data_1RVY # _model_server_result.job_id zE_kmvjWT4o3FZSxqctPrQ _model_server_result.datetime_utc '2024-11-25 04:40:20' _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":"C","auth_seq_id":500}' # _entry.id 1RVY # _exptl.entry_id 1RVY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 306.209 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE] _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 2 _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 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 'C10 H15 N2 O7 P' _chem_comp.formula_weight 306.209 _chem_comp.id PLG _chem_comp.mon_nstd_flag . _chem_comp.name N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE] _chem_comp.type non-polymer _chem_comp.pdbx_synonyms N-PYRIDOXYL-GLYCINE-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 PLG doub 260 n y N1 C6 PLG sing 261 n y C2 C2A PLG sing 262 n n C2 C3 PLG sing 263 n y C2A H2A1 PLG sing 264 n n C2A H2A2 PLG sing 265 n n C2A H2A3 PLG sing 266 n n C3 O3 PLG sing 267 n n C3 C4 PLG doub 268 n y O3 HO3 PLG sing 269 n n C4 C4A PLG sing 270 n n C4 C5 PLG sing 271 n y C4A N PLG sing 272 n n C4A H4A1 PLG sing 273 n n C4A H4A2 PLG sing 274 n n C5 C6 PLG doub 275 n y C5 C5A PLG sing 276 n n C6 H6 PLG sing 277 n n C5A OP4 PLG sing 278 n n C5A H5A1 PLG sing 279 n n C5A H5A2 PLG sing 280 n n OP4 P PLG sing 281 n n P OP1 PLG doub 282 n n P OP2 PLG sing 283 n n P OP3 PLG sing 284 n n OP2 HOP2 PLG sing 285 n n OP3 HOP3 PLG sing 286 n n C O PLG doub 287 n n C OXT PLG sing 288 n n C CA PLG sing 289 n n OXT HXT PLG sing 290 n n CA N PLG sing 291 n n CA HA2 PLG sing 292 n n CA HA1 PLG sing 293 n n N H PLG sing 294 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 PLG . A . C 2 52.624 80.053 68.691 0.5 29.51 ? N1 PLG 500 A 1 HETATM 2 N N1 PLG . B . C 2 52.6 80.144 68.397 0.5 27.3 ? N1 PLG 500 A 1 HETATM 3 C C2 PLG . A . C 2 53.14 81.361 68.638 0.5 32.07 ? C2 PLG 500 A 1 HETATM 4 C C2 PLG . B . C 2 53.084 81.462 68.549 0.5 29.86 ? C2 PLG 500 A 1 HETATM 5 C C2A PLG . A . C 2 54.57 81.59 68.28 0.5 30.79 ? C2A PLG 500 A 1 HETATM 6 C C2A PLG . B . C 2 54.467 81.789 68.135 0.5 28.58 ? C2A PLG 500 A 1 HETATM 7 C C3 PLG . A . C 2 52.214 82.488 68.944 0.5 32.6 ? C3 PLG 500 A 1 HETATM 8 C C3 PLG . B . C 2 52.169 82.488 69.122 0.5 30.39 ? C3 PLG 500 A 1 HETATM 9 O O3 PLG . A . C 2 52.555 83.795 68.929 0.5 34.95 ? O3 PLG 500 A 1 HETATM 10 O O3 PLG . B . C 2 52.483 83.794 69.329 0.5 32.74 ? O3 PLG 500 A 1 HETATM 11 C C4 PLG . A . C 2 50.743 82.139 69.305 0.5 34.75 ? C4 PLG 500 A 1 HETATM 12 C C4 PLG . B . C 2 50.744 82.019 69.516 0.5 32.54 ? C4 PLG 500 A 1 HETATM 13 C C4A PLG . A . C 2 49.694 83.242 69.631 0.5 35.93 ? C4A PLG 500 A 1 HETATM 14 C C4A PLG . B . C 2 49.842 82.825 70.034 0.5 33.72 ? C4A PLG 500 A 1 HETATM 15 C C5 PLG . A . C 2 50.32 80.72 69.342 0.5 33.6 ? C5 PLG 500 A 1 HETATM 16 C C5 PLG . B . C 2 50.351 80.604 69.315 0.5 31.39 ? C5 PLG 500 A 1 HETATM 17 C C6 PLG . A . C 2 51.308 79.688 69.017 0.5 32.95 ? C6 PLG 500 A 1 HETATM 18 C C6 PLG . B . C 2 51.327 79.675 68.741 0.5 30.74 ? C6 PLG 500 A 1 HETATM 19 C C5A PLG . A . C 2 48.89 80.236 69.726 0.5 33.99 ? C5A PLG 500 A 1 HETATM 20 C C5A PLG . B . C 2 48.946 80.026 69.702 0.5 31.78 ? C5A PLG 500 A 1 HETATM 21 O OP4 PLG . A . C 2 47.709 80.519 68.939 0.5 32.5 ? OP4 PLG 500 A 1 HETATM 22 O OP4 PLG . B . C 2 47.743 80.401 68.954 0.5 30.29 ? OP4 PLG 500 A 1 HETATM 23 P P PLG . A . C 2 46.382 80.162 69.321 0.5 31.12 ? P PLG 500 A 1 HETATM 24 P P PLG . B . C 2 46.391 80.137 69.349 0.5 28.91 ? P PLG 500 A 1 HETATM 25 O OP1 PLG . A . C 2 46.168 80.997 70.562 0.5 29.08 ? OP1 PLG 500 A 1 HETATM 26 O OP1 PLG . B . C 2 46.22 80.957 70.605 0.5 26.87 ? OP1 PLG 500 A 1 HETATM 27 O OP2 PLG . A . C 2 45.524 80.632 68.277 0.5 30.82 ? OP2 PLG 500 A 1 HETATM 28 O OP2 PLG . B . C 2 45.581 80.676 68.308 0.5 28.61 ? OP2 PLG 500 A 1 HETATM 29 O OP3 PLG . A . C 2 45.902 78.905 69.699 0.5 31.82 ? OP3 PLG 500 A 1 HETATM 30 O OP3 PLG . B . C 2 45.825 78.918 69.708 0.5 29.61 ? OP3 PLG 500 A 1 HETATM 31 C C PLG . A . C 2 50.175 85.692 72.456 0.5 53.11 ? C PLG 500 A 1 HETATM 32 C C PLG . B . C 2 49.683 85.766 72.474 0.5 68.25 ? C PLG 500 A 1 HETATM 33 O O PLG . A . C 2 51.006 86.314 73.086 0.5 53.11 ? O PLG 500 A 1 HETATM 34 O O PLG . B . C 2 50.852 86.095 72.635 0.5 68.25 ? O PLG 500 A 1 HETATM 35 O OXT PLG . A . C 2 48.957 85.781 72.82 0.5 53.11 ? OXT PLG 500 A 1 HETATM 36 O OXT PLG . B . C 2 48.821 86.237 73.258 0.5 68.25 ? OXT PLG 500 A 1 HETATM 37 C CA PLG . A . C 2 50.632 84.806 71.218 0.5 53.11 ? CA PLG 500 A 1 HETATM 38 C CA PLG . B . C 2 49.268 84.771 71.297 0.5 68.25 ? CA PLG 500 A 1 HETATM 39 N N PLG . A . C 2 49.73 83.616 71.04 0.5 53.11 ? N PLG 500 A 1 HETATM 40 N N PLG . B . C 2 50.23 83.954 70.748 0.5 68.25 ? N PLG 500 A 1 # _model_server_stats.io_time_ms 57 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 266 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 40 #