data_5VER # _model_server_result.job_id E827JvUCyC1FU9046jYuQA _model_server_result.datetime_utc '2024-12-01 10:31:57' _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 5ver # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":501}' # _entry.id 5VER # _exptl.entry_id 5VER _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 248.173 _entity.id 7 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE" _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 5VER _cell.length_a 91.49 _cell.length_b 91.49 _cell.length_c 233.501 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VER _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 43 21 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA tetrameric 4 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R 1 1 A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R 2 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' 8_555 -y,-x,-z+1/2 0 -1 0 -1 0 0 0 0 -1 0 0 116.7505 # _struct_asym.details ? _struct_asym.entity_id 7 _struct_asym.id K _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 NZ LYS 240 A LYS 281 1_555 C C4A PLP . A PLP 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.511 doub metalc ? metalc1 A OE1 GLU 6 A GLU 47 1_555 J CA CA . A CA 708 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.093 ? metalc ? metalc2 A OE2 GLU 6 A GLU 47 1_555 J CA CA . A CA 708 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.788 ? metalc ? metalc3 A OE1 GLN 81 A GLN 122 1_555 H CA CA . A CA 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? metalc ? metalc4 A OE1 GLN 81 A GLN 122 1_555 H CA CA . A CA 706 8_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.813 ? metalc ? metalc5 A O HIS 199 A HIS 240 1_555 I CA CA . A CA 707 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.255 ? metalc ? metalc6 A OD2 ASP 396 A ASP 437 1_555 J CA CA . A CA 708 6_455 ? ? ? ? ? ? ? ? ? ? ? ? 2.857 ? metalc ? metalc7 H CA CA . A CA 706 1_555 Q O HOH . A HOH 824 8_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.539 ? metalc ? metalc8 H CA CA . A CA 706 1_555 Q O HOH . A HOH 825 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? metalc ? metalc9 H CA CA . A CA 706 1_555 Q O HOH . A HOH 825 8_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.406 ? metalc ? metalc10 H CA CA . A CA 706 1_555 Q O HOH . A HOH 855 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.539 ? metalc ? metalc11 H CA CA . A CA 706 1_555 Q O HOH . A HOH 855 8_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.548 ? metalc ? metalc12 I CA CA . A CA 707 1_555 Q O HOH . A HOH 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.903 ? metalc ? metalc13 I CA CA . A CA 707 1_555 Q O HOH . A HOH 812 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.195 ? metalc ? metalc14 I CA CA . A CA 707 1_555 Q O HOH . A HOH 820 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.36 ? metalc ? metalc15 I CA CA . A CA 707 1_555 Q O HOH . A HOH 833 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.838 ? metalc ? metalc16 I CA CA . A CA 707 1_555 Q O HOH . A HOH 853 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.581 ? metalc ? metalc17 J CA CA . A CA 708 1_555 Q O HOH . A HOH 801 