data_1D7R # _model_server_result.job_id F-cLu4mreHr40z823gQSHg _model_server_result.datetime_utc '2025-02-27 01:16:42' _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 1d7r # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":500}' # _entry.id 1D7R # _exptl.entry_id 1D7R _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 332.246 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'N-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-Y-LMETHYL]-1-AMINO-CYCLOPROPANECARBOXYLIC ACID' _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 1D7R _cell.length_a 152.65 _cell.length_b 152.65 _cell.length_c 86.22 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1D7R _symmetry.cell_setting ? _symmetry.Int_Tables_number 181 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 64 2 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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4 # 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' 4_665 -x+1,-y+1,z -1 0 0 0 -1 0 0 0 1 76.325 132.198778 0 3 'crystal symmetry operation' 7_555 y,x,-z+1/3 -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 28.74 4 'crystal symmetry operation' 10_665 -y+1,-x+1,-z+1/3 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 76.325 132.198778 28.74 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _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 LEU 78 A LEU 78 1_555 C K K . A K 436 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.653 ? metalc ? metalc2 A OG SER 80 A SER 80 1_555 C K K . A K 436 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.662 ? metalc ? metalc3 A O ALA 95 A ALA 95 1_555 B NA NA . A NA 435 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.476 ? metalc ? metalc4 A O THR 98 A THR 98 1_555 B NA NA . A NA 435 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.547 ? metalc ? metalc5 A OG1 THR 98 A THR 98 1_555 B NA NA . A NA 435 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.885 ? metalc ? metalc6 A O PRO 99 A PRO 99 1_555 B NA NA . A NA 435 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.681 ? metalc ? metalc7 A O LEU 102 A LEU 102 1_555 B NA NA . A NA 435 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.726 ? metalc ? metalc8 A O THR 303 A THR 303 1_555 C K K . A K 436 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.871 ? metalc ? metalc9 A O VAL 305 A VAL 305 1_555 C K K . A K 436 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.812 ? metalc ? metalc10 A OD1 ASP 307 A ASP 307 1_555 C K K . A K 436 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.536 ? metalc ? metalc11 C K K . A K 436 1_555 E O HOH . A HOH 529 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.857 ? # _chem_comp.formula 'C12 H17 N2 O7 P' _chem_comp.formula_weight 332.246 _chem_comp.id 5PA _chem_comp.mon_nstd_flag . _chem_comp.name 'N-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-Y-LMETHYL]-1-AMINO-CYCLOPROPANECARBOXYLIC ACID' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'N-PYRIDOXYL-1-AMINO-CYCLOPROPANECARBOXYLIC ACID-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 C4 C4A 5PA sing 1 n n C4 C5 5PA doub 2 n y C4 C3 5PA sing 