data_6VEB # _model_server_result.job_id F9uDQGmBAopHwA9Mwa617g _model_server_result.datetime_utc '2024-11-15 13:48:49' _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 6veb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":501}' # _entry.id 6VEB # _exptl.entry_id 6VEB _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 6VEB _cell.length_a 59.682 _cell.length_b 99.489 _cell.length_c 146.037 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6VEB _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,K,L,M,N,O _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 J N N # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id B _struct_conn.ptnr1_label_atom_id N _struct_conn.ptnr1_label_comp_id GLY _struct_conn.ptnr1_label_seq_id 130 _struct_conn.ptnr1_auth_asym_id B _struct_conn.ptnr1_auth_comp_id GLY _struct_conn.ptnr1_auth_seq_id 130 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id K _struct_conn.ptnr2_label_atom_id O2A _struct_conn.ptnr2_label_comp_id PQ2 _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id B _struct_conn.ptnr2_auth_comp_id PQ2 _struct_conn.ptnr2_auth_seq_id 502 _struct_conn.ptnr2_symmetry 1_555 _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 1.301 _struct_conn.pdbx_value_order ? # _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 466 n n N HN1 SAH sing 467 n n N HN2 SAH sing 468 n n CA CB SAH sing 469 n n CA C SAH sing 470 n n CA HA SAH sing 471 n n CB CG SAH sing 472 n n CB HB1 SAH sing 473 n n CB HB2 SAH sing 474 n n CG SD SAH sing 475 n n CG HG1 SAH sing 476 n n CG HG2 SAH sing 477 n n SD C5' SAH sing 478 n n C O SAH doub 479 n n C OXT SAH sing 480 n n OXT HXT SAH sing 481 n n C5' C4' SAH sing 482 n n C5' "H5'1" SAH sing 483 n n C5' "H5'2" SAH sing 484 n n C4' O4' SAH sing 485 n n C4' C3' SAH sing 486 n n C4' H4' SAH sing 487 n n O4' C1' SAH sing 488 n n C3' O3' SAH sing 489 n n C3' C2' SAH sing 490 n n C3' H3' SAH sing 491 n n O3' HO3' SAH sing 492 n n C2' O2' SAH sing 493 n n C2' C1' SAH sing 494 n n C2' H2' SAH sing 495 n n O2' HO2' SAH sing 496 n n C1' N9 SAH sing 497 n n C1' H1' SAH sing 498 n n N9 C8 SAH sing 499 n y N9 C4 SAH sing 500 n y C8 N7 SAH doub 501 n y C8 H8 SAH sing 502 n n N7 C5 SAH sing 503 n y C5 C6 SAH sing 504 n y C5 C4 SAH doub 505 n y C6 N6 SAH sing 506 n n C6 N1 SAH doub 507 n y N6 HN61 SAH sing 508 n n N6 HN62 SAH sing 509 n n N1 C2 SAH sing 510 n y C2 N3 SAH doub 511 n y C2 H2 SAH sing 512 n n N3 C4 SAH sing 513 n y # _atom_sites.entry_id 6VEB _atom_sites.fract_transf_matrix[1][1] 0.016755 _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] 0.010051 _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] 0.006848 _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 NAD A 1 502 1 NAD NAI . E 4 CL A 1 503 210 CL CL . F 4 CL A 1 504 211 CL CL . G 4 CL A 1 505 212 CL CL . H 4 CL A 1 506 213 CL CL . I 4 CL