data_5V3H # _model_server_result.job_id Xxw3E2wZmg9GMBAejoCTjA _model_server_result.datetime_utc '2025-02-17 22:10:39' _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 5v3h # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 5V3H # _exptl.entry_id 5V3H _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 398.437 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description S-ADENOSYLMETHIONINE _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 114.22 _cell.angle_gamma 90 _cell.entry_id 5V3H _cell.length_a 157.56 _cell.length_b 54.775 _cell.length_c 79.702 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5V3H _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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,K,L,M _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 2 _struct_asym.id B _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 metalc ? metalc1 A SG CYS 63 A CYS 52 1_555 D ZN ZN . A ZN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? metalc ? metalc2 A SG CYS 66 A CYS 55 1_555 D ZN ZN . A ZN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.375 ? metalc ? metalc3 A SG CYS 76 A CYS 65 1_555 E ZN ZN . A ZN 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.351 ? metalc ? metalc4 A SG CYS 79 A CYS 68 1_555 E ZN ZN . A ZN 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.335 ? metalc ? metalc5 A SG CYS 85 A CYS 74 1_555 D ZN ZN . A ZN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.336 ? metalc ? metalc6 A SG CYS 89 A CYS 78 1_555 D ZN ZN . A ZN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.354 ? metalc ? metalc7 A NE2 HIS 97 A HIS 86 1_555 E ZN ZN . A ZN 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc8 A SG CYS 101 A CYS 90 1_555 E ZN ZN . A ZN 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.352 ? metalc ? metalc9 A SG CYS 220 A CYS 209 1_555 C ZN ZN . A ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.345 ? metalc ? metalc10 A SG CYS 273 A CYS 262 1_555 C ZN ZN . A ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? metalc ? metalc11 A SG CYS 275 A CYS 264 1_555 C ZN ZN . A ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.352 ? metalc ? metalc12 A SG CYS 278 A CYS 267 1_555 C ZN ZN . A ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.333 ? # _chem_comp.formula 'C15 H22 N6 O5 S' _chem_comp.formula_weight 398.437 _chem_comp.id SAM _chem_comp.mon_nstd_flag . _chem_comp.name S-ADENOSYLMETHIONINE _chem_comp.type non-polymer _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 SAM sing 370 n n N HN1 SAM sing 371 n n N HN2 SAM sing 372 n n CA C SAM sing 373 n n CA CB SAM sing 374 n