data_1RVY # _model_server_result.job_id Ywe2kOzTx0AFNF921AnS6g _model_server_result.datetime_utc '2024-12-05 06:12:54' _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 1rvy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":600}' # _entry.id 1RVY # _exptl.entry_id 1RVY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 247.142 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "PYRIDOXAL-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 1RVY _cell.length_a 114.7 _cell.length_b 114.7 _cell.length_c 156.37 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1RVY _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,G _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' 7_556 y,x,-z+1 0 1 0 1 0 0 0 0 -1 0 0 156.37 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id E _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 256 A LYS 257 1_555 C C4A PLG . A PLG 500 1_555 ? A ? ? A ? ? ? ? ? ? ? 1.479 ? covale ? covale2 B NZ LYS 256 B LYS 257 1_555 E C4A PLP . B PLP 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.478 ? # _chem_comp.formula 'C8 H10 N O6 P' _chem_comp.formula_weight 247.142 _chem_comp.id PLP _chem_comp.mon_nstd_flag . _chem_comp.name "PYRIDOXAL-5'-PHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'VITAMIN B6 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 PLP doub 295 n y N1 C6 PLP sing 296 n y C2 C2A PLP sing 297 n n C2 C3 PLP sing 298 n y C2A H2A1 PLP sing 299 n n C2A H2A2 PLP sing 300 n n C2A H2A3 PLP sing 301 n n C3 O3 PLP sing 302 n n C3 C4 PLP doub 303 n y O3 HO3 PLP sing 304 n n C4 C4A PLP sing 305 n n C4 C5 PLP sing 306 n y C4A O4A PLP doub 307 n n C4A H4A PLP sing 308 n n C5 C6 PLP doub 309 n y C5 C5A PLP sing 310 n n C6 H6 PLP sing 311 n n C5A O4P PLP sing 312 n n C5A H5A1 PLP sing 313 n n C5A H5A2 PLP sing 314 n n O4P P PLP sing 315 n n P O1P PLP doub 316 n n P O2P PLP sing 317 n n P O3P PLP sing 318 n n O2P HOP2 PLP sing 319 n n O3P HOP3 PLP sing 320 n n # _atom_sites.entry_id 1RVY _atom_sites.fract_transf_matrix[1][1] 0.008718 _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] 0.008718 _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] 0.006395 _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 PLG A 1 500 500 PLG PLH . D 3 PO4 B 1 601 601 PO4 PO4 . E 4 PLP B 1 600 600 PLP PLP . F 5 HOH A 1 511 511 HOH HOH . F 5 HOH A 2 512 512 HOH HOH . F 5 HOH A 3 513 513 HOH HOH . F 5 HOH A 4 514 514 HOH HOH . F 5 HOH A 5 515 515 HOH HOH . F 5 HOH A 6 516 516 HOH HOH . F 5 HOH A 7 517 517 HOH HOH . F 5 HOH A 8 518 518 HOH HOH . F 5 HOH A 9 519 519 HOH HOH . F 5 HOH A 10 520 520 HOH HOH . F 5 HOH A 11 521 521 HOH HOH . F 5 HOH A 12 522 522 HOH HOH . F 5 HOH A 13 523 523 HOH HOH . F 5 HOH A 14 524 524 HOH HOH . F 5 HOH A 15 526 526 HOH HOH . F 5 HOH A 16 527 527 HOH HOH . F 5 HOH A 17 528 528 HOH HOH . F 5 HOH A 18 529 529 HOH HOH . F 5 HOH A 19 530 530 HOH HOH . F 5 HOH A 20 531 531 HOH HOH . F 5 HOH A 21 532 532 HOH HOH . F 5 HOH A 22 533 533 HOH HOH . F 5 HOH A 23 534 534 HOH HOH . F 5 HOH A 24 535 535 HOH HOH . F 5 HOH A 25 536 536 HOH HOH . F 5 HOH A 26 537 537 HOH HOH . F 5 HOH A 27 538 538 HOH HOH . F 5 HOH A 28 539 539 HOH HOH . F 5 HOH A 29 541 541 HOH HOH . F 5 HOH A 30 542 542 HOH HOH . F 5 HOH A 31 543 543 HOH HOH . F 5 HOH A 32 544 544 HOH HOH . F 5 HOH A 33 545 545 HOH HOH . F 5 HOH A 34 546 546 HOH HOH . F 5 HOH A 35 547 547 