data_4U7T # _model_server_result.job_id AiF_0WYXQbj-UWNyFxqAUQ _model_server_result.datetime_utc '2024-11-04 22:32:48' _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 4u7t # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":1004}' # _entry.id 4U7T # _exptl.entry_id 4U7T _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 384.411 _entity.id 5 _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 120 _cell.entry_id 4U7T _cell.length_a 183.823 _cell.length_b 183.823 _cell.length_c 123.265 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4U7T _symmetry.cell_setting ? _symmetry.Int_Tables_number 170 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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 _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 ? 5 J N N ? 5 N 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 27 A CYS 494 1_555 G ZN ZN . A ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? metalc ? metalc2 A SG CYS 30 A CYS 497 1_555 G ZN ZN . A ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.264 ? metalc ? metalc3 A SG CYS 47 A CYS 514 1_555 G ZN ZN . A ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.421 ? metalc ? metalc4 A SG CYS 50 A CYS 517 1_555 G ZN ZN . A ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.281 ? metalc ? metalc5 A SG CYS 70 A CYS 537 1_555 H ZN ZN . A ZN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.566 ? metalc ? metalc6 A SG CYS 73 A CYS 540 1_555 H ZN ZN . A ZN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.244 ? metalc ? metalc7 A SG CYS 82 A CYS 549 1_555 I ZN ZN . A ZN 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.518 ? metalc ? metalc8 A SG CYS 87 A CYS 554 1_555 I ZN ZN . A ZN 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.218 ? metalc ? metalc9 A SG CYS 92 A CYS 559 1_555 H ZN ZN . A ZN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.417 ? metalc ? metalc10 A SG CYS 95 A CYS 562 1_555 H ZN ZN . A ZN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.157 ? metalc ? metalc11 A SG CYS 116 A CYS 583 1_555 I ZN ZN . A ZN 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.13 ? metalc ? metalc12 A SG CYS 119 A CYS 586 1_555 I ZN ZN . A ZN 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.298 ? metalc ? metalc13 C SG CYS 27 C CYS 494 1_555 K ZN ZN . C ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.228 ? metalc ? metalc14 C SG CYS 30 C CYS 497 1_555 K ZN ZN . C ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? metalc ? metalc15 C SG CYS 47 C CYS 514 1_555 K ZN ZN . C ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.479 ? metalc ? metalc16 C SG CYS 50 C CYS 517 1_555 K ZN ZN . C ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? metalc ? metalc17 C SG CYS 70 C CYS 537 1_555 L ZN ZN . C ZN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.479 ? metalc ? metalc18 C SG CYS 73 C CYS 540 1_555 L ZN ZN . C ZN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.423 ? metalc ? metalc19 C SG CYS 82 C CYS 549 1_555 M ZN ZN . C ZN 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.484 ? metalc ? metalc20 C SG CYS 87 C CYS 554 1_555 M ZN ZN . C ZN 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? metalc ? metalc21 C SG CYS 92 C CYS 559 1_555 L ZN ZN . C ZN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.324 ? metalc ? metalc22 C SG CYS 95 C CYS 562 1_555 L ZN ZN . C ZN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.096 ? metalc ? metalc23 C SG CYS 116 C CYS 583 1_555 M ZN ZN . C ZN 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.12 ? metalc ? metalc24 C SG CYS 119 C CYS 586 1_555 M ZN ZN . C ZN 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.27 ? # _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 277 n n N HN1 SAH sing 278 n n N HN2 SAH sing 279 n n CA CB SAH sing 280 n n CA C SAH sing 281 n n CA HA SAH sing 282 n n CB CG SAH sing 283 n n CB HB1 SAH sing 284 n n CB HB2 SAH