data_2PGR # _model_server_result.job_id F_F9ijhC0HD8lo43f7TFEA _model_server_result.datetime_utc '2024-12-02 15:41:10' _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 2pgr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":501}' # _entry.id 2PGR # _exptl.entry_id 2PGR _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 268.269 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYCOFORMYCIN" _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 2PGR _cell.length_a 143.488 _cell.length_b 146.386 _cell.length_c 50.034 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2PGR _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F _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 3 _struct_asym.id C _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 A C GLN 31 A GLN 23 1_555 A N MSE 32 A MSE 24 1_555 ? ? ? ? A ? ? ? ? ? ? ? 1.328 ? covale ? covale2 A C GLN 31 A GLN 23 1_555 A N MSE 32 A MSE 24 1_555 ? ? ? ? B ? ? ? ? ? ? ? 1.333 ? covale ? covale3 A C MSE 32 A MSE 24 1_555 A N SER 33 A SER 25 1_555 ? A ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale4 A C MSE 32 A MSE 24 1_555 A N SER 33 A SER 25 1_555 ? B ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale5 A C LEU 131 A LEU 123 1_555 A N MSE 132 A MSE 124 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale6 A C MSE 132 A MSE 124 1_555 A N GLU 133 A GLU 125 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale7 A C LEU 175 A LEU 167 1_555 A N MSE 176 A MSE 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale8 A C MSE 176 A MSE 168 1_555 A N CYS 177 A CYS 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale9 A C ASP 273 A ASP 265 1_555 A N MSE 274 A MSE 266 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale10 A C MSE 274 A MSE 266 1_555 A N VAL 275 A VAL 267 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale11 A C SER 297 A SER 289 1_555 A N MSE 298 A MSE 290 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale12 A C MSE 298 A MSE 290 1_555 A N ASP 299 A ASP 291 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale13 A C GLY 321 A GLY 313 1_555 A N MSE 322 A MSE 314 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale14 A C MSE 322 A MSE 314 1_555 A N PHE 323 A PHE 315 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale15 A C PHE 345 A PHE 337 1_555 A N MSE 346 A MSE 338 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale16 A C MSE 346 A MSE 338 1_555 A N LYS 347 A LYS 339 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale17 A C LYS 347 A LYS 339 1_555 A N MSE 348 A MSE 340 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale18 A C MSE 348 A MSE 340 1_555 A N ASN 349 A ASN 341 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale19 A C PHE 357 A PHE 349 1_555 A N MSE 358 A MSE 350 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale20 A C MSE 358 A MSE 350 1_555 A N ASP 359 A ASP 351 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? metalc ? metalc1 A NE2 HIS 50 A HIS 42 1_555 B ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? metalc ? metalc2 A NE2 HIS 52 A HIS 44 1_555 B ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? metalc ? metalc3 A NE2 HIS 234 A HIS 226 1_555 B ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.328 ? metalc ? metalc4 A OD1 