HOH HOH . F 5 HOH A 36 548 548 HOH HOH . F 5 HOH A 37 549 549 HOH HOH . F 5 HOH A 38 550 550 HOH HOH . F 5 HOH A 39 551 551 HOH HOH . F 5 HOH A 40 552 552 HOH HOH . F 5 HOH A 41 553 553 HOH HOH . F 5 HOH A 42 560 560 HOH HOH . F 5 HOH A 43 561 561 HOH HOH . F 5 HOH A 44 562 562 HOH HOH . F 5 HOH A 45 564 564 HOH HOH . F 5 HOH A 46 613 613 HOH HOH . F 5 HOH A 47 625 625 HOH HOH . F 5 HOH A 48 640 640 HOH HOH . F 5 HOH A 49 651 651 HOH HOH . F 5 HOH A 50 655 655 HOH HOH . F 5 HOH A 51 657 657 HOH HOH . F 5 HOH A 52 663 663 HOH HOH . G 5 HOH B 1 525 525 HOH HOH . G 5 HOH B 2 540 540 HOH HOH . G 5 HOH B 3 556 556 HOH HOH . G 5 HOH B 4 557 557 HOH HOH . G 5 HOH B 5 611 611 HOH HOH . G 5 HOH B 6 612 612 HOH HOH . G 5 HOH B 7 614 614 HOH HOH . G 5 HOH B 8 615 615 HOH HOH . G 5 HOH B 9 616 616 HOH HOH . G 5 HOH B 10 617 617 HOH HOH . G 5 HOH B 11 618 618 HOH HOH . G 5 HOH B 12 619 619 HOH HOH . G 5 HOH B 13 620 620 HOH HOH . G 5 HOH B 14 621 621 HOH HOH . G 5 HOH B 15 622 622 HOH HOH . G 5 HOH B 16 623 623 HOH HOH . G 5 HOH B 17 624 624 HOH HOH . G 5 HOH B 18 626 626 HOH HOH . G 5 HOH B 19 627 627 HOH HOH . G 5 HOH B 20 628 628 HOH HOH . G 5 HOH B 21 629 629 HOH HOH . G 5 HOH B 22 630 630 HOH HOH . G 5 HOH B 23 631 631 HOH HOH . G 5 HOH B 24 632 632 HOH HOH . G 5 HOH B 25 633 633 HOH HOH . G 5 HOH B 26 634 634 HOH HOH . G 5 HOH B 27 635 635 HOH HOH . G 5 HOH B 28 636 636 HOH HOH . G 5 HOH B 29 637 637 HOH HOH . G 5 HOH B 30 638 638 HOH HOH . G 5 HOH B 31 639 639 HOH HOH . G 5 HOH B 32 641 641 HOH HOH . G 5 HOH B 33 642 642 HOH HOH . G 5 HOH B 34 643 643 HOH HOH . G 5 HOH B 35 644 644 HOH HOH . G 5 HOH B 36 645 645 HOH HOH . G 5 HOH B 37 646 646 HOH HOH . G 5 HOH B 38 647 647 HOH HOH . G 5 HOH B 39 648 648 HOH HOH . G 5 HOH B 40 649 649 HOH HOH . G 5 HOH B 41 650 650 HOH HOH . G 5 HOH B 42 652 652 HOH HOH . G 5 HOH B 43 653 653 HOH HOH . G 5 HOH B 44 654 654 HOH HOH . G 5 HOH B 45 656 656 HOH HOH . G 5 HOH B 46 658 658 HOH HOH . G 5 HOH B 47 659 659 HOH HOH . G 5 HOH B 48 660 660 HOH HOH . G 5 HOH B 49 661 661 HOH HOH . G 5 HOH B 50 694 694 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 PLP . . . E 4 33.717 61.927 69.993 1 26.63 ? N1 PLP 600 B 1 HETATM 2 C C2 PLP . . . E 4 32.517 61.215 69.792 1 28.38 ? C2 PLP 600 B 1 HETATM 3 C C2A PLP . . . E 4 32.047 60.239 70.805 1 26.03 ? C2A PLP 600 B 1 HETATM 4 C C3 PLP . . . E 4 31.752 61.475 68.554 1 28.56 ? C3 PLP 600 B 1 HETATM 5 O O3 PLP . . . E 4 30.591 60.874 68.225 1 30.95 ? O3 PLP 600 B 1 HETATM 6 C C4 PLP . . . E 4 32.338 62.515 67.568 1 28.94 ? C4 PLP 600 B 1 HETATM 7 C C4A PLP . . . E 4 31.748 62.85 66.422 1 28.89 ? C4A PLP 600 B 1 HETATM 8 C C5 PLP . . . E 4 33.606 63.184 67.884 1 29.04 ? C5 PLP 600 B 1 HETATM 9 C C6 PLP . . . E 4 34.282 62.866 69.125 1 28.08 ? C6 PLP 600 B 1 HETATM 10 C C5A PLP . . . E 4 34.251 64.196 66.939 1 28.95 ? C5A PLP 600 B 1 HETATM 11 O O4P PLP . . . E 4 34.052 65.582 67.161 1 26.9 ? O4P PLP 600 B 1 HETATM 12 P P PLP . . . E 4 34.823 66.588 66.576 1 26.53 ? P PLP 600 B 1 HETATM 13 O O1P PLP . . . E 4 34.518 66.448 65.117 1 25.12 ? O1P PLP 600 B 1 HETATM 14 O O2P PLP . . . E 4 34.267 67.788 67.08 1 24.52 ? O2P PLP 600 B 1 HETATM 15 O O3P PLP . . . E 4 36.21 66.726 66.567 1 25.8 ? O3P PLP 600 B 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 313 _model_server_stats.encode_time_ms 20 _model_server_stats.element_count 15 #