6_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? metalc ? metalc18 J CA CA . A CA 708 1_555 Q O HOH . A HOH 846 6_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.951 ? metalc ? metalc19 B O HIS 199 B HIS 240 1_555 P CA CA . B CA 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? metalc ? metalc20 P CA CA . B CA 506 1_555 R O HOH . B HOH 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.352 ? metalc ? metalc21 P CA CA . B CA 506 1_555 R O HOH . B HOH 631 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.43 ? metalc ? metalc22 P CA CA . B CA 506 1_555 R O HOH . B HOH 638 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.032 ? metalc ? metalc23 P CA CA . B CA 506 1_555 R O HOH . B HOH 640 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.076 ? metalc ? metalc24 P CA CA . B CA 506 1_555 R O HOH . B HOH 641 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.167 ? metalc ? metalc25 P CA CA . B CA 506 1_555 R O HOH . B HOH 645 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.366 ? # _chem_comp.formula 'C8 H13 N2 O5 P' _chem_comp.formula_weight 248.173 _chem_comp.id PMP _chem_comp.mon_nstd_flag . _chem_comp.name "4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "PYRIDOXAMINE-5'-PHOSPHATE" # _atom_sites.entry_id 5VER _atom_sites.fract_transf_matrix[1][1] 0.01093 _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] 0.01093 _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] 0.004283 _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 PLP A 1 701 701 PLP PLP . D 3 EPE A 1 702 702 EPE EPE . E 4 PGE A 1 703 703 PGE PGE . F 5 GOL A 1 704 704 GOL GOL . G 5 GOL A 1 705 705 GOL GOL . H 6 CA A 1 706 706 CA CA . I 6 CA A 1 707 707 CA CA . J 6 CA A 1 708 708 CA CA . K 7 PMP B 1 501 501 PMP PMP . L 3 EPE B 1 502 502 EPE EPE . M 8 PEG B 1 503 503 PEG PEG . N 5 GOL B 1 504 504 GOL GOL . O 5 GOL B 1 505 505 GOL GOL . P 6 CA B 1 506 506 CA CA . Q 9 HOH A 1 801 801 HOH HOH . Q 9 HOH A 2 802 802 HOH HOH . Q 9 HOH A 3 803 803 HOH HOH . Q 9 HOH A 4 804 804 HOH HOH . Q 9 HOH A 5 805 805 HOH HOH . Q 9 HOH A 6 806 806 HOH HOH . Q 9 HOH A 7 807 807 HOH HOH . Q 9 HOH A 8 808 808 HOH HOH . Q 9 HOH A 9 809 809 HOH HOH . Q 9 HOH A 10 810 810 HOH HOH . Q 9 HOH A 11 811 811 HOH HOH . Q 9 HOH A 12 812 812 HOH HOH . Q 9 HOH A 13 813 813 HOH HOH . Q 9 HOH A 14 814 814 HOH HOH . Q 9 HOH A 15 815 815 HOH HOH . Q 9 HOH A 16 816 816 HOH HOH . Q 9 HOH A 17 817 817 HOH HOH . Q 9 HOH A 18 818 818 HOH HOH . Q 9 HOH A 19 819 819 HOH HOH . Q 9 HOH A 20 820 820 HOH HOH . Q 9 HOH A 21 821 821 HOH HOH . Q 9 HOH A 22 822 822 HOH HOH . Q 9 HOH A 23 823 823 HOH HOH . Q 9 HOH A 24 824 824 HOH HOH . Q 9 HOH A 25 825 825 HOH HOH . Q 9 HOH A 26 826 826 HOH HOH . Q 9 HOH A 27 827 827 HOH HOH . Q 9 HOH A 28 828 828 HOH HOH . Q 9 HOH A 29 829 829 HOH HOH . Q 9 HOH A 30 830 830 HOH HOH . Q 9 HOH A 31 831 831 HOH HOH . Q 9 HOH A 32 832 832 HOH HOH . Q 9 HOH A 33 833 833 HOH HOH . Q 9 HOH A 34 834 834 HOH HOH . Q 9 HOH A 35 835 835 HOH HOH . Q 9 HOH A 36 836 836 HOH HOH . Q 9 HOH A 37 837 837 HOH HOH . Q 9 HOH A 38 838 838 HOH HOH . Q 9 HOH A 39 839 839 HOH HOH . Q 9 HOH A 40 840 840 HOH HOH . Q 9 HOH A 41 841 841 HOH HOH . Q 9 HOH A 