sing 285 n n CG SD SAH sing 286 n n CG HG1 SAH sing 287 n n CG HG2 SAH sing 288 n n SD C5' SAH sing 289 n n C O SAH doub 290 n n C OXT SAH sing 291 n n OXT HXT SAH sing 292 n n C5' C4' SAH sing 293 n n C5' "H5'1" SAH sing 294 n n C5' "H5'2" SAH sing 295 n n C4' O4' SAH sing 296 n n C4' C3' SAH sing 297 n n C4' H4' SAH sing 298 n n O4' C1' SAH sing 299 n n C3' O3' SAH sing 300 n n C3' C2' SAH sing 301 n n C3' H3' SAH sing 302 n n O3' HO3' SAH sing 303 n n C2' O2' SAH sing 304 n n C2' C1' SAH sing 305 n n C2' H2' SAH sing 306 n n O2' HO2' SAH sing 307 n n C1' N9 SAH sing 308 n n C1' H1' SAH sing 309 n n N9 C8 SAH sing 310 n y N9 C4 SAH sing 311 n y C8 N7 SAH doub 312 n y C8 H8 SAH sing 313 n n N7 C5 SAH sing 314 n y C5 C6 SAH sing 315 n y C5 C4 SAH doub 316 n y C6 N6 SAH sing 317 n n C6 N1 SAH doub 318 n y N6 HN61 SAH sing 319 n n N6 HN62 SAH sing 320 n n N1 C2 SAH sing 321 n y C2 N3 SAH doub 322 n y C2 H2 SAH sing 323 n n N3 C4 SAH sing 324 n y # _atom_sites.entry_id 4U7T _atom_sites.fract_transf_matrix[1][1] 0.00544 _atom_sites.fract_transf_matrix[1][2] 0.003141 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006282 _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] 0.008113 _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 G 4 ZN A 1 1001 1 ZN ZN . H 4 ZN A 1 1002 2 ZN ZN . I 4 ZN A 1 1003 3 ZN ZN . J 5 SAH A 1 1004 4 SAH SAH . K 4 ZN C 1 1001 1 ZN ZN . L 4 ZN C 1 1002 2 ZN ZN . M 4 ZN C 1 1003 3 ZN ZN . N 5 SAH C 1 1004 4 SAH SAH . O 6 HOH A 1 1101 1 HOH HOH . O 6 HOH A 2 1102 2 HOH HOH . O 6 HOH A 3 1103 3 HOH HOH . O 6 HOH A 4 1104 4 HOH HOH . O 6 HOH A 5 1105 5 HOH HOH . O 6 HOH A 6 1106 11 HOH HOH . P 6 HOH C 1 1101 6 HOH HOH . P 6 HOH C 2 1102 7 HOH HOH . P 6 HOH C 3 1103 8 HOH HOH . Q 6 HOH D 1 401 9 HOH HOH . Q 6 HOH D 2 402 10 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 . . . N 5 -20.298 66.792 3.568 1 52.66 ? N SAH 1004 C 1 HETATM 2 C CA SAH . . . N 5 -19.15 66.08 4.082 1 46.82 ? CA SAH 1004 C 1 HETATM 3 C CB SAH . . . N 5 -19.213 64.566 3.856 1 48.9 ? CB SAH 1004 C 1 HETATM 4 C CG SAH . . . N 5 -20.587 63.923 3.785 1 54.59 ? CG SAH 1004 C 1 HETATM 5 S SD SAH . . . N 5 -20.371 62.134 3.674 1 75.89 ? SD SAH 1004 C 1 HETATM 6 C C SAH . . . N 5 -17.903 66.705 3.475 1 54.08 ? C SAH 1004 C 1 HETATM 7 O O SAH . . . N 5 -18.005 67.854 3.006 1 51.86 ? O SAH 1004 C 1 HETATM 8 O OXT SAH . . . N 5 -16.803 66.099 3.455 1 54.52 ? OXT SAH 1004 C 1 HETATM 9 C C5' SAH . . . N 5 -21.058 61.715 5.315 1 64.68 ? C5' SAH 1004 C 1 HETATM 10 C C4' SAH . . . N 5 -20.109 61.543 6.519 1 61.27 ? C4' SAH 1004 C 1 HETATM 11 O O4' SAH . . . N 5 -20.824 61.032 7.634 1 62.52 ? O4' SAH 1004 C 1 HETATM 12 C C3' SAH . . . N 5 -18.937 60.581 6.362 1 61.38 ? C3' SAH 1004 C 1 HETATM 13 O O3' SAH . . . N 5 -17.761 61.348 6.478 1 66.72 ? O3' SAH 1004 C 1 HETATM 14 C C2' SAH . . . N 5 -19.004 59.621 7.54 1 62.16 ? C2' SAH 1004 C 1 HETATM 15 O O2' SAH . . . N 5 -17.768 59.433 8.195 1 58.16 ? O2' SAH 1004 C 1 HETATM 16 C C1' SAH . . . N 5 -19.934 60.335 8.494 1 61.8 ? C1' SAH 1004 C 1 HETATM 17 N N9 SAH . . . N 5 -20.612 59.429 9.461 1 59.2 ? N9 SAH 1004 C 1 HETATM 18 C C8 SAH . . . N 5 -20.884 58.091 9.334 1 56.5 ? C8 SAH 1004 C 1 HETATM 19 N N7 SAH . . . N 5 -21.52 57.656 10.448 1 50.62 ? N7 SAH 1004 C 1 HETATM 20 C C5 SAH . . . N 5 -21.66 58.71 11.285 1 55.4 ? C5 SAH 1004 C 1 HETATM 21 C C6 SAH . . . N 5 -22.23 58.833 12.547 1 55.88 ? C6 SAH 1004 C 1 HETATM 22 N N6 SAH . . . N 5 -22.782 57.777 13.144 1 53.42 ? N6 SAH 1004 C 1 HETATM 23 N N1 SAH . . . N 5 -22.215 60.059 13.17 1 56.24 ? N1 SAH 1004 C 1 HETATM 24 C C2 SAH . . . N 5 -21.648 61.161 12.553 1 55.53 ? C2 SAH 1004 C 1 HETATM 25 N N3 SAH . . . N 5 -21.09 61.034 11.303 1 56.26 ? N3 SAH 1004 C 1 HETATM 26 C C4 SAH . . . N 5 -21.091 59.824 10.685 1 55.52 ? C4 SAH 1004 C 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 310 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 26 #