data_6C4P # _model_server_result.job_id 7NVqko7hIxsoz8MMbuXZqg _model_server_result.datetime_utc '2024-11-30 23:26:46' _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 6c4p # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 6C4P # _exptl.entry_id 6C4P _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 248.173 _entity.id 2 _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 120 _cell.entry_id 6C4P _cell.length_a 80.733 _cell.length_b 80.733 _cell.length_c 207.923 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6C4P _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65 2 2' # _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 _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' 12_564 x,x-y+1,-z-1/6 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 -40.3665 69.916829 -34.653833 # _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 O GLY 142 A GLY 120 1_555 D NA NA . A NA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.453 ? metalc ? metalc2 A O ASN 205 A ASN 183 1_555 C CA CA . A CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.407 ? metalc ? metalc3 A OD1 ASP 208 A ASP 186 1_555 C CA CA . A CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.351 ? metalc ? metalc4 A OD2 ASP 208 A ASP 186 1_555 C CA CA . A CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.735 ? metalc ? metalc5 A OD1 ASN 209 A ASN 187 1_555 C CA CA . A CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.374 ? metalc ? metalc6 A OE1 GLN 275 A GLN 253 1_555 C CA CA . A CA 502 5_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.523 ? metalc ? metalc7 C CA CA . A CA 502 1_555 K O HOH . A HOH 647 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? metalc ? metalc8 D NA NA . A NA 503 1_555 K O HOH . A HOH 606 12_564 ? ? ? ? ? ? ? ? ? ? ? ? 2.48 ? metalc ? metalc9 D NA NA . A NA 503 1_555 K O HOH . A HOH 634 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.213 ? metalc ? metalc10 D NA NA . A NA 503 1_555 K O HOH . A HOH 637 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.241 ? metalc ? metalc11 D NA NA . A NA 503 1_555 K O HOH . A HOH 651 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.763 ? metalc ? metalc12 D NA NA . A NA 503 1_555 K O HOH . A HOH 679 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.393 ? # _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" # 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 PMP doub 285 n y N1 C6 PMP sing 286 n y C2 C2A PMP sing 287 n n C2 C3 PMP sing 288 n y C2A H2A1 PMP sing 289 n n C2A H2A2 PMP sing 290 n n C2A H2A3 PMP sing 291 n n C3 O3 PMP sing 292 n n C3 C4 PMP doub 293 n y O3 HO3 PMP sing 294 n n C4 C4A PMP sing 295 n n C4 C5 PMP sing 296 n y C4A N4A PMP sing 297 n n C4A H4A1 PMP sing 298 n n C4A H4A2 PMP sing 299 n n N4A HNA1 PMP sing 300 n n N4A HNA2 PMP sing 301 n n C5 C6 PMP doub 302 n y C5 C5A PMP sing 303 n n C6 H6 PMP sing 304 n n C5A O4P PMP sing 305 n n C5A H5A1 PMP sing 306 n n C5A H5A2 PMP sing 307 n n O4P P PMP sing 308 n n P O1P PMP doub 309 n n P O2P PMP sing 310 n n P O3P PMP sing 311 n n O2P HOP2 PMP sing 312 n n O3P HOP3 PMP sing 313 n n # _atom_sites.entry_id 6C4P _atom_sites.fract_transf_matrix[1][1] 0.012387 _atom_sites.fract_transf_matrix[1][2] 0.007151 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014303 _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] 0.004809 _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 PMP A 1 501 501 PMP PMP . C 3 CA A 1 502 502 CA CA . D 4 NA A 1 503 503 NA NA . E 5 CL A 1 504 504 CL CL . F 6 PEG A 1 505 1 PEG PEG . G 6 PEG A 1 506 2 PEG PEG . H 7 EDO A 1 507 1 EDO EDO . I 7 EDO A 1 508 2 EDO EDO . J 7 EDO A 1 509 3 EDO EDO . K 8 HOH A 1 601 51 HOH HOH . K 8 HOH A 2 602 25 HOH HOH . K 8 HOH A 3 603 17 HOH HOH . K 8 HOH A 4 604 50 HOH HOH . K 8 HOH A 5 605 21 HOH HOH . K 