ASP 318 A ASP 310 1_555 B ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.353 ? metalc ? metalc5 B ZN ZN . A ZN 401 1_555 C O8 DCF . A DCF 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.922 ? # _chem_comp.formula 'C11 H16 N4 O4' _chem_comp.formula_weight 268.269 _chem_comp.id DCF _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYCOFORMYCIN" _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 N1 C2 DCF doub 88 n y N1 C9 DCF sing 89 n y C2 N3 DCF sing 90 n y C2 H2 DCF sing 91 n n N3 C10 DCF sing 92 n y N3 C1S DCF sing 93 n n C9 C10 DCF doub 94 n y C9 C8 DCF sing 95 n n C10 N4 DCF sing 96 n n N4 C5 DCF doub 97 n n C5 N6 DCF sing 98 n n C5 H5 DCF sing 99 n n N6 C7 DCF sing 100 n n N6 HN6 DCF sing 101 n n C7 C8 DCF sing 102 n n C7 H71 DCF sing 103 n n C7 H72 DCF sing 104 n n C8 O8 DCF sing 105 n n C8 H8 DCF sing 106 n n O8 HO8 DCF sing 107 n n C2S C3S DCF sing 108 n n C2S C1S DCF sing 109 n n C2S H2S1 DCF sing 110 n n C2S H2S2 DCF sing 111 n n C3S O3S DCF sing 112 n n C3S C4S DCF sing 113 n n C3S H3S DCF sing 114 n n O3S HO3 DCF sing 115 n n O5S C5S DCF sing 116 n n O5S HO5 DCF sing 117 n n C5S C4S DCF sing 118 n n C5S H5S1 DCF sing 119 n n C5S H5S2 DCF sing 120 n n C4S O4S DCF sing 121 n n C4S H4S DCF sing 122 n n O4S C1S DCF sing 123 n n C1S H1S DCF sing 124 n n # _atom_sites.entry_id 2PGR _atom_sites.fract_transf_matrix[1][1] 0.006969 _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] 0.006831 _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] 0.019986 _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 ZN A 1 401 401 ZN ZN . C 3 DCF A 1 501 501 DCF DCF . D 4 CCN A 1 601 601 CCN CCN . E 4 CCN A 1 602 602 CCN CCN . F 5 HOH A 1 603 1 HOH HOH . F 5 HOH A 2 604 2 HOH HOH . F 5 HOH A 3 605 3 HOH HOH . F 5 HOH A 4 606 4 HOH HOH . F 5 HOH A 5 607 5 HOH HOH . F 5 HOH A 6 608 6 HOH HOH . F 5 HOH A 7 609 7 HOH HOH . F 5 HOH A 8 610 8 HOH HOH . F 5 HOH A 9 611 9 HOH HOH . F 5 HOH A 10 612 10 HOH HOH . F 5 HOH A 11 613 11 HOH HOH . F 5 HOH A 12 614 12 HOH HOH . F 5 HOH A 13 615 13 HOH HOH . F 5 HOH A 14 616 14 HOH HOH . F 5 HOH A 15 617 16 HOH HOH . F 5 HOH A 16 618 17 HOH HOH . F 5 HOH A 17 619 18 HOH HOH . F 5 HOH A 18 620 19 HOH HOH . F 5 HOH A 19 621 20 HOH HOH . F 5 HOH A 20 622 21 HOH HOH . F 5 HOH A 21 623 22 HOH HOH . F 5 HOH A 22 624 23 HOH HOH . F 5 HOH A 23 625 24 HOH HOH . F 5 HOH A 24 626 25 HOH HOH . F 5 HOH A 25 627 26 HOH HOH . F 5 HOH A 26 628 27 HOH HOH . F 5 HOH A 27 629 28 HOH HOH . F 5 HOH A 28 630 29 HOH HOH . F 5 HOH A 29 631 30 HOH HOH . F 5 HOH A 30 632 31 HOH HOH . F 5 HOH A 31 633 32 HOH HOH . F 5 HOH A 32 634 33 HOH HOH . F 5 HOH A 33 635 34 HOH HOH . F 5 HOH A 34 636 35 HOH HOH . F 5 HOH A 35 637 36 HOH HOH . F 5 HOH A 36 638 37 HOH HOH . F 5 HOH A 37 639 38 HOH HOH . F 5 HOH A 38 640 39 HOH HOH . F 5 HOH A 39 641 40 HOH HOH . F 5 HOH A 40 642 41 HOH HOH . F 5 HOH A 41 643 43 HOH HOH . F 5 HOH A 42 644 44 HOH HOH . F 5 HOH A 43 645 46 HOH HOH . F 5 HOH A 44 646 47 HOH HOH . F 5 HOH A 45 647 48 HOH HOH . F 5 HOH A 46 648 49 HOH HOH . F 5 HOH A 47 649 50 HOH HOH . F 5 HOH A 48 650 52 HOH HOH . F 5 HOH A 49 651 53 HOH HOH . F 5 HOH A 50 652 54 HOH HOH . F 5 HOH A 51 653 56 HOH HOH . F 5 HOH A 52 654 57 HOH HOH . F 5 HOH A 53 655 58 HOH HOH . F 5 HOH A 54 656 60 HOH HOH . F 