOH A 39 839 69 HOH HOH . E 5 HOH A 40 840 58 HOH HOH . E 5 HOH A 41 841 26 HOH HOH . E 5 HOH A 42 842 21 HOH HOH . E 5 HOH A 43 843 72 HOH HOH . E 5 HOH A 44 844 60 HOH HOH . E 5 HOH A 45 845 10 HOH HOH . E 5 HOH A 46 846 83 HOH HOH . E 5 HOH A 47 847 19 HOH HOH . E 5 HOH A 48 848 88 HOH HOH . E 5 HOH A 49 849 76 HOH HOH . E 5 HOH A 50 850 2 HOH HOH . E 5 HOH A 51 851 27 HOH HOH . E 5 HOH A 52 852 9 HOH HOH . E 5 HOH A 53 853 37 HOH HOH . E 5 HOH A 54 854 33 HOH HOH . E 5 HOH A 55 855 38 HOH HOH . E 5 HOH A 56 856 80 HOH HOH . E 5 HOH A 57 857 68 HOH HOH . E 5 HOH A 58 858 46 HOH HOH . E 5 HOH A 59 859 91 HOH HOH . E 5 HOH A 60 860 82 HOH HOH . E 5 HOH A 61 861 29 HOH HOH . E 5 HOH A 62 862 90 HOH HOH . E 5 HOH A 63 863 14 HOH HOH . F 5 HOH B 1 201 15 HOH HOH . F 5 HOH B 2 202 87 HOH HOH . F 5 HOH B 3 203 79 HOH HOH . F 5 HOH B 4 204 62 HOH HOH . F 5 HOH B 5 205 31 HOH HOH . F 5 HOH B 6 206 36 HOH HOH . F 5 HOH B 7 207 77 HOH HOH . F 5 HOH B 8 208 51 HOH HOH . F 5 HOH B 9 209 44 HOH HOH . F 5 HOH B 10 210 66 HOH HOH . F 5 HOH B 11 211 25 HOH HOH . F 5 HOH B 12 212 5 HOH HOH . F 5 HOH B 13 213 34 HOH HOH . F 5 HOH B 14 214 61 HOH HOH . F 5 HOH B 15 215 65 HOH HOH . F 5 HOH B 16 216 17 HOH HOH . F 5 HOH B 17 217 40 HOH HOH . F 5 HOH B 18 218 20 HOH HOH . F 5 HOH B 19 219 28 HOH HOH . F 5 HOH B 20 220 63 HOH HOH . F 5 HOH B 21 221 53 HOH HOH . F 5 HOH B 22 222 86 HOH HOH . F 5 HOH B 23 223 6 HOH HOH . F 5 HOH B 24 224 75 HOH HOH . F 5 HOH B 25 225 55 HOH HOH . F 5 HOH B 26 226 30 HOH HOH . F 5 HOH B 27 227 74 HOH HOH . F 5 HOH B 28 228 73 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 . . . C 3 -57.163 9.599 0.103 1 37.34 ? N SAH 701 A 1 HETATM 2 C CA SAH . . . C 3 -57.739 9.402 -1.241 1 40.14 ? CA SAH 701 A 1 HETATM 3 C CB SAH . . . C 3 -57.848 10.721 -2.009 1 36.59 ? CB SAH 701 A 1 HETATM 4 C CG SAH . . . C 3 -56.656 11.661 -2.022 1 33.86 ? CG SAH 701 A 1 HETATM 5 S SD SAH . . . C 3 -57.12 13.265 -2.781 1 36.85 ? SD SAH 701 A 1 HETATM 6 C C SAH . . . C 3 -56.947 8.402 -2.072 1 38.68 ? C SAH 701 A 1 HETATM 7 O O SAH . . . C 3 -57.442 7.894 -3.097 1 39.43 ? O SAH 701 A 1 HETATM 8 O OXT SAH . . . C 3 -55.802 8.084 -1.737 1 41.7 ? OXT SAH 701 A 1 HETATM 9 C C5' SAH . . . C 3 -56.656 14.181 -1.273 1 33.52 ? C5' SAH 701 A 1 HETATM 10 C C4' SAH . . . C 3 -57.907 14.696 -0.56 1 30.64 ? C4' SAH 701 A 1 HETATM 11 O O4' SAH . . . C 3 -57.569 15.239 0.694 1 32.99 ? O4' SAH 701 A 1 HETATM 12 C C3' SAH . . . C 3 -58.541 15.846 -1.334 1 34.48 ? C3' SAH 701 A 1 HETATM 13 O O3' SAH . . . C 3 -59.821 15.44 -1.732 1 33.69 ? O3' SAH 701 A 1 HETATM 14 C C2' SAH . . . C 3 -58.574 17.022 -0.365 1 32.69 ? C2' SAH 701 A 1 HETATM 15 O O2' SAH . . . C 3 -59.757 17.781 -0.414 1 31.06 ? O2' SAH 701 A 1 HETATM 16 C C1' SAH . . . C 3 -58.424 16.317 0.977 1 28.95 ? C1' SAH 701 A 1 HETATM 17 N N9 SAH . . . C 3 -57.822 17.156 2.031 1 29.64 ? N9 SAH 701 A 1 HETATM 18 C C8 SAH . . . C 3 -56.733 17.985 1.93 1 30.65 ? C8 SAH 701 A 1 HETATM 19 N N7 SAH . . . C 3 -56.509 18.541 3.158 1 34.16 ? N7 SAH 701 A 1 HETATM 20 C C5 SAH . . . C 3 -57.445 18.082 4.019 1 36.11 ? C5 SAH 701 A 1 HETATM 21 C C6 SAH . . . C 3 -57.695 18.329 5.369 1 33.21 ? C6 SAH 701 A 1 HETATM 22 N N6 SAH . . . C 3 -56.931 19.167 6.075 1 33.23 ? N6 SAH 701 A 1 HETATM 23 N N1 SAH . . . C 3 -58.735 17.679 5.97 1 36.78 ? N1 SAH 701 A 1 HETATM 24 C C2 SAH . . . C 3 -59.546 16.814 5.259 1 34.57 ? C2 SAH 701 A 1 HETATM 25 N N3 SAH . . . C 3 -59.299 16.575 3.924 1 33.07 ? N3 SAH 701 A 1 HETATM 26 C C4 SAH . . . C 3 -58.267 17.202 3.318 1 33.64 ? C4 SAH 701 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 286 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 26 #