n CA HA SAM sing 375 n n C O SAM doub 376 n n C OXT SAM sing 377 n n CB CG SAM sing 378 n n CB HB1 SAM sing 379 n n CB HB2 SAM sing 380 n n CG SD SAM sing 381 n n CG HG1 SAM sing 382 n n CG HG2 SAM sing 383 n n SD CE SAM sing 384 n n SD C5' SAM sing 385 n n CE HE1 SAM sing 386 n n CE HE2 SAM sing 387 n n CE HE3 SAM sing 388 n n C5' C4' SAM sing 389 n n C5' "H5'1" SAM sing 390 n n C5' "H5'2" SAM sing 391 n n C4' O4' SAM sing 392 n n C4' C3' SAM sing 393 n n C4' H4' SAM sing 394 n n O4' C1' SAM sing 395 n n C3' O3' SAM sing 396 n n C3' C2' SAM sing 397 n n C3' H3' SAM sing 398 n n O3' HO3' SAM sing 399 n n C2' O2' SAM sing 400 n n C2' C1' SAM sing 401 n n C2' H2' SAM sing 402 n n O2' HO2' SAM sing 403 n n C1' N9 SAM sing 404 n n C1' H1' SAM sing 405 n n N9 C8 SAM sing 406 n y N9 C4 SAM sing 407 n y C8 N7 SAM doub 408 n y C8 H8 SAM sing 409 n n N7 C5 SAM sing 410 n y C5 C6 SAM sing 411 n y C5 C4 SAM doub 412 n y C6 N6 SAM sing 413 n n C6 N1 SAM doub 414 n y N6 HN61 SAM sing 415 n n N6 HN62 SAM sing 416 n n N1 C2 SAM sing 417 n y C2 N3 SAM doub 418 n y C2 H2 SAM sing 419 n n N3 C4 SAM sing 420 n y # _atom_sites.entry_id 5V3H _atom_sites.fract_transf_matrix[1][1] 0.006347 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002855 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018257 _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] 0.013757 _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 B 2 SAM A 1 501 1 SAM SAM . C 3 ZN A 1 502 1 ZN ZN . D 3 ZN A 1 503 2 ZN ZN . E 3 ZN A 1 504 3 ZN ZN . F 4 8WG A 1 505 1 8WG EPZ . G 4 8WG A 1 506 2 8WG EPZ . H 5 PEG A 1 507 1 PEG PEG . I 5 PEG A 1 508 2 PEG PEG . J 6 EDO A 1 509 3 EDO EDO . K 7 GOL A 1 510 1 GOL GOL . L 7 GOL A 1 511 2 GOL GOL . M 8 HOH A 1 601 74 HOH HOH . M 8 HOH A 2 602 1 HOH HOH . M 8 HOH A 3 603 96 HOH HOH . M 8 HOH A 4 604 105 HOH HOH . M 8 HOH A 5 605 43 HOH HOH . M 8 HOH A 6 606 110 HOH HOH . M 8 HOH A 7 607 23 HOH HOH . M 8 HOH A 8 608 16 HOH HOH . M 8 HOH A 9 609 13 HOH HOH . M 8 HOH A 10 610 68 HOH HOH . M 8 HOH A 11 611 115 HOH HOH . M 8 HOH A 12 612 93 HOH HOH . M 8 HOH A 13 613 41 HOH HOH . M 8 HOH A 14 614 129 HOH HOH . M 8 HOH A 15 615 106 HOH HOH . M 8 HOH A 16 616 114 HOH HOH . M 8 HOH A 17 617 73 HOH HOH . M 8 HOH A 18 618 11 HOH HOH . M 8 HOH A 19 619 17 HOH HOH . M 8 HOH A 20 620 33 HOH HOH . M 8 HOH A 21 621 6 HOH HOH . M 8 HOH A 22 622 15 HOH HOH . M 8 HOH A 23 623 85 HOH HOH . M 8 HOH A 24 624 51 HOH HOH . M 8 HOH A 25 625 80 HOH HOH . M 8 HOH A 26 626 4 HOH HOH . M 8 HOH A 27 627 22 HOH HOH . M 8 HOH A 28 628 52 HOH HOH . M 8 HOH A 29 629 10 HOH HOH . M 8 HOH A 30 630 25 HOH HOH . M 