data_6P5Z # _model_server_result.job_id WOdJERQxsaAiCfAC1ITHSw _model_server_result.datetime_utc '2024-10-15 11:22:15' _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 6p5z # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":501}' # _entry.id 6P5Z # _exptl.entry_id 6P5Z _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 6P5Z _cell.length_a 59.601 _cell.length_b 100.446 _cell.length_c 146.4 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6P5Z _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall 'P 2ac 2ab' _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 G 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 covale ? covale1 A NE2 GLN 291 A GLN 291 1_555 D O59 F0X . A F0X 502 3_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.297 ? covale ? covale2 A NH2 ARG 309 A ARG 309 1_555 E O39 F0X . A F0X 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.301 ? metalc ? metalc1 A NE2 HIS 359 A HIS 359 1_555 E CO F0X . A F0X 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.711 ? # _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 391 n n N HN1 SAH sing 392 n n N HN2 SAH sing 393 n n CA CB SAH sing 394 n n CA C SAH sing 395 n n CA HA SAH sing 396 n n CB CG SAH sing 397 n n CB HB1 SAH sing 398 n n CB HB2 SAH sing 399 n n CG SD SAH sing 400 n n CG HG1 SAH sing 401 n n CG HG2 SAH sing 402 n n SD C5' SAH sing 403 n n C O SAH doub 404 n n C OXT SAH sing 405 n n OXT HXT SAH sing 406 n n C5' C4' SAH sing 407 n n C5' "H5'1" SAH sing 408 n n C5' "H5'2" SAH sing 409 n n C4' O4' SAH sing 410 n n C4' C3' SAH sing 411 n n C4' H4' SAH sing 412 n n O4' C1' SAH sing 413 n n C3' O3' SAH sing 414 n n C3' C2' SAH sing 415 n n C3' H3' SAH sing 416 n n O3' HO3' SAH sing 417 n n C2' O2' SAH sing 418 n n C2' C1' SAH sing 419 n n C2' H2' SAH sing 420 n n O2' HO2' SAH sing 421 n n C1' N9 SAH sing 422 n n C1' H1' SAH sing 423 n n N9 C8 SAH sing 424 n y N9 C4 SAH sing 425 n y C8 N7 SAH doub 426 n y C8 H8 SAH sing 427 n n N7 C5 SAH sing 428 n y C5 C6 SAH sing 429 n y C5 C4 SAH doub 430 n y C6 N6 SAH sing 431 n n C6 N1 SAH doub 432 n y N6 HN61 SAH sing 433 n n N6 HN62 SAH sing 434 n n N1 C2 SAH sing 435 n y C2 N3 SAH doub 436 n y C2 H2 SAH sing 437 n n N3 C4 SAH sing 438 n y # _atom_sites.entry_id 6P5Z _atom_sites.fract_transf_matrix[1][1] 0.016778 _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] 0.009956 _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] 0.006831 _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 1 501 458 SAH SAH . D 3 F0X A 1 502 1 F0X SIR . E 3 F0X A 1 503 2 F0X SIR . F 4 CL A 1 504 2 CL CL . G 2 SAH B 1 501 458 SAH SAH . H 4 CL B 1 502 1 CL CL . I 5 HOH A 1 601 8 HOH HOH . I 5 HOH A 2 602 24 HOH HOH . I 5 HOH A 3 603 12 HOH HOH . I 5 HOH A 4 604 48 HOH HOH . I 5 HOH A 5 605 23 HOH HOH . I 5 HOH A 6 606 30 HOH HOH . I 5 HOH A 7 607 19 HOH HOH . I 5 HOH A 8 608 21 HOH HOH . I 5 HOH A 9 609 28 HOH HOH . I 5 HOH A 10 610 29 HOH HOH . I 5 HOH A 11 611 13 HOH HOH . I 5 HOH A 12 612 49 HOH HOH . I 5 HOH A 13 613 32 HOH HOH . I 5 HOH A 14 614 22 HOH HOH . I 5 HOH A 15 615 37 HOH HOH . I 5 HOH A 16 616 9 HOH HOH . I 5 HOH A 17 617 36 HOH HOH . I 5 HOH A 18 618 7 HOH HOH . I 5 HOH A 19 619 