data_4QEP # _model_server_result.job_id sigEg6lcbJsPJ1a6Iv2h3Q _model_server_result.datetime_utc '2024-11-16 11:02:33' _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 4qep # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":801}' # _entry.id 4QEP # _exptl.entry_id 4QEP _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 384.411 _entity.id 4 _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 90 _cell.entry_id 4QEP _cell.length_a 54.346 _cell.length_b 95.569 _cell.length_c 121.754 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4QEP _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 trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _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' DT 6 C DT 6 1_555 B P 5CM 7 C 5CM 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.521 ? covale ? covale2 B O3' 5CM 7 C 5CM 7 1_555 B P DA 8 C DA 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.61 ? metalc ? metalc1 A SG CYS 292 A CYS 383 1_555 E ZN ZN . A ZN 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.399 ? metalc ? metalc2 A SG CYS 292 A CYS 383 1_555 G ZN ZN . A ZN 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.361 ? metalc ? metalc3 A SG CYS 294 A CYS 385 1_555 G ZN ZN . A ZN 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.463 ? metalc ? metalc4 A SG CYS 298 A CYS 389 1_555 F ZN ZN . A ZN 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.382 ? metalc ? metalc5 A SG CYS 298 A CYS 389 1_555 G ZN ZN . A ZN 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.371 ? metalc ? metalc6 A SG CYS 304 A CYS 395 1_555 G ZN ZN . A ZN 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.105 ? metalc ? metalc7 A SG CYS 306 A CYS 397 1_555 E ZN ZN . A ZN 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.602 ? metalc ? metalc8 A SG CYS 334 A CYS 425 1_555 E ZN ZN . A ZN 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.571 ? metalc ? metalc9 A SG CYS 334 A CYS 425 1_555 F ZN ZN . A ZN 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.171 ? metalc ? metalc10 A SG CYS 338 A CYS 429 1_555 E ZN ZN . A ZN 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.323 ? metalc ? metalc11 A SG CYS 340 A CYS 431 1_555 F ZN ZN . A ZN 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.219 ? metalc ? metalc12 A SG CYS 344 A CYS 435 1_555 F ZN ZN . A ZN 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.28 ? metalc ? metalc13 A SG CYS 463 A CYS 554 1_555 H ZN ZN . A ZN 805 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.752 ? metalc ? metalc14 A SG CYS 521 A CYS 612 1_555 H ZN ZN . A ZN 805 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.365 ? metalc ? metalc15 A SG CYS 523 A CYS 614 1_555 H ZN ZN . A ZN 805 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.731 ? metalc ? metalc16 A SG CYS 528 A CYS 619 1_555 H ZN ZN . A ZN 805 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.406 ? hydrog WATSON-CRICK hydrog1 B N1 DG 1 C DG 1 1_555 C N3 DC 13 D DC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N2 DG 1 C DG 1 1_555 C O2 DC 13 D DC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B O6 DG 1 C DG 1 1_555 C N4 DC 13 D DC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N1 DG 2 C DG 2 1_555 C N3 DC 12 D DC 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B N2 DG 2 C DG 2 1_555 C O2 DC 12 D DC 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B O6 DG 2 C DG 2 1_555 C N4 DC 12 D DC 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DG-DC PAIR' hydrog7 B N2 DG 2 C DG 2 1_555 C O2 DC 13 D DC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B N3 DT 3 C DT 3 1_555 C N1 DA 11 D DA 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B O4 DT 3 C DT 3 1_555 C N6 DA 11 D DA 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B N1 DA 4 C DA 4 1_555 C N3 DT 10 D DT 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B N6 DA 4 C DA 4 1_555 C O4 DT 10 D DT 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B N3 DC 5 C DC 5 1_555 C N1 DG 9 D DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B N4 DC 5 C DC 5 1_555 C O6 DG 9 D DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B O2 DC 5 C DC 5 1_555 C N2 DG 9 D DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B N3 DT 6 C DT 6 1_555 C N1 DA 8 D DA 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B O4 DT 6 C DT 6 1_555 C N6 DA 8 D DA 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DA-DT PAIR' hydrog17 B N1 DA 8 C DA 8 1_555 C N3 DT 6 D DT 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B N1 DG 9 C DG 9 1_555 C N3 DC 5 D DC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 B N2 DG 9 C DG 9 1_555 C O2 DC 5 D DC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 B O6 DG 9 C DG 9 1_555 C N4 DC 5 D DC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DC-DG PAIR' hydrog21 B O2 DC 10 C DC 10 1_555 C N1 DG 4 D DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_8_PAIR hydrog22 B N1 DA 11 C DA 11 1_555 C N1 DG 4 D DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_8_PAIR hydrog23 B N6 DA 11 C DA 11 1_555 C O6 DG 4 D DG 4 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 462 n n N HN1 SAH sing 463 n n N HN2 SAH sing 464 n n CA CB SAH sing 465 n n CA C SAH sing 466 n n CA HA SAH sing 467 n n CB CG SAH sing 468 n n CB HB1 SAH sing 469 n n CB HB2 SAH sing 470 n n CG SD SAH sing 471 n n CG HG1 SAH sing 472 n n CG HG2 SAH sing 473 n n SD C5' SAH sing 474 n n C O SAH doub 475 n n C OXT SAH sing 476 n n OXT HXT SAH sing 477 n n C5' C4' SAH sing 478 n n C5' "H5'1" SAH sing 479 n n C5' "H5'2" SAH sing 480 n n C4' O4' SAH sing 481 n n C4' C3' SAH sing 482 n n C4' H4' SAH sing 483 n n O4' C1' SAH sing 484 n n C3' O3' SAH sing 485 n n C3' C2' SAH sing 486 n n C3' H3' SAH sing 487 n n O3' HO3' SAH sing 488 n n C2' O2' SAH sing 489 n n C2' C1' SAH sing 490 n n C2' H2' SAH sing 491 n n O2' HO2' SAH sing 492 n n C1' N9 SAH sing 493 n n C1' H1' SAH sing 494 n n N9 C8 SAH sing 495 n y N9 C4 SAH sing 496 n y C8 N7 SAH doub 497 n y C8 H8 SAH sing 498 n n N7 C5 SAH sing 499 n y C5 C6 SAH sing 500 n y C5 C4 SAH doub 501 n y C6 N6 SAH sing 502 n n C6 N1 SAH doub 503 n y N6 HN61 SAH sing 504 n n N6 HN62 SAH sing 505 n n N1 C2 SAH sing 506 n y C2 N3 SAH doub 507 n y C2 H2 SAH sing 508 n n N3 C4 SAH sing 509 n y # _atom_sites.entry_id 4QEP _atom_sites.fract_transf_matrix[1][1] 0.018401 _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] 0.010464 _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] 0.008213 _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 D 4 SAH A 1 801 801 SAH SAH . E 5 ZN A 1 802 802 ZN ZN . F 5 ZN A 1 803 803 ZN ZN . G 5 ZN A 1 804 804 ZN ZN . H 5 ZN A 1 805 805 ZN ZN . # 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 . . . D 4 -41.168 6.105 -38.618 1 56.12 ? N SAH 801 A 1 HETATM 2 C CA SAH . . . D 4 -39.947 5.619 -39.202 1 56.35 ? CA SAH 801 A 1 HETATM 3 C CB SAH . . . D 4 -38.844 6.631 -39.02 1 67.21 ? CB SAH 801 A 1 HETATM 4 C CG SAH . . . D 4 -37.741 6.362 -40.026 1 68.01 ? CG SAH 801 A 1 HETATM 5 S SD SAH . . . D 4 -37.972 7.098 -41.596 1 54.57 ? SD SAH 801 A 1 HETATM 6 C C SAH . . . D 4 -39.603 4.34 -38.566 1 56.3 ? C SAH 801 A 1 HETATM 7 O O SAH . . . D 4 -39.822 3.33 -39.212 1 55.13 ? O SAH 801 A 1 HETATM 8 O OXT SAH . . . D 4 -39.109 4.32 -37.439 1 67.23 ? OXT SAH 801 A 1 HETATM 9 C C5' SAH . . . D 4 -38.431 8.701 -41.087 1 89.22 ? C5' SAH 801 A 1 HETATM 10 C C4' SAH . . . D 4 -39.921 8.972 -40.998 1 88.53 ? C4' SAH 801 A 1 HETATM 11 O O4' SAH . . . D 4 -40.293 8.83 -39.637 1 88.33 ? O4' SAH 801 A 1 HETATM 12 C C3' SAH . . . D 4 -40.227 10.419 -41.315 1 87.12 ? C3' SAH 801 A 1 HETATM 13 O O3' SAH . . . D 4 -40.775 10.604 -42.603 1 86.27 ? O3' SAH 801 A 1 HETATM 14 C C2' SAH . . . D 4 -41.201 10.87 -40.273 1 86.52 ? C2' SAH 801 A 1 HETATM 15 O O2' SAH . . . D 4 -42.539 10.634 -40.653 1 86.19 ? O2' SAH 801 A 1 HETATM 16 C C1' SAH . . . D 4 -40.824 10.025 -39.104 1 86.89 ? C1' SAH 801 A 1 HETATM 17 N N9 SAH . . . D 4 -39.783 10.926 -38.632 1 86.21 ? N9 SAH 801 A 1 HETATM 18 C C8 SAH . . . D 4 -38.517 10.967 -38.986 1 86.34 ? C8 SAH 801 A 1 HETATM 19 N N7 SAH . . . D 4 -37.86 11.98 -38.394 1 85.78 ? N7 SAH 801 A 1 HETATM 20 C C5 SAH . . . D 4 -38.75 12.617 -37.656 1 85.71 ? C5 SAH 801 A 1 HETATM 21 C C6 SAH . . . D 4 -38.765 13.766 -36.763 1 85.58 ? C6 SAH 801 A 1 HETATM 22 N N6 SAH . . . D 4 -37.665 14.479 -36.509 1 85.83 ? N6 SAH 801 A 1 HETATM 23 N N1 SAH . . . D 4 -39.914 14.076 -36.196 1 84.93 ? N1 SAH 801 A 1 HETATM 24 C C2 SAH . . . D 4 -41.025 13.393 -36.398 1 84.92 ? C2 SAH 801 A 1 HETATM 25 N N3 SAH . . . D 4 -41.092 12.349 -37.187 1 85.29 ? N3 SAH 801 A 1 HETATM 26 C C4 SAH . . . D 4 -40.008 11.926 -37.829 1 85.63 ? C4 SAH 801 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 272 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 26 #