5 HOH A 55 657 61 HOH HOH . F 5 HOH A 56 658 62 HOH HOH . F 5 HOH A 57 659 63 HOH HOH . F 5 HOH A 58 660 64 HOH HOH . F 5 HOH A 59 661 66 HOH HOH . F 5 HOH A 60 662 67 HOH HOH . F 5 HOH A 61 663 68 HOH HOH . F 5 HOH A 62 664 69 HOH HOH . F 5 HOH A 63 665 70 HOH HOH . F 5 HOH A 64 666 71 HOH HOH . F 5 HOH A 65 667 72 HOH HOH . F 5 HOH A 66 668 73 HOH HOH . F 5 HOH A 67 669 74 HOH HOH . F 5 HOH A 68 670 75 HOH HOH . F 5 HOH A 69 671 76 HOH HOH . F 5 HOH A 70 672 77 HOH HOH . F 5 HOH A 71 673 78 HOH HOH . F 5 HOH A 72 674 79 HOH HOH . F 5 HOH A 73 675 80 HOH HOH . F 5 HOH A 74 676 81 HOH HOH . F 5 HOH A 75 677 82 HOH HOH . F 5 HOH A 76 678 83 HOH HOH . F 5 HOH A 77 679 84 HOH HOH . F 5 HOH A 78 680 85 HOH HOH . F 5 HOH A 79 681 86 HOH HOH . F 5 HOH A 80 682 87 HOH HOH . F 5 HOH A 81 683 88 HOH HOH . F 5 HOH A 82 684 89 HOH HOH . F 5 HOH A 83 685 90 HOH HOH . F 5 HOH A 84 686 91 HOH HOH . F 5 HOH A 85 687 92 HOH HOH . F 5 HOH A 86 688 93 HOH HOH . F 5 HOH A 87 689 94 HOH HOH . F 5 HOH A 88 690 95 HOH HOH . F 5 HOH A 89 691 96 HOH HOH . F 5 HOH A 90 692 97 HOH HOH . F 5 HOH A 91 693 98 HOH HOH . F 5 HOH A 92 694 99 HOH HOH . F 5 HOH A 93 695 100 HOH HOH . F 5 HOH A 94 696 101 HOH HOH . F 5 HOH A 95 697 102 HOH HOH . F 5 HOH A 96 698 103 HOH HOH . F 5 HOH A 97 699 104 HOH HOH . F 5 HOH A 98 700 107 HOH HOH . F 5 HOH A 99 701 109 HOH HOH . F 5 HOH A 100 702 110 HOH HOH . F 5 HOH A 101 703 112 HOH HOH . F 5 HOH A 102 704 114 HOH HOH . F 5 HOH A 103 705 115 HOH HOH . F 5 HOH A 104 706 116 HOH HOH . F 5 HOH A 105 707 117 HOH HOH . F 5 HOH A 106 708 118 HOH HOH . F 5 HOH A 107 709 119 HOH HOH . F 5 HOH A 108 710 120 HOH HOH . F 5 HOH A 109 711 121 HOH HOH . F 5 HOH A 110 712 122 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 DCF . . . C 3 27.859 22.211 37.532 1 22.92 ? N1 DCF 501 A 1 HETATM 2 C C2 DCF . . . C 3 29.191 22.225 37.482 1 20.99 ? C2 DCF 501 A 1 HETATM 3 N N3 DCF . . . C 3 29.633 23.48 37.531 1 19.23 ? N3 DCF 501 A 1 HETATM 4 C C9 DCF . . . C 3 27.445 23.464 37.611 1 22.48 ? C9 DCF 501 A 1 HETATM 5 C C10 DCF . . . C 3 28.562 24.269 37.619 1 20.71 ? C10 DCF 501 A 1 HETATM 6 N N4 DCF . . . C 3 28.608 25.59 37.656 1 21.92 ? N4 DCF 501 A 1 HETATM 7 C C5 DCF . . . C 3 27.664 26.414 38.068 1 19.18 ? C5 DCF 501 A 1 HETATM 8 N N6 DCF . . . C 3 26.47 26.161 38.566 1 23.07 ? N6 DCF 501 A 1 HETATM 9 C C7 DCF . . . C 3 25.805 24.87 38.835 1 23.75 ? C7 DCF 501 A 1 HETATM 10 C C8 DCF . . . C 3 25.978 23.867 37.697 1 23.4 ? C8 DCF 501 A 1 HETATM 11 O O8 DCF . . . C 3 25.538 24.439 36.465 1 29.6 ? O8 DCF 501 A 1 HETATM 12 C C2S DCF . . . C 3 31.877 23.244 38.629 1 22.96 ? C2S DCF 501 A 1 HETATM 13 C C3S DCF . . . C 3 33.255 23.077 38.009 1 22.69 ? C3S DCF 501 A 1 HETATM 14 O O3S DCF . . . C 3 33.972 24.32 38.087 1 22.14 ? O3S DCF 501 A 1 HETATM 15 O O5S DCF . . . C 3 32.31 21.029 34.948 1 20.02 ? O5S DCF 501 A 1 HETATM 16 C C5S DCF . . . C 3 32.858 21.242 36.261 1 21.72 ? C5S DCF 501 A 1 HETATM 17 C C4S DCF . . . C 3 32.932 22.754 36.546 1 21.57 ? C4S DCF 501 A 1 HETATM 18 O O4S DCF . . . C 3 31.624 23.342 36.264 1 21.48 ? O4S DCF 501 A 1 HETATM 19 C C1S DCF . . . C 3 31.068 23.879 37.486 1 21.36 ? C1S DCF 501 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 286 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 19 #