53 HOH HOH . I 5 HOH A 20 620 15 HOH HOH . I 5 HOH A 21 621 46 HOH HOH . I 5 HOH A 22 622 11 HOH HOH . I 5 HOH A 23 623 25 HOH HOH . I 5 HOH A 24 624 26 HOH HOH . I 5 HOH A 25 625 44 HOH HOH . I 5 HOH A 26 626 45 HOH HOH . I 5 HOH A 27 627 50 HOH HOH . I 5 HOH A 28 628 27 HOH HOH . I 5 HOH A 29 629 52 HOH HOH . J 5 HOH B 1 601 51 HOH HOH . J 5 HOH B 2 602 43 HOH HOH . J 5 HOH B 3 603 16 HOH HOH . J 5 HOH B 4 604 34 HOH HOH . J 5 HOH B 5 605 33 HOH HOH . J 5 HOH B 6 606 17 HOH HOH . J 5 HOH B 7 607 6 HOH HOH . J 5 HOH B 8 608 41 HOH HOH . J 5 HOH B 9 609 10 HOH HOH . J 5 HOH B 10 610 1 HOH HOH . J 5 HOH B 11 611 18 HOH HOH . J 5 HOH B 12 612 39 HOH HOH . J 5 HOH B 13 613 4 HOH HOH . J 5 HOH B 14 614 14 HOH HOH . J 5 HOH B 15 615 20 HOH HOH . J 5 HOH B 16 616 31 HOH HOH . J 5 HOH B 17 617 40 HOH HOH . J 5 HOH B 18 618 35 HOH HOH . J 5 HOH B 19 619 2 HOH HOH . J 5 HOH B 20 620 5 HOH HOH . J 5 HOH B 21 621 3 HOH HOH . J 5 HOH B 22 622 38 HOH HOH . J 5 HOH B 23 623 42 HOH HOH . J 5 HOH B 24 624 47 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 . . . G 2 16.769 -15.659 13.452 1 54.21 ? N SAH 501 B 1 HETATM 2 C CA SAH . . . G 2 17.82 -15.189 14.351 1 56.42 ? CA SAH 501 B 1 HETATM 3 C CB SAH . . . G 2 19.174 -15.162 13.647 1 56.45 ? CB SAH 501 B 1 HETATM 4 C CG SAH . . . G 2 19.753 -16.498 13.192 1 65.59 ? CG SAH 501 B 1 HETATM 5 S SD SAH . . . G 2 21.315 -16.249 12.294 1 67.13 ? SD SAH 501 B 1 HETATM 6 C C SAH . . . G 2 17.53 -13.793 14.913 1 60.68 ? C SAH 501 B 1 HETATM 7 O O SAH . . . G 2 16.52 -13.147 14.604 1 54.36 ? O SAH 501 B 1 HETATM 8 O OXT SAH . . . G 2 18.331 -13.27 15.69 1 48.54 ? OXT SAH 501 B 1 HETATM 9 C C5' SAH . . . G 2 22.337 -16.533 13.761 1 69.11 ? C5' SAH 501 B 1 HETATM 10 C C4' SAH . . . G 2 23.148 -15.279 14.085 1 67.39 ? C4' SAH 501 B 1 HETATM 11 O O4' SAH . . . G 2 22.358 -14.377 14.84 1 60.22 ? O4' SAH 501 B 1 HETATM 12 C C3' SAH . . . G 2 24.421 -15.524 14.888 1 64.2 ? C3' SAH 501 B 1 HETATM 13 O O3' SAH . . . G 2 25.554 -15.681 14.068 1 67.54 ? O3' SAH 501 B 1 HETATM 14 C C2' SAH . . . G 2 24.561 -14.25 15.691 1 63.67 ? C2' SAH 501 B 1 HETATM 15 O O2' SAH . . . G 2 25.321 -13.28 15.002 1 61.11 ? O2' SAH 501 B 1 HETATM 16 C C1' SAH . . . G 2 23.152 -13.725 15.8 1 56.73 ? C1' SAH 501 B 1 HETATM 17 N N9 SAH . . . G 2 22.641 -14.071 17.131 1 55.76 ? N9 SAH 501 B 1 HETATM 18 C C8 SAH . . . G 2 21.656 -14.983 17.436 1 43.93 ? C8 SAH 501 B 1 HETATM 19 N N7 SAH . . . G 2 21.479 -14.993 18.775 1 45.9 ? N7 SAH 501 B 1 HETATM 20 C C5 SAH . . . G 2 22.352 -14.115 19.337 1 52.74 ? C5 SAH 501 B 1 HETATM 21 C C6 SAH . . . G 2 22.603 -13.746 20.657 1 48.9 ? C6 SAH 501 B 1 HETATM 22 N N6 SAH . . . G 2 21.92 -14.288 21.667 1 61.21 ? N6 SAH 501 B 1 HETATM 23 N N1 SAH . . . G 2 23.571 -12.801 20.906 1 53.61 ? N1 SAH 501 B 1 HETATM 24 C C2 SAH . . . G 2 24.293 -12.226 19.868 1 54.01 ? C2 SAH 501 B 1 HETATM 25 N N3 SAH . . . G 2 24.048 -12.603 18.557 1 50.89 ? N3 SAH 501 B 1 HETATM 26 C C4 SAH . . . G 2 23.091 -13.528 18.305 1 52.23 ? C4 SAH 501 B 1 # _model_server_stats.io_time_ms 26 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 301 _model_server_stats.encode_time_ms 15 _model_server_stats.element_count 26 #