A 1 507 215 CL CL . J 2 SAH B 1 501 502 SAH SAH . K 5 PQ2 B 1 502 2 PQ2 PQ2 . L 4 CL B 1 503 214 CL CL . M 4 CL B 1 504 216 CL CL . N 6 HOH A 1 601 80 HOH HOH . N 6 HOH A 2 602 87 HOH HOH . N 6 HOH A 3 603 208 HOH HOH . N 6 HOH A 4 604 119 HOH HOH . N 6 HOH A 5 605 113 HOH HOH . N 6 HOH A 6 606 195 HOH HOH . N 6 HOH A 7 607 32 HOH HOH . N 6 HOH A 8 608 207 HOH HOH . N 6 HOH A 9 609 181 HOH HOH . N 6 HOH A 10 610 70 HOH HOH . N 6 HOH A 11 611 89 HOH HOH . N 6 HOH A 12 612 133 HOH HOH . N 6 HOH A 13 613 111 HOH HOH . N 6 HOH A 14 614 130 HOH HOH . N 6 HOH A 15 615 43 HOH HOH . N 6 HOH A 16 616 96 HOH HOH . N 6 HOH A 17 617 21 HOH HOH . N 6 HOH A 18 618 146 HOH HOH . N 6 HOH A 19 619 115 HOH HOH . N 6 HOH A 20 620 2 HOH HOH . N 6 HOH A 21 621 177 HOH HOH . N 6 HOH A 22 622 17 HOH HOH . N 6 HOH A 23 623 66 HOH HOH . N 6 HOH A 24 624 69 HOH HOH . N 6 HOH A 25 625 7 HOH HOH . N 6 HOH A 26 626 12 HOH HOH . N 6 HOH A 27 627 11 HOH HOH . N 6 HOH A 28 628 75 HOH HOH . N 6 HOH A 29 629 28 HOH HOH . N 6 HOH A 30 630 155 HOH HOH . N 6 HOH A 31 631 109 HOH HOH . N 6 HOH A 32 632 76 HOH HOH . N 6 HOH A 33 633 98 HOH HOH . N 6 HOH A 34 634 4 HOH HOH . N 6 HOH A 35 635 25 HOH HOH . N 6 HOH A 36 636 104 HOH HOH . N 6 HOH A 37 637 50 HOH HOH . N 6 HOH A 38 638 82 HOH HOH . N 6 HOH A 39 639 99 HOH HOH . N 6 HOH A 40 640 6 HOH HOH . N 6 HOH A 41 641 112 HOH HOH . N 6 HOH A 42 642 124 HOH HOH . N 6 HOH A 43 643 81 HOH HOH . N 6 HOH A 44 644 156 HOH HOH . N 6 HOH A 45 645 39 HOH HOH . N 6 HOH A 46 646 16 HOH HOH . N 6 HOH A 47 647 101 HOH HOH . N 6 HOH A 48 648 34 HOH HOH . N 6 HOH A 49 649 26 HOH HOH . N 6 HOH A 50 650 45 HOH HOH . N 6 HOH A 51 651 31 HOH HOH . N 6 HOH A 52 652 29 HOH HOH . N 6 HOH A 53 653 27 HOH HOH . N 6 HOH A 54 654 180 HOH HOH . N 6 HOH A 55 655 94 HOH HOH . N 6 HOH A 56 656 88 HOH HOH . N 6 HOH A 57 657 151 HOH HOH . N 6 HOH A 58 658 20 HOH HOH . N 6 HOH A 59 659 171 HOH HOH . N 6 HOH A 60 660 106 HOH HOH . N 6 HOH A 61 661 169 HOH HOH . N 6 HOH A 62 662 117 HOH HOH . N 6 HOH A 63 663 205 HOH HOH . N 6 HOH A 64 664 193 HOH HOH . N 6 HOH A 65 665 23 HOH HOH . N 6 HOH A 66 666 150 HOH HOH . N 6 HOH A 67 667 84 HOH HOH . N 6 HOH A 68 668 134 HOH HOH . N 6 HOH A 69 669 147 HOH HOH . N 6 HOH A 70 670 198 HOH HOH . N 6 HOH A 71 671 158 HOH HOH . N 6 HOH A 72 672 15 HOH HOH . N 6 HOH A 73 673 51 HOH HOH . N 6 HOH A 74 674 33 HOH HOH . N 6 HOH A 75 675 91 HOH HOH . N 6 HOH A 76 676 52 HOH HOH . N 6 HOH A 77 677 182 HOH HOH . N 6 HOH A 78 678 179 HOH HOH . N 6 HOH A 79 679 120 HOH HOH . N 6 HOH A 80 680 118 HOH HOH . N 6 HOH A 81 681 132 HOH HOH . N 6 HOH A 82 682 78 HOH HOH . N 6 HOH A 83 683 186 HOH HOH . N 6 HOH A 84 684 141 HOH HOH . N 6 HOH A 85 685 160 HOH HOH . N 6 HOH A 86 686 77 HOH HOH . N 6 HOH A 87 687 199 HOH HOH . N 6 HOH A 88 688 122 HOH HOH . N 6 HOH A 89 689 187 HOH HOH . N 6 HOH A 90 