42 842 842 HOH HOH . Q 9 HOH A 43 843 843 HOH HOH . Q 9 HOH A 44 844 844 HOH HOH . Q 9 HOH A 45 845 845 HOH HOH . Q 9 HOH A 46 846 846 HOH HOH . Q 9 HOH A 47 847 847 HOH HOH . Q 9 HOH A 48 848 848 HOH HOH . Q 9 HOH A 49 849 849 HOH HOH . Q 9 HOH A 50 850 850 HOH HOH . Q 9 HOH A 51 851 851 HOH HOH . Q 9 HOH A 52 852 852 HOH HOH . Q 9 HOH A 53 853 853 HOH HOH . Q 9 HOH A 54 854 854 HOH HOH . Q 9 HOH A 55 855 855 HOH HOH . R 9 HOH B 1 601 601 HOH HOH . R 9 HOH B 2 602 602 HOH HOH . R 9 HOH B 3 603 603 HOH HOH . R 9 HOH B 4 604 604 HOH HOH . R 9 HOH B 5 605 605 HOH HOH . R 9 HOH B 6 606 606 HOH HOH . R 9 HOH B 7 607 607 HOH HOH . R 9 HOH B 8 608 608 HOH HOH . R 9 HOH B 9 609 609 HOH HOH . R 9 HOH B 10 610 610 HOH HOH . R 9 HOH B 11 611 611 HOH HOH . R 9 HOH B 12 612 612 HOH HOH . R 9 HOH B 13 613 613 HOH HOH . R 9 HOH B 14 614 614 HOH HOH . R 9 HOH B 15 615 615 HOH HOH . R 9 HOH B 16 616 616 HOH HOH . R 9 HOH B 17 617 617 HOH HOH . R 9 HOH B 18 618 618 HOH HOH . R 9 HOH B 19 619 619 HOH HOH . R 9 HOH B 20 620 620 HOH HOH . R 9 HOH B 21 621 621 HOH HOH . R 9 HOH B 22 622 622 HOH HOH . R 9 HOH B 23 623 623 HOH HOH . R 9 HOH B 24 624 624 HOH HOH . R 9 HOH B 25 625 625 HOH HOH . R 9 HOH B 26 626 626 HOH HOH . R 9 HOH B 27 627 627 HOH HOH . R 9 HOH B 28 628 628 HOH HOH . R 9 HOH B 29 629 629 HOH HOH . R 9 HOH B 30 630 630 HOH HOH . R 9 HOH B 31 631 631 HOH HOH . R 9 HOH B 32 632 632 HOH HOH . R 9 HOH B 33 633 633 HOH HOH . R 9 HOH B 34 634 634 HOH HOH . R 9 HOH B 35 635 635 HOH HOH . R 9 HOH B 36 636 636 HOH HOH . R 9 HOH B 37 637 637 HOH HOH . R 9 HOH B 38 638 638 HOH HOH . R 9 HOH B 39 639 639 HOH HOH . R 9 HOH B 40 640 640 HOH HOH . R 9 HOH B 41 641 641 HOH HOH . R 9 HOH B 42 642 642 HOH HOH . R 9 HOH B 43 643 643 HOH HOH . R 9 HOH B 44 644 644 HOH HOH . R 9 HOH B 45 645 645 HOH HOH . R 9 HOH B 46 646 646 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 PMP . . . K 7 22.161 26.985 61.71 1 28.1 ? N1 PMP 501 B 1 HETATM 2 C C2 PMP . . . K 7 21.85 27.36 62.974 1 30.13 ? C2 PMP 501 B 1 HETATM 3 C C2A PMP . . . K 7 22.926 27.959 63.846 1 21.35 ? C2A PMP 501 B 1 HETATM 4 C C3 PMP . . . K 7 20.453 27.13 63.477 1 33.48 ? C3 PMP 501 B 1 HETATM 5 O O3 PMP . . . K 7 20.094 27.475 64.733 1 32.86 ? O3 PMP 501 B 1 HETATM 6 C C4 PMP . . . K 7 19.458 26.509 62.571 1 32.64 ? C4 PMP 501 B 1 HETATM 7 C C4A PMP . . . K 7 18.029 26.241 63.006 1 32.57 ? C4A PMP 501 B 1 HETATM 8 N N4A PMP . . . K 7 17.513 27.298 63.854 1 43.79 ? N4A PMP 501 B 1 HETATM 9 C C5 PMP . . . K 7 19.956 26.156 61.203 1 39.24 ? C5 PMP 501 B 1 HETATM 10 C C6 PMP . . . K 7 21.285 26.416 60.859 1 32.68 ? C6 PMP 501 B 1 HETATM 11 C C5A PMP . . . K 7 19.051 25.532 60.159 1 38.57 ? C5A PMP 501 B 1 HETATM 12 O O4P PMP . . . K 7 18.129 26.51 59.674 1 30.6 ? O4P PMP 501 B 1 HETATM 13 P P PMP . . . K 7 17.323 26.326 58.297 1 29.66 ? P PMP 501 B 1 HETATM 14 O O1P PMP . . . K 7 17.939 25.214 57.471 1 32.31 ? O1P PMP 501 B 1 HETATM 15 O O2P PMP . . . K 7 17.51 27.694 57.688 1 22.6 ? O2P PMP 501 B 1 HETATM 16 O O3P PMP . . . K 7 15.946 25.945 58.768 1 33.95 ? O3P PMP 501 B 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 325 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 16 #