3 n y C4A N 5PA sing 4 n n C4A H4A1 5PA sing 5 n n C4A H4A2 5PA sing 6 n n P O1P 5PA doub 7 n n P O2P 5PA sing 8 n n P O3P 5PA sing 9 n n P O4P 5PA sing 10 n n O2P HOP2 5PA sing 11 n n O3P HOP3 5PA sing 12 n n O4P C5A 5PA sing 13 n n C5A C5 5PA sing 14 n n C5A H5A1 5PA sing 15 n n C5A H5A2 5PA sing 16 n n C5 C6 5PA sing 17 n y N1 C6 5PA doub 18 n y N1 C2 5PA sing 19 n y C6 H6 5PA sing 20 n n C2 C2A 5PA sing 21 n n C2 C3 5PA doub 22 n y C2A H2A1 5PA sing 23 n n C2A H2A2 5PA sing 24 n n C2A H2A3 5PA sing 25 n n C3 O3 5PA sing 26 n n O3 HO3 5PA sing 27 n n N C8 5PA sing 28 n n N HN 5PA sing 29 n n C8 C7 5PA sing 30 n n C8 C9 5PA sing 31 n n C8 C10 5PA sing 32 n n C7 O7 5PA doub 33 n n C7 O8 5PA sing 34 n n O8 HO8 5PA sing 35 n n C9 C10 5PA sing 36 n n C9 H91 5PA sing 37 n n C9 H92 5PA sing 38 n n C10 H101 5PA sing 39 n n C10 H102 5PA sing 40 n n # _atom_sites.entry_id 1D7R _atom_sites.fract_transf_matrix[1][1] 0.006551 _atom_sites.fract_transf_matrix[1][2] 0.003782 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007564 _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] 0.011598 _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 NA A 1 435 435 NA NA+ . C 3 K A 1 436 436 K K+ . D 4 5PA A 1 500 500 5PA ACC . E 5 HOH A 1 501 501 HOH WAT . E 5 HOH A 2 502 502 HOH WAT . E 5 HOH A 3 503 503 HOH WAT . E 5 HOH A 4 504 504 HOH WAT . E 5 HOH A 5 505 505 HOH WAT . E 5 HOH A 6 506 506 HOH WAT . E 5 HOH A 7 507 507 HOH WAT . E 5 HOH A 8 508 508 HOH WAT . E 5 HOH A 9 509 509 HOH WAT . E 5 HOH A 10 510 510 HOH WAT . E 5 HOH A 11 511 511 HOH WAT . E 5 HOH A 12 512 512 HOH WAT . E 5 HOH A 13 513 513 HOH WAT . E 5 HOH A 14 514 514 HOH WAT . E 5 HOH A 15 515 515 HOH WAT . E 5 HOH A 16 516 516 HOH WAT . E 5 HOH A 17 517 517 HOH WAT . E 5 HOH A 18 518 518 HOH WAT . E 5 HOH A 19 519 519 HOH WAT . E 5 HOH A 20 520 520 HOH WAT . E 5 HOH A 21 521 521 HOH WAT . E 5 HOH A 22 522 522 HOH WAT . E 5 HOH A 23 523 523 HOH WAT . E 5 HOH A 24 524 524 HOH WAT . E 5 HOH A 25 525 525 HOH WAT . E 5 HOH A 26 526 526 HOH WAT . E 5 HOH A 27 527 527 HOH WAT . E 5 HOH A 28 528 528 HOH WAT . E 5 HOH A 29 529 529 HOH WAT . E 5 HOH A 30 530 530 HOH WAT . E 5 HOH A 31 531 531 HOH WAT . E 5 HOH A 32 532 532 HOH WAT . E 5 HOH A 33 533 533 HOH WAT . E 5 HOH A 34 534 534 HOH WAT . E 5 HOH A 35 535 535 HOH WAT . E 5 HOH A 36 536 536 HOH WAT . E 5 HOH A 37 537 537 HOH WAT . E 5 HOH A 38 538 538 HOH WAT . E 5 HOH A 39 539 539 HOH WAT . E 5 HOH A 40 540 540 HOH WAT . E 5 HOH A 41 541 541 HOH WAT . E 5 HOH A 42 542 542 HOH WAT . E 5 HOH A 43 543 543 HOH WAT . E 5 HOH A 44 544 544 HOH WAT . E 5 HOH A 45 545 545 HOH WAT . E 5 HOH A 46 546 546 HOH WAT . E 5 HOH A 47 547 547 HOH WAT . E 5 HOH A 48 548 548 HOH WAT . E 5 HOH A 49 549 549 HOH WAT . E 5 HOH A 50 550 550 HOH WAT . E 5 HOH A 51 551 551 HOH WAT . E 5 HOH A 52 552 552 HOH WAT . E 5 HOH A 53 553 553 HOH WAT . E 5 HOH A 54 554 554 HOH WAT . E 5 HOH A 55 555 555 HOH WAT . E 5 HOH A 56 556 556 HOH WAT . E 5 HOH A 57 557 557 HOH WAT . E 5 HOH A 58 558 558 HOH WAT . E 5 HOH A 59 559 559 HOH WAT . E 5 HOH A 60 560 560 HOH WAT . E 5 HOH A 61 561 561 HOH WAT . E 5 HOH A 62 562 562 HOH