8 HOH A 6 606 85 HOH HOH . K 8 HOH A 7 607 8 HOH HOH . K 8 HOH A 8 608 20 HOH HOH . K 8 HOH A 9 609 56 HOH HOH . K 8 HOH A 10 610 16 HOH HOH . K 8 HOH A 11 611 15 HOH HOH . K 8 HOH A 12 612 73 HOH HOH . K 8 HOH A 13 613 76 HOH HOH . K 8 HOH A 14 614 22 HOH HOH . K 8 HOH A 15 615 26 HOH HOH . K 8 HOH A 16 616 43 HOH HOH . K 8 HOH A 17 617 42 HOH HOH . K 8 HOH A 18 618 86 HOH HOH . K 8 HOH A 19 619 49 HOH HOH . K 8 HOH A 20 620 74 HOH HOH . K 8 HOH A 21 621 46 HOH HOH . K 8 HOH A 22 622 12 HOH HOH . K 8 HOH A 23 623 38 HOH HOH . K 8 HOH A 24 624 4 HOH HOH . K 8 HOH A 25 625 18 HOH HOH . K 8 HOH A 26 626 53 HOH HOH . K 8 HOH A 27 627 39 HOH HOH . K 8 HOH A 28 628 35 HOH HOH . K 8 HOH A 29 629 63 HOH HOH . K 8 HOH A 30 630 28 HOH HOH . K 8 HOH A 31 631 75 HOH HOH . K 8 HOH A 32 632 33 HOH HOH . K 8 HOH A 33 633 2 HOH HOH . K 8 HOH A 34 634 82 HOH HOH . K 8 HOH A 35 635 67 HOH HOH . K 8 HOH A 36 636 54 HOH HOH . K 8 HOH A 37 637 80 HOH HOH . K 8 HOH A 38 638 57 HOH HOH . K 8 HOH A 39 639 36 HOH HOH . K 8 HOH A 40 640 27 HOH HOH . K 8 HOH A 41 641 3 HOH HOH . K 8 HOH A 42 642 1 HOH HOH . K 8 HOH A 43 643 5 HOH HOH . K 8 HOH A 44 644 84 HOH HOH . K 8 HOH A 45 645 9 HOH HOH . K 8 HOH A 46 646 14 HOH HOH . K 8 HOH A 47 647 64 HOH HOH . K 8 HOH A 48 648 37 HOH HOH . K 8 HOH A 49 649 10 HOH HOH . K 8 HOH A 50 650 11 HOH HOH . K 8 HOH A 51 651 81 HOH HOH . K 8 HOH A 52 652 13 HOH HOH . K 8 HOH A 53 653 59 HOH HOH . K 8 HOH A 54 654 61 HOH HOH . K 8 HOH A 55 655 72 HOH HOH . K 8 HOH A 56 656 34 HOH HOH . K 8 HOH A 57 657 7 HOH HOH . K 8 HOH A 58 658 40 HOH HOH . K 8 HOH A 59 659 52 HOH HOH . K 8 HOH A 60 660 62 HOH HOH . K 8 HOH A 61 661 24 HOH HOH . K 8 HOH A 62 662 6 HOH HOH . K 8 HOH A 63 663 60 HOH HOH . K 8 HOH A 64 664 44 HOH HOH . K 8 HOH A 65 665 41 HOH HOH . K 8 HOH A 66 666 30 HOH HOH . K 8 HOH A 67 667 70 HOH HOH . K 8 HOH A 68 668 45 HOH HOH . K 8 HOH A 69 669 47 HOH HOH . K 8 HOH A 70 670 71 HOH HOH . K 8 HOH A 71 671 31 HOH HOH . K 8 HOH A 72 672 68 HOH HOH . K 8 HOH A 73 673 78 HOH HOH . K 8 HOH A 74 674 29 HOH HOH . K 8 HOH A 75 675 32 HOH HOH . K 8 HOH A 76 676 19 HOH HOH . K 8 HOH A 77 677 48 HOH HOH . K 8 HOH A 78 678 77 HOH HOH . K 8 HOH A 79 679 83 HOH HOH . K 8 HOH A 80 680 65 HOH HOH . K 8 HOH A 81 681 66 HOH HOH . K 8 HOH A 82 682 55 HOH HOH . K 8 HOH A 83 683 23 HOH HOH . K 8 HOH A 84 684 58 HOH HOH . K 8 HOH A 85 685 79 HOH HOH . K 8 HOH A 86 686 69 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 . . . B 2 3.532 31.832 -13.436 1 39.25 ? N1 PMP 501 A 1 HETATM 2 C C2 PMP . . . B 2 3.477 33.012 -12.771 1 39.02 ? C2 PMP 501 A 1 HETATM 3 C C2A PMP . . . B 2 3.524 34.301 -13.529 1 38.9 ? C2A PMP 501 A 1 HETATM 4 C C3 PMP . . . B 2 3.374 33.011 -11.362 1 40.05 ? C3 PMP 501 A 1 HETATM 5 O O3 PMP . . . B 2 3.325 34.249 -10.698 1 37.93 ? O3 PMP 501 A 1 HETATM 6 C C4 PMP . . . B 2 3.336 31.817 -10.669 1 42.68 ? C4 PMP 501 A 1 HETATM 7 C C4A PMP . . . B 2 3.231 31.879 -9.081 1 44.91 ? C4A PMP 501 A 1 HETATM 8 N N4A PMP . . . B 2 4.23 32.713 -8.517 1 47.55 ? N4A PMP 501 A 1 HETATM 9 C C5 PMP . . . B 2 3.373 30.596 -11.375 1 41.79 ? C5 PMP 501 A 1 HETATM 10 C C6 PMP . . . B 2 3.485 30.637 -12.772 1 40.28 ? C6 PMP 501 A 1 HETATM 11 C C5A PMP . . . B 2 3.363 29.225 -10.717 1 40.59 ? C5A PMP 501 A 1 HETATM 12 O O4P PMP . . . B 2 2.121 28.939 -10.066 1 41.83 ? O4P PMP 501 A 1 HETATM 13 P P PMP . . . B 2 2.097 27.859 -8.89 1 39.97 ? P PMP 501 A 1 HETATM 14 O O1P PMP . . . B 2 2.982 26.659 -9.284 1 39.55 ? O1P PMP 501 A 1 HETATM 15 O O2P PMP . . . B 2 0.679 27.428 -8.584 1 36.16 ? O2P PMP 501 A 1 HETATM 16 O O3P PMP . . . B 2 2.741 28.507 -7.7 1 39.83 ? O3P PMP 501 A 1 # _model_server_stats.io_time_ms 62 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 990 _model_server_stats.encode_time_ms 21 _model_server_stats.element_count 16 #