8 HOH A 31 631 39 HOH HOH . M 8 HOH A 32 632 18 HOH HOH . M 8 HOH A 33 633 5 HOH HOH . M 8 HOH A 34 634 77 HOH HOH . M 8 HOH A 35 635 29 HOH HOH . M 8 HOH A 36 636 59 HOH HOH . M 8 HOH A 37 637 53 HOH HOH . M 8 HOH A 38 638 48 HOH HOH . M 8 HOH A 39 639 32 HOH HOH . M 8 HOH A 40 640 55 HOH HOH . M 8 HOH A 41 641 66 HOH HOH . M 8 HOH A 42 642 58 HOH HOH . M 8 HOH A 43 643 30 HOH HOH . M 8 HOH A 44 644 79 HOH HOH . M 8 HOH A 45 645 37 HOH HOH . M 8 HOH A 46 646 14 HOH HOH . M 8 HOH A 47 647 2 HOH HOH . M 8 HOH A 48 648 83 HOH HOH . M 8 HOH A 49 649 8 HOH HOH . M 8 HOH A 50 650 71 HOH HOH . M 8 HOH A 51 651 119 HOH HOH . M 8 HOH A 52 652 81 HOH HOH . M 8 HOH A 53 653 98 HOH HOH . M 8 HOH A 54 654 12 HOH HOH . M 8 HOH A 55 655 95 HOH HOH . M 8 HOH A 56 656 126 HOH HOH . M 8 HOH A 57 657 40 HOH HOH . M 8 HOH A 58 658 94 HOH HOH . M 8 HOH A 59 659 122 HOH HOH . M 8 HOH A 60 660 24 HOH HOH . M 8 HOH A 61 661 19 HOH HOH . M 8 HOH A 62 662 102 HOH HOH . M 8 HOH A 63 663 118 HOH HOH . M 8 HOH A 64 664 50 HOH HOH . M 8 HOH A 65 665 63 HOH HOH . M 8 HOH A 66 666 113 HOH HOH . M 8 HOH A 67 667 46 HOH HOH . M 8 HOH A 68 668 125 HOH HOH . M 8 HOH A 69 669 107 HOH HOH . M 8 HOH A 70 670 60 HOH HOH . M 8 HOH A 71 671 86 HOH HOH . M 8 HOH A 72 672 3 HOH HOH . M 8 HOH A 73 673 111 HOH HOH . M 8 HOH A 74 674 75 HOH HOH . M 8 HOH A 75 675 67 HOH HOH . M 8 HOH A 76 676 127 HOH HOH . M 8 HOH A 77 677 20 HOH HOH . M 8 HOH A 78 678 21 HOH HOH . M 8 HOH A 79 679 26 HOH HOH . M 8 HOH A 80 680 56 HOH HOH . M 8 HOH A 81 681 7 HOH HOH . M 8 HOH A 82 682 45 HOH HOH . M 8 HOH A 83 683 57 HOH HOH . M 8 HOH A 84 684 44 HOH HOH . M 8 HOH A 85 685 84 HOH HOH . M 8 HOH A 86 686 61 HOH HOH . M 8 HOH A 87 687 34 HOH HOH . M 8 HOH A 88 688 78 HOH HOH . M 8 HOH A 89 689 128 HOH HOH . M 8 HOH A 90 690 35 HOH HOH . M 8 HOH A 91 691 36 HOH HOH . M 8 HOH A 92 692 116 HOH HOH . M 8 HOH A 93 693 120 HOH HOH . M 8 HOH A 94 694 72 HOH HOH . M 8 HOH A 95 695 76 HOH HOH . M 8 HOH A 96 696 62 HOH HOH . M 8 HOH A 97 697 9 HOH HOH . M 8 HOH A 98 698 31 HOH HOH . M 8 HOH A 99 699 64 HOH HOH . M 8 HOH A 100 700 65 HOH HOH . M 8 HOH A 101 701 42 HOH HOH . M 8 HOH A 102 702 112 HOH HOH . M 8 HOH A 103 703 49 HOH HOH . M 8 HOH A 104 704 103 HOH HOH . M 8 HOH A 105 705 109 HOH HOH . M 8 HOH A 106 706 82 HOH HOH . M 8 HOH A 107 707 101 HOH HOH . M 8 HOH A 108 708 90 HOH HOH . M 8 HOH A 109 709 54 HOH HOH . M 8 HOH A 110 710 89 HOH HOH . M 8 HOH A 111 711 92 HOH HOH . M 8 HOH A 112 712 108 HOH HOH . M 8 HOH A 113 713 27 HOH HOH . M 8 HOH A 114 714 87 HOH HOH . M 8 HOH A 115 715 47 HOH HOH . M 8 HOH A 116 716 97 HOH HOH . M 8 HOH A 117 