data_6GKV # _model_server_result.job_id BY1pQODrU9lH1MTCp7NgEg _model_server_result.datetime_utc '2024-12-27 08:56:05' _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 6gkv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":402}' # _entry.id 6GKV # _exptl.entry_id 6GKV _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 6GKV _cell.length_a 48.47 _cell.length_b 96.05 _cell.length_c 154.63 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6GKV _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 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 _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 # _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 311 n n N HN1 SAH sing 312 n n N HN2 SAH sing 313 n n CA CB SAH sing 314 n n CA C SAH sing 315 n n CA HA SAH sing 316 n n CB CG SAH sing 317 n n CB HB1 SAH sing 318 n n CB HB2 SAH sing 319 n n CG SD SAH sing 320 n n CG HG1 SAH sing 321 n n CG HG2 SAH sing 322 n n SD C5' SAH sing 323 n n C O SAH doub 324 n n C OXT SAH sing 325 n n OXT HXT SAH sing 326 n n C5' C4' SAH sing 327 n n C5' "H5'1" SAH sing 328 n n C5' "H5'2" SAH sing 329 n n C4' O4' SAH sing 330 n n C4' C3' SAH sing 331 n n C4' H4' SAH sing 332 n n O4' C1' SAH sing 333 n n C3' O3' SAH sing 334 n n C3' C2' SAH sing 335 n n C3' H3' SAH sing 336 n n O3' HO3' SAH sing 337 n n C2' O2' SAH sing 338 n n C2' C1' SAH sing 339 n n C2' H2' SAH sing 340 n n O2' HO2' SAH sing 341 n n C1' N9 SAH sing 342 n n C1' H1' SAH sing 343 n n N9 C8 SAH sing 344 n y N9 C4 SAH sing 345 n y C8 N7 SAH doub 346 n y C8 H8 SAH sing 347 n n N7 C5 SAH sing 348 n y C5 C6 SAH sing 349 n y C5 C4 SAH doub 350 n y C6 N6 SAH sing 351 n n C6 N1 SAH doub 352 n y N6 HN61 SAH sing 353 n n N6 HN62 SAH sing 354 n n N1 C2 SAH sing 355 n y C2 N3 SAH doub 356 n y C2 H2 SAH sing 357 n n N3 C4 SAH sing 358 n y # _atom_sites.entry_id 6GKV _atom_sites.fract_transf_matrix[1][1] 0.020631 _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] 0.010411 _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] 0.006467 _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 1 501 501 SAH SAH . D 3 F2W A 1 502 502 F2W DRG . E 3 F2W B 1 401 502 F2W DRG . F 2 SAH B 1 402 501 SAH SAH . G 4 HOH A 1 601 80 HOH HOH . G 4 HOH A 2 602 5 HOH HOH . G 4 HOH A 3 603 21 HOH HOH . G 4 HOH A 4 604 66 HOH HOH . G 4 HOH A 5 605 51 HOH HOH . G 4 HOH A 6 606 69 HOH HOH . G 4 HOH A 7 607 32 HOH HOH . G 4 HOH A 8 608 46 HOH HOH . G 4 HOH A 9 609 3 HOH HOH . G 4 HOH A 10 610 17 HOH HOH . G 4 HOH A 11 611 31 HOH HOH . G 4 HOH A 12 612 10 HOH HOH . G 4 HOH A 13 613 7 HOH HOH . G 4 HOH A 14 614 20 HOH HOH . G 4 HOH A 15 615 1 HOH HOH . G 4 HOH A 16 616 68 HOH HOH . G 4 HOH A 17 617 37 HOH HOH . G 4 HOH A 18 618 4 HOH HOH . G 4 HOH A 19 619 25 HOH HOH . G 4 HOH A 20 620 15 HOH HOH . G 4 HOH A 21 621 71 HOH HOH . G 4 HOH A 22 622 35 HOH HOH . G 4 HOH A 23 623 8 HOH HOH . G 4 HOH A 24 624 2 HOH HOH . G 4 HOH A 25 625 49 HOH HOH . G 4 HOH A 26 626 24 HOH HOH . G 4 HOH A 27 627 40 HOH HOH . G 4 HOH A 28 628 28 HOH HOH . G 4 HOH A 29 629 26 HOH HOH . G 4 HOH A 30 630 76 HOH HOH . G 4 HOH A 31 631 72 HOH HOH . G 4 HOH A 32 632 57 HOH HOH . G 4 HOH A 33 633 62 HOH HOH . G 4 HOH A 34 634 42 HOH HOH . G 4 HOH A 35 635 41 HOH HOH . G 4 HOH A 36 636 43 HOH HOH . G 4 HOH A 37 637 38 HOH HOH . G 4 HOH A 38 638 44 HOH HOH . G 4 HOH A 39 639 78 HOH HOH . G 4 HOH A 40 640 74 HOH HOH . G 4 HOH A 41 641 55 HOH HOH . G 4 HOH A 42 642 75 HOH HOH . H 4 HOH B 1 501 77 HOH HOH . H 4 HOH B 2 502 18 HOH HOH . H 4 HOH B 3 503 45 HOH HOH . H 4 HOH B 4 504 30 HOH HOH . H 4 HOH B 5 505 53 HOH HOH . H 4 HOH B 6 506 19 HOH HOH . H 4 HOH B 7 507 6 HOH HOH . H 4 HOH B 8 508 52 HOH HOH . H 4 HOH B 9 509 13 HOH HOH . H 4 HOH B 10 510 16 HOH HOH . H 4 HOH B 11 511 22 HOH HOH . H 4 HOH B 12 512 14 HOH HOH . H 4 HOH B 13 513 23 HOH HOH . H 4 HOH B 14 514 27 HOH HOH . H 4 HOH B 15 515 60 HOH HOH . H 4 HOH B 16 516 9 HOH HOH . H 4 HOH B 17 517 34 HOH HOH . H 4 HOH B 18 518 50 HOH HOH . H 4 HOH B 19 519 11 HOH HOH . H 4 HOH B 20 520 58 HOH HOH . H 4 HOH B 21 521 29 HOH HOH . H 4 HOH B 22 522 79 HOH HOH . H 4 HOH B 23 523 36 HOH HOH . H 4 HOH B 24 524 12 HOH HOH . H 4 HOH B 25 525 54 HOH HOH . H 4 HOH B 26 526 65 HOH HOH . H 4 HOH B 27 527 56 HOH HOH . H 4 HOH B 28 528 33 HOH HOH . H 4 HOH B 29 529 61 HOH HOH . H 4 HOH B 30 530 47 HOH HOH . H 4 HOH B 31 531 63 HOH HOH . H 4 HOH B 32 532 67 HOH HOH . H 4 HOH B 33 533 39 HOH HOH . H 4 HOH B 34 534 59 HOH HOH . H 4 HOH B 35 535 81 HOH HOH . H 4 HOH B 36 536 48 HOH HOH . H 4 HOH B 37 537 73 HOH HOH . H 4 HOH B 38 538 64 HOH HOH . H 4 HOH B 39 539 70 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 -3.82 27.934 -57.431 1 58.77 ? N SAH 402 B 1 HETATM 2 C CA SAH . . . F 2 -4.664 27.154 -58.334 1 64.3 ? CA SAH 402 B 1 HETATM 3 C CB SAH . . . F 2 -3.785 26.279 -59.209 1 68.32 ? CB SAH 402 B 1 HETATM 4 C CG SAH . . . F 2 -2.408 26.059 -58.612 1 70.02 ? CG SAH 402 B 1 HETATM 5 S SD SAH . . . F 2 -1.283 25.299 -59.797 1 90.86 ? SD SAH 402 B 1 HETATM 6 C C SAH . . . F 2 -5.692 26.304 -57.601 1 70.2 ? C SAH 402 B 1 HETATM 7 O O SAH . . . F 2 -6.506 25.597 -58.199 1 65.31 ? O SAH 402 B 1 HETATM 8 O OXT SAH . . . F 2 -5.73 26.313 -56.372 1 85.58 ? OXT SAH 402 B 1 HETATM 9 C C5' SAH . . . F 2 -0.268 26.795 -59.845 1 93.78 ? C5' SAH 402 B 1 HETATM 10 C C4' SAH . . . F 2 -0.873 27.907 -60.703 1 98.55 ? C4' SAH 402 B 1 HETATM 11 O O4' SAH . . . F 2 -0.029 29.042 -60.67 1 96.28 ? O4' SAH 402 B 1 HETATM 12 C C3' SAH . . . F 2 -1.042 27.519 -62.165 1 102.64 ? C3' SAH 402 B 1 HETATM 13 O O3' SAH . . . F 2 -2.41 27.362 -62.468 1 108.39 ? O3' SAH 402 B 1 HETATM 14 C C2' SAH . . . F 2 -0.457 28.668 -62.963 1 97.76 ? C2' SAH 402 B 1 HETATM 15 O O2' SAH . . . F 2 -1.491 29.352 -63.622 1 102.08 ? O2' SAH 402 B 1 HETATM 16 C C1' SAH . . . F 2 0.128 29.623 -61.947 1 87.47 ? C1' SAH 402 B 1 HETATM 17 N N9 SAH . . . F 2 1.564 29.876 -62.163 1 78.64 ? N9 SAH 402 B 1 HETATM 18 C C8 SAH . . . F 2 2.585 28.955 -62.17 1 80.5 ? C8 SAH 402 B 1 HETATM 19 N N7 SAH . . . F 2 3.755 29.608 -62.384 1 80.25 ? N7 SAH 402 B 1 HETATM 20 C C5 SAH . . . F 2 3.498 30.937 -62.512 1 77.96 ? C5 SAH 402 B 1 HETATM 21 C C6 SAH . . . F 2 4.309 32.052 -62.744 1 69.82 ? C6 SAH 402 B 1 HETATM 22 N N6 SAH . . . F 2 5.63 31.934 -62.885 1 63.56 ? N6 SAH 402 B 1 HETATM 23 N N1 SAH . . . F 2 3.73 33.304 -62.827 1 69.05 ? N1 SAH 402 B 1 HETATM 24 C C2 SAH . . . F 2 2.361 33.452 -62.687 1 64.88 ? C2 SAH 402 B 1 HETATM 25 N N3 SAH . . . F 2 1.564 32.35 -62.457 1 65.4 ? N3 SAH 402 B 1 HETATM 26 C C4 SAH . . . F 2 2.121 31.115 -62.366 1 76.63 ? C4 SAH 402 B 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 110 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 288 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 26 #