690 154 HOH HOH . N 6 HOH A 91 691 194 HOH HOH . N 6 HOH A 92 692 197 HOH HOH . N 6 HOH A 93 693 173 HOH HOH . N 6 HOH A 94 694 142 HOH HOH . N 6 HOH A 95 695 206 HOH HOH . N 6 HOH A 96 696 176 HOH HOH . N 6 HOH A 97 697 121 HOH HOH . N 6 HOH A 98 698 178 HOH HOH . N 6 HOH A 99 699 135 HOH HOH . N 6 HOH A 100 700 108 HOH HOH . N 6 HOH A 101 701 138 HOH HOH . N 6 HOH A 102 702 183 HOH HOH . N 6 HOH A 103 703 148 HOH HOH . N 6 HOH A 104 704 85 HOH HOH . N 6 HOH A 105 705 165 HOH HOH . O 6 HOH B 1 601 200 HOH HOH . O 6 HOH B 2 602 188 HOH HOH . O 6 HOH B 3 603 68 HOH HOH . O 6 HOH B 4 604 79 HOH HOH . O 6 HOH B 5 605 57 HOH HOH . O 6 HOH B 6 606 56 HOH HOH . O 6 HOH B 7 607 175 HOH HOH . O 6 HOH B 8 608 209 HOH HOH . O 6 HOH B 9 609 184 HOH HOH . O 6 HOH B 10 610 48 HOH HOH . O 6 HOH B 11 611 42 HOH HOH . O 6 HOH B 12 612 49 HOH HOH . O 6 HOH B 13 613 196 HOH HOH . O 6 HOH B 14 614 8 HOH HOH . O 6 HOH B 15 615 30 HOH HOH . O 6 HOH B 16 616 40 HOH HOH . O 6 HOH B 17 617 1 HOH HOH . O 6 HOH B 18 618 13 HOH HOH . O 6 HOH B 19 619 72 HOH HOH . O 6 HOH B 20 620 53 HOH HOH . O 6 HOH B 21 621 71 HOH HOH . O 6 HOH B 22 622 152 HOH HOH . O 6 HOH B 23 623 164 HOH HOH . O 6 HOH B 24 624 19 HOH HOH . O 6 HOH B 25 625 95 HOH HOH . O 6 HOH B 26 626 74 HOH HOH . O 6 HOH B 27 627 201 HOH HOH . O 6 HOH B 28 628 5 HOH HOH . O 6 HOH B 29 629 18 HOH HOH . O 6 HOH B 30 630 24 HOH HOH . O 6 HOH B 31 631 92 HOH HOH . O 6 HOH B 32 632 3 HOH HOH . O 6 HOH B 33 633 100 HOH HOH . O 6 HOH B 34 634 37 HOH HOH . O 6 HOH B 35 635 62 HOH HOH . O 6 HOH B 36 636 10 HOH HOH . O 6 HOH B 37 637 14 HOH HOH . O 6 HOH B 38 638 204 HOH HOH . O 6 HOH B 39 639 159 HOH HOH . O 6 HOH B 40 640 185 HOH HOH . O 6 HOH B 41 641 58 HOH HOH . O 6 HOH B 42 642 44 HOH HOH . O 6 HOH B 43 643 162 HOH HOH . O 6 HOH B 44 644 9 HOH HOH . O 6 HOH B 45 645 153 HOH HOH . O 6 HOH B 46 646 110 HOH HOH . O 6 HOH B 47 647 97 HOH HOH . O 6 HOH B 48 648 36 HOH HOH . O 6 HOH B 49 649 54 HOH HOH . O 6 HOH B 50 650 38 HOH HOH . O 6 HOH B 51 651 170 HOH HOH . O 6 HOH B 52 652 59 HOH HOH . O 6 HOH B 53 653 60 HOH HOH . O 6 HOH B 54 654 35 HOH HOH . O 6 HOH B 55 655 73 HOH HOH . O 6 HOH B 56 656 102 HOH HOH . O 6 HOH B 57 657 125 HOH HOH . O 6 HOH B 58 658 203 HOH HOH . O 6 HOH B 59 659 145 HOH HOH . O 6 HOH B 60 660 103 HOH HOH . O 6 HOH B 61 661 83 HOH HOH . O 6 HOH B 62 662 105 HOH HOH . O 6 HOH B 63 663 144 HOH HOH . O 6 HOH B 64 664 41 HOH HOH . O 6 HOH B 65 665 114 HOH HOH . O 6 HOH B 66 666 157 HOH HOH . O 6 HOH B 67 667 127 HOH HOH . O 6 HOH B 68 668 149 HOH HOH . O 6 HOH B 69 669 90 HOH HOH . O 6 HOH B 70 670 22 HOH HOH . O 6 HOH B 71 671 61 HOH HOH . O 6 HOH B 72 672 65 HOH HOH . O 6 HOH B 73 673 168 HOH HOH . O 6 HOH B 74 674 47 HOH HOH . O 6 HOH B 75 675 161 HOH HOH . O 6 HOH B 76 676 166 HOH HOH . O 6 HOH B 77 677 55 HOH HOH . O 6 HOH B 78 678 140 HOH HOH . O 6 HOH B 79 679 46 HOH HOH . O 6 HOH B 80 680 190 HOH HOH . O 6 HOH B 81 681 64 HOH HOH . O 6 HOH B 82 682 172 HOH HOH . O 6 HOH B 83 683 163 HOH HOH . O 6 HOH B 84 684 139 HOH HOH . O 6 HOH B 85 685 93 HOH HOH . O 6 HOH B 86 686 202 HOH HOH . O 6 HOH B 87 687 116 HOH HOH . O 6 HOH B 88 688 189 HOH HOH . O 6 HOH B 89 689 136 HOH HOH . O 6 HOH B 90 690 67 HOH HOH . O 6 HOH B 91 691 107 HOH HOH . O 6 HOH B 92 692 137 HOH HOH . O 6 HOH B 93 693 143 HOH HOH . O 6 HOH B 94 694 192 HOH HOH . O 6 HOH B 95 695 191 HOH HOH . O 6 HOH B 96 696 126 HOH HOH . O 6 HOH B 97 697 63 HOH HOH . O 6 HOH B 98 698 131 HOH HOH . O 6 HOH B 99 699 167 HOH HOH . O 6 HOH B 100 700 86 HOH HOH . O 6 HOH B 101 701 174 HOH HOH . O 6 HOH B 102 702 123 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 . . . C 2 69.049 1.803 17.795 1 23.11 ? N SAH 501 A 1 HETATM 2 C CA SAH . . . C 2 68.022 1.338 16.882 1 24.32 ? CA SAH 501 A 1 HETATM 3 C CB SAH . . . C 2 67.815 2.367 15.789 1 22.79 ? CB SAH 501 A 1 HETATM 4 C CG SAH . . . C 2 67.585 3.789 16.289 1 28.69 ? CG SAH 501 A 1 HETATM 5 S SD SAH . . . C 2 67.639 5.001 14.939 1 36.18 ? SD SAH 501 A 1 HETATM 6 C C SAH . . . C 2 68.4 -0.032 16.315 1 30.05 ? C SAH 501 A 1 HETATM 7 O O SAH . . . C 2 69.444 -0.579 16.688 1 26.95 ? O SAH 501 A 1 HETATM 8 O OXT SAH . . . C 2 67.684 -0.618 15.492 1 30.57 ? OXT SAH 501 A 1 HETATM 9 C C5' SAH . . . C 2 65.875 4.822 14.544 1 30.03 ? C5' SAH 501 A 1 HETATM 10 C C4' SAH . . . C 2 65.642 4.11 13.216 1 33.63 ? C4' SAH 501 A 1 HETATM 11 O O4' SAH . . . C 2 65.603 2.697 13.393 1 42.05 ? O4' SAH 501 A 1 HETATM 12 C C3' SAH . . . C 2 64.308 4.459 12.57 1 32.51 ? C3' SAH 501 A 1 HETATM 13 O O3' SAH . . . C 2 64.417 5.539 11.695 1 36.43 ? O3' SAH 501 A 1 HETATM 14 C C2' SAH . . . C 2 63.98 3.26 11.73 1 42.8 ? C2' SAH 501 A 1 HETATM 15 O O2' SAH . . . C 2 64.582 3.431 10.463 1 50.14 ? O2' SAH 501 A 1 HETATM 16 C C1' SAH . . . C 2 64.71 2.138 12.434 1 42.37 ? C1' SAH 501 A 1 HETATM 17 N N9 SAH . . . C 2 63.781 1.196 13.084 1 36.34 ? N9 SAH 501 A 1 HETATM 18 C C8 SAH . . . C 2 63.629 1.009 14.433 1 35.49 ? C8 SAH 501 A 1 HETATM 19 N N7 SAH . . . C 2 62.68 0.06 14.663 1 23.16 ? N7 SAH 501 A 1 HETATM 20 C C5 SAH . . . C 2 62.229 -0.366 13.467 1 31.9 ? C5 SAH 501 A 1 HETATM 21 C C6 SAH . . . C 2 61.285 -1.335 13.121 1 33.16 ? C6 SAH 501 A 1 HETATM 22 N N6 SAH . . . C 2 60.636 -2.049 14.056 1 26.41 ? N6 SAH 501 A 1 HETATM 23 N N1 SAH . . . C 2 61.032 -1.555 11.782 1 32.58 ? N1 SAH 501 A 1 HETATM 24 C C2 SAH . . . C 2 61.712 -0.828 10.836 1 29.57 ? C2 SAH 501 A 1 HETATM 25 N N3 SAH . . . C 2 62.65 0.119 11.201 1 23.59 ? N3 SAH 501 A 1 HETATM 26 C C4 SAH . . . C 2 62.905 0.349 12.482 1 23.15 ? C4 SAH 501 A 1 # _model_server_stats.io_time_ms 27 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 261 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 26 #