717 104 HOH HOH . M 8 HOH A 118 718 100 HOH HOH . M 8 HOH A 119 719 91 HOH HOH . M 8 HOH A 120 720 99 HOH HOH . M 8 HOH A 121 721 28 HOH HOH . M 8 HOH A 122 722 38 HOH HOH . M 8 HOH A 123 723 124 HOH HOH . M 8 HOH A 124 724 117 HOH HOH . M 8 HOH A 125 725 69 HOH HOH . M 8 HOH A 126 726 121 HOH HOH . M 8 HOH A 127 727 123 HOH HOH . M 8 HOH A 128 728 70 HOH HOH . M 8 HOH A 129 729 88 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 SAM . . . B 2 -26.595 0.465 25.062 1 42.65 ? N SAM 501 A 1 HETATM 2 C CA SAM . . . B 2 -26.266 -0.632 24.168 1 42.95 ? CA SAM 501 A 1 HETATM 3 C C SAM . . . B 2 -25.363 -0.114 23.094 1 43.75 ? C SAM 501 A 1 HETATM 4 O O SAM . . . B 2 -24.25 -0.659 22.942 1 45.03 ? O SAM 501 A 1 HETATM 5 O OXT SAM . . . B 2 -25.747 0.838 22.385 1 44.91 ? OXT SAM 501 A 1 HETATM 6 C CB SAM . . . B 2 -27.518 -1.264 23.55 1 41.94 ? CB SAM 501 A 1 HETATM 7 C CG SAM . . . B 2 -28.091 -2.371 24.427 1 41.09 ? CG SAM 501 A 1 HETATM 8 S SD SAM . . . B 2 -27.197 -3.764 24.303 1 40.54 ? SD SAM 501 A 1 HETATM 9 C CE SAM . . . B 2 -28.134 -4.92 23.565 1 40.75 ? CE SAM 501 A 1 HETATM 10 C C5' SAM . . . B 2 -26.774 -4.351 25.805 1 42.7 ? C5' SAM 501 A 1 HETATM 11 C C4' SAM . . . B 2 -25.761 -3.497 26.566 1 43.74 ? C4' SAM 501 A 1 HETATM 12 O O4' SAM . . . B 2 -26.305 -2.25 27.017 1 45.37 ? O4' SAM 501 A 1 HETATM 13 C C3' SAM . . . B 2 -25.298 -4.203 27.825 1 44.43 ? C3' SAM 501 A 1 HETATM 14 O O3' SAM . . . B 2 -24.178 -5.048 27.566 1 44.31 ? O3' SAM 501 A 1 HETATM 15 C C2' SAM . . . B 2 -24.975 -3.069 28.774 1 46.13 ? C2' SAM 501 A 1 HETATM 16 O O2' SAM . . . B 2 -23.628 -2.614 28.601 1 47.02 ? O2' SAM 501 A 1 HETATM 17 C C1' SAM . . . B 2 -25.921 -1.956 28.365 1 47.59 ? C1' SAM 501 A 1 HETATM 18 N N9 SAM . . . B 2 -27.108 -1.858 29.262 1 49.43 ? N9 SAM 501 A 1 HETATM 19 C C8 SAM . . . B 2 -28.363 -2.254 28.981 1 49.59 ? C8 SAM 501 A 1 HETATM 20 N N7 SAM . . . B 2 -29.203 -2.009 30.016 1 49.14 ? N7 SAM 501 A 1 HETATM 21 C C5 SAM . . . B 2 -28.484 -1.435 30.989 1 50.84 ? C5 SAM 501 A 1 HETATM 22 C C6 SAM . . . B 2 -28.751 -0.912 32.355 1 51.34 ? C6 SAM 501 A 1 HETATM 23 N N6 SAM . . . B 2 -29.992 -0.974 32.888 1 51.48 ? N6 SAM 501 A 1 HETATM 24 N N1 SAM . . . B 2 -27.708 -0.391 33.052 1 51.66 ? N1 SAM 501 A 1 HETATM 25 C C2 SAM . . . B 2 -26.457 -0.329 32.532 1 51.99 ? C2 SAM 501 A 1 HETATM 26 N N3 SAM . . . B 2 -26.15 -0.782 31.293 1 52.06 ? N3 SAM 501 A 1 HETATM 27 C C4 SAM . . . B 2 -27.1 -1.334 30.488 1 51.09 ? C4 SAM 501 A 1 # _model_server_stats.io_time_ms 64 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 325 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #