data_7CER # _model_server_result.job_id ndKUmhsBHiBWLyZu0oSNUA _model_server_result.datetime_utc '2024-11-24 08:38:02' _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 7cer # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 7CER # _exptl.entry_id 7CER _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 333.234 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description D-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-N,O-CYCLOSERYLAMIDE _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 120 _cell.entry_id 7CER _cell.length_a 92.5 _cell.length_b 92.5 _cell.length_c 128.2 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7CER _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 5_554 x-y,-y,-z-1/3 1 0 0 0 -1 0 0 0 -1 0 0 -42.733333 # _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 # _chem_comp.formula 'C11 H16 N3 O7 P' _chem_comp.formula_weight 333.234 _chem_comp.id DCS _chem_comp.mon_nstd_flag . _chem_comp.name D-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-N,O-CYCLOSERYLAMIDE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms D-PYRIDOXYL-N,O-CYCLOSERYLAMIDE-5-MONOPHOSPHATE # 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 N1 C2 DCS doub 83 n y N1 C6 DCS sing 84 n y C2 C2A DCS sing 85 n n C2 C3 DCS sing 86 n y C2A H2A1 DCS sing 87 n n C2A H2A2 DCS sing 88 n n C2A H2A3 DCS sing 89 n n C3 O3 DCS sing 90 n n C3 C4 DCS doub 91 n y O3 HO3 DCS sing 92 n n C4 C4A DCS sing 93 n n C4 C5 DCS sing 94 n y C4A N DCS sing 95 n n C4A H4A1 DCS sing 96 n n C4A H4A2 DCS sing 97 n n C5 C6 DCS doub 98 n y C5 C5A DCS sing 99 n n C6 H6 DCS sing 100 n n C5A O4P DCS sing 101 n n C5A H5A1 DCS sing 102 n n C5A H5A2 DCS sing 103 n n O4P P DCS sing 104 n n P O1P DCS doub 105 n n P O2P DCS sing 106 n n P O3P DCS sing 107 n n O2P HOP2 DCS sing 108 n n O3P HOP3 DCS sing 109 n n N CA DCS sing 110 n n N HN DCS sing 111 n n CA C DCS sing 112 n n CA CB DCS sing 113 n n CA HA DCS sing 114 n n C O DCS doub 115 n n C ND DCS sing 116 n n ND OG DCS sing 117 n n ND HND DCS sing 118 n n OG CB DCS sing 119 n n CB HB1 DCS sing 120 n n CB HB2 DCS sing 121 n n # _atom_sites.entry_id 7CER _atom_sites.fract_transf_matrix[1][1] 0.010811 _atom_sites.fract_transf_matrix[1][2] 0.006242 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012483 _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] 0.0078 _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 DCS A 1 501 501 DCS DCS . C 3 PGE A 1 502 601 PGE PGE . D 4 PEG A 1 503 701 PEG PEG . E 5 HOH A 1 601 58 HOH HOH . E 5 HOH A 2 602 20 HOH HOH . E 5 HOH A 3 603 64 HOH HOH . E 5 HOH A 4 604 68 HOH HOH . E 5 HOH A 5 605 137 HOH HOH . E 5 HOH A 6 606 8 HOH HOH . E 5 HOH A 7 607 80 HOH HOH . E 5 HOH A 8 608 50 HOH HOH . E 5 HOH A 9 609 91 HOH HOH . E 5 HOH A 10 610 32 HOH HOH . E 5 HOH A 11 611 33 HOH HOH . E 5 HOH A 12 612 110 HOH HOH . E 5 HOH A 13 613 127 HOH HOH . E 5 HOH A 14 614 5 HOH HOH . E 5 HOH A 15 615 118 HOH HOH . E 5 HOH A 16 616 126 HOH HOH . E 5 HOH A 17 617 37 HOH HOH . E 5 HOH A 18 618 53 HOH HOH . E 5 HOH A 19 619 65 HOH HOH . E 5 HOH A 20 620 59 HOH HOH . E 5 HOH A 21 621 30 HOH HOH . E 5 HOH A 22 622 67 HOH HOH . E 5 HOH A 23 623 45 HOH HOH . E 5 HOH A 24 624 44 HOH HOH . E 5 HOH A 25 625 107 HOH HOH . E 5 HOH A 26 626 90 HOH HOH . E 5 HOH A 27 627 88 HOH HOH . E 5 HOH A 28 628 36 HOH HOH . E 5 HOH A 29 629 52 HOH HOH . E 5 HOH A 30 630 15 HOH HOH . E 5 HOH A 31 631 26 HOH HOH . E 5 HOH A 32 632 61 HOH HOH . E 5 HOH A 33 633 3 HOH HOH . E 5 HOH A 34 634 87 HOH HOH . E 5 HOH A 35 635 35 HOH HOH . E 5 HOH A 36 636 39 HOH HOH . E 5 HOH A 37 637 85 HOH HOH . E 5 HOH A 38 638 28 HOH HOH . E 5 HOH A 39 639 23 HOH HOH . E 5 HOH A 40 640 129 HOH HOH . E 5 HOH A 41 641 10 HOH HOH . E 5 HOH A 42 642 109 HOH HOH . E 5 HOH A 43 643 42 HOH HOH . E 5 HOH A 44 644 77 HOH HOH . E 5 HOH A 45 645 79 HOH HOH . E 5 HOH A 46 646 73 HOH HOH . E 5 HOH A 47 647 29 HOH HOH . E 5 HOH A 48 648 21 HOH HOH . E 5 HOH A 49 649 19 HOH HOH . E 5 HOH A 50 650 38 HOH HOH . E 5 HOH A 51 651 76 HOH HOH . E 5 HOH A 52 652 9 HOH HOH . E 5 HOH A 53 653 7 HOH HOH . E 5 HOH A 54 654 46 HOH HOH . E 5 HOH A 55 655 106 HOH HOH . E 5 HOH A 56 656 22 HOH HOH . E 5 HOH A 57 657 84 HOH HOH . E 5 HOH A 58 658 134 HOH HOH . E 5 HOH A 59 659 48 HOH HOH . E 5 HOH A 60 660 63 HOH HOH . E 5 HOH A 61 661 31 HOH HOH . E 5 HOH A 62 662 89 HOH HOH . E 5 HOH A 63 663 66 HOH HOH . E 5 HOH A 64 664 4 HOH HOH . E 5 HOH A 65 665 11 HOH HOH . E 5 HOH A 66 666 27 HOH HOH . E 5 HOH A 67 667 55 HOH HOH . E 5 HOH A 68 668 94 HOH HOH . E 5 HOH A 69 669 14 HOH HOH . E 5 HOH A 70 670 56 HOH HOH . E 5 HOH A 71 671 69 HOH HOH . E 5 HOH A 72 672 97 HOH HOH . E 5 HOH A 73 673 13 HOH HOH . E 5 HOH A 74 674 24 HOH HOH . E 5 HOH A 75 675 57 HOH HOH . E 5 HOH A 76 676 83 HOH HOH . E 5 HOH A 77 677 54 HOH HOH . E 5 HOH A 78 678 113 HOH HOH . E 5 HOH A 79 679 2 HOH HOH . E 5 HOH A 80 680 6 HOH HOH . E 5 HOH A 81 681 122 HOH HOH . E 5 HOH A 82 682 101 HOH HOH . E 5 HOH A 83 683 116 HOH HOH . E 5 HOH A 84 684 43 HOH HOH . E 5 HOH A 85 685 74 HOH HOH . E 5 HOH A 86 686 82 HOH HOH . E 5 HOH A 87 687 34 HOH HOH . E 5 HOH A 88 688 60 HOH HOH . E 5 HOH A 89 689 128 HOH HOH . E 5 HOH A 90 690 17 HOH HOH . E 5 HOH A 91 691 131 HOH HOH . E 5 HOH A 92 692 78 HOH HOH . E 5 HOH A 93 693 119 HOH HOH . E 5 HOH A 94 694 111 HOH HOH . E 5 HOH A 95 695 93 HOH HOH . E 5 HOH A 96 696 98 HOH HOH . E 5 HOH A 97 697 25 HOH HOH . E 5 HOH A 98 698 75 HOH HOH . E 5 HOH A 99 699 130 HOH HOH . E 5 HOH A 100 700 95 HOH HOH . E 5 HOH A 101 701 100 HOH HOH . E 5 HOH A 102 702 70 HOH HOH . E 5 HOH A 103 703 40 HOH HOH . E 5 HOH A 104 704 16 HOH HOH . E 5 HOH A 105 705 103 HOH HOH . E 5 HOH A 106 706 1 HOH HOH . E 5 HOH A 107 707 92 HOH HOH . E 5 HOH A 108 708 104 HOH HOH . E 5 HOH A 109 709 12 HOH HOH . E 5 HOH A 110 710 120 HOH HOH . E 5 HOH A 111 711 51 HOH HOH . E 5 HOH A 112 712 112 HOH HOH . E 5 HOH A 113 713 41 HOH HOH . E 5 HOH A 114 714 135 HOH HOH . E 5 HOH A 115 715 121 HOH HOH . E 5 HOH A 116 716 71 HOH HOH . E 5 HOH A 117 717 47 HOH HOH . E 5 HOH A 118 718 18 HOH HOH . E 5 HOH A 119 719 72 HOH HOH . E 5 HOH A 120 720 114 HOH HOH . E 5 HOH A 121 721 133 HOH HOH . E 5 HOH A 122 722 81 HOH HOH . E 5 HOH A 123 723 124 HOH HOH . E 5 HOH A 124 724 123 HOH HOH . E 5 HOH A 125 725 132 HOH HOH . E 5 HOH A 126 726 108 HOH HOH . E 5 HOH A 127 727 62 HOH HOH . E 5 HOH A 128 728 117 HOH HOH . E 5 HOH A 129 729 105 HOH HOH . E 5 HOH A 130 730 125 HOH HOH . E 5 HOH A 131 731 115 HOH HOH . E 5 HOH A 132 732 136 HOH HOH . E 5 HOH A 133 733 86 HOH HOH . E 5 HOH A 134 734 99 HOH HOH . E 5 HOH A 135 735 49 HOH HOH . E 5 HOH A 136 736 96 HOH HOH . E 5 HOH A 137 737 102 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 N1 DCS . . . B 2 -48.752 13.428 -12.763 1 50.89 ? N1 DCS 501 A 1 HETATM 2 C C2 DCS . . . B 2 -47.802 14.345 -12.425 1 67.11 ? C2 DCS 501 A 1 HETATM 3 C C2A DCS . . . B 2 -47.959 15.182 -11.129 1 66.47 ? C2A DCS 501 A 1 HETATM 4 C C3 DCS . . . B 2 -46.694 14.527 -13.243 1 70.34 ? C3 DCS 501 A 1 HETATM 5 O O3 DCS . . . B 2 -45.719 15.466 -12.901 1 74.38 ? O3 DCS 501 A 1 HETATM 6 C C4 DCS . . . B 2 -46.561 13.789 -14.383 1 71.58 ? C4 DCS 501 A 1 HETATM 7 C C4A DCS . . . B 2 -45.312 13.995 -15.305 1 74.26 ? C4A DCS 501 A 1 HETATM 8 C C5 DCS . . . B 2 -47.518 12.87 -14.714 1 61.26 ? C5 DCS 501 A 1 HETATM 9 C C6 DCS . . . B 2 -48.623 12.689 -13.897 1 50.25 ? C6 DCS 501 A 1 HETATM 10 C C5A DCS . . . B 2 -47.374 12.021 -16.013 1 64.39 ? C5A DCS 501 A 1 HETATM 11 O O4P DCS . . . B 2 -47.006 10.71 -15.665 1 59.9 ? O4P DCS 501 A 1 HETATM 12 P P DCS . . . B 2 -46.386 9.761 -16.864 1 38.45 ? P DCS 501 A 1 HETATM 13 O O1P DCS . . . B 2 -46.123 10.634 -18.066 1 49.69 ? O1P DCS 501 A 1 HETATM 14 O O2P DCS . . . B 2 -47.377 8.7 -17.224 1 44.33 ? O2P DCS 501 A 1 HETATM 15 O O3P DCS . . . B 2 -45.104 9.123 -16.405 1 36.5 ? O3P DCS 501 A 1 HETATM 16 N N DCS . . . B 2 -45.684 14.872 -16.439 1 86.96 ? N DCS 501 A 1 HETATM 17 C CA DCS . . . B 2 -44.543 15.788 -16.753 1 96.59 ? CA DCS 501 A 1 HETATM 18 C C DCS . . . B 2 -44.549 16.095 -18.081 1 102.31 ? C DCS 501 A 1 HETATM 19 O O DCS . . . B 2 -44.709 15.335 -18.976 1 105.86 ? O DCS 501 A 1 HETATM 20 N ND DCS . . . B 2 -44.317 17.559 -18.202 1 90.05 ? ND DCS 501 A 1 HETATM 21 O OG DCS . . . B 2 -44.168 18.124 -16.774 1 83.26 ? OG DCS 501 A 1 HETATM 22 C CB DCS . . . B 2 -44.725 17.171 -15.97 1 92.45 ? CB DCS 501 A 1 # _model_server_stats.io_time_ms 27 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 302 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 22 #