WAT . E 5 HOH A 63 563 563 HOH WAT . E 5 HOH A 64 564 564 HOH WAT . E 5 HOH A 65 565 565 HOH WAT . E 5 HOH A 66 566 566 HOH WAT . E 5 HOH A 67 568 568 HOH WAT . E 5 HOH A 68 569 569 HOH WAT . E 5 HOH A 69 570 570 HOH WAT . E 5 HOH A 70 571 571 HOH WAT . E 5 HOH A 71 572 572 HOH WAT . E 5 HOH A 72 573 573 HOH WAT . E 5 HOH A 73 574 574 HOH WAT . E 5 HOH A 74 575 575 HOH WAT . E 5 HOH A 75 576 576 HOH WAT . E 5 HOH A 76 577 577 HOH WAT . E 5 HOH A 77 578 578 HOH WAT . E 5 HOH A 78 579 579 HOH WAT . E 5 HOH A 79 580 580 HOH WAT . E 5 HOH A 80 581 581 HOH WAT . E 5 HOH A 81 582 582 HOH WAT . E 5 HOH A 82 583 583 HOH WAT . E 5 HOH A 83 584 584 HOH WAT . E 5 HOH A 84 585 585 HOH WAT . E 5 HOH A 85 586 586 HOH WAT . E 5 HOH A 86 587 587 HOH WAT . E 5 HOH A 87 588 588 HOH WAT . E 5 HOH A 88 589 589 HOH WAT . E 5 HOH A 89 590 590 HOH WAT . E 5 HOH A 90 591 591 HOH WAT . E 5 HOH A 91 601 601 HOH WAT . E 5 HOH A 92 602 602 HOH WAT . E 5 HOH A 93 603 603 HOH WAT . E 5 HOH A 94 604 604 HOH WAT . E 5 HOH A 95 605 605 HOH WAT . E 5 HOH A 96 606 606 HOH WAT . E 5 HOH A 97 607 607 HOH WAT . E 5 HOH A 98 608 608 HOH WAT . E 5 HOH A 99 609 609 HOH WAT . E 5 HOH A 100 610 610 HOH WAT . E 5 HOH A 101 611 611 HOH WAT . E 5 HOH A 102 612 612 HOH WAT . E 5 HOH A 103 613 613 HOH WAT . E 5 HOH A 104 614 614 HOH WAT . E 5 HOH A 105 615 615 HOH WAT . E 5 HOH A 106 616 616 HOH WAT . E 5 HOH A 107 617 617 HOH WAT . E 5 HOH A 108 618 618 HOH WAT . E 5 HOH A 109 619 619 HOH WAT . E 5 HOH A 110 620 620 HOH WAT . E 5 HOH A 111 621 621 HOH WAT . E 5 HOH A 112 622 622 HOH WAT . E 5 HOH A 113 623 623 HOH WAT . E 5 HOH A 114 624 624 HOH WAT . E 5 HOH A 115 625 625 HOH WAT . E 5 HOH A 116 626 626 HOH WAT . E 5 HOH A 117 627 627 HOH WAT . E 5 HOH A 118 628 628 HOH WAT . E 5 HOH A 119 629 629 HOH WAT . E 5 HOH A 120 630 630 HOH WAT . E 5 HOH A 121 631 631 HOH WAT . E 5 HOH A 122 632 632 HOH WAT . E 5 HOH A 123 633 633 HOH WAT . E 5 HOH A 124 634 634 HOH WAT . E 5 HOH A 125 635 635 HOH WAT . E 5 HOH A 126 636 636 HOH WAT . E 5 HOH A 127 637 637 HOH WAT . E 5 HOH A 128 638 638 HOH WAT . E 5 HOH A 129 639 639 HOH WAT . E 5 HOH A 130 640 500 HOH ACC . # 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 C C4 5PA . . . D 4 17.072 52.06 16.443 1 100 ? C4 5PA 500 A 1 HETATM 2 C C4A 5PA . . . D 4 16.803 51.423 17.735 1 42.24 ? C4A 5PA 500 A 1 HETATM 3 P P 5PA . . . D 4 20.044 48.554 16.643 1 28.99 ? P 5PA 500 A 1 HETATM 4 O O1P 5PA . . . D 4 19.703 48.897 18.069 1 34.6 ? O1P 5PA 500 A 1 HETATM 5 O O2P 5PA . . . D 4 19.54 47.128 16.272 1 35.89 ? O2P 5PA 500 A 1 HETATM 6 O O3P 5PA . . . D 4 21.407 48.694 16.126 1 26.47 ? O3P 5PA 500 A 1 HETATM 7 O O4P 5PA . . . D 4 19.271 49.665 15.767 1 37.27 ? O4P 5PA 500 A 1 HETATM 8 C C5A 5PA . . . D 4 19.447 51.015 16.163 1 24.45 ? C5A 5PA 500 A 1 HETATM 9 C C5 5PA . . . D 4 18.279 51.871 15.674 1 34.11 ? C5 5PA 500 A 1 HETATM 10 N N1 5PA . . . D 4 17.557 53.293 13.967 1 30.09 ? N1 5PA 500 A 1 HETATM 11 C C6 5PA . . . D 4 18.505 52.479 14.477 1 38.47 ? C6 5PA 500 A 1 HETATM 12 C C2 5PA . . . D 4 16.379 53.542 14.608 1 42.64 ? C2 5PA 500 A 1 HETATM 13 C C2A 5PA . . . D 4 15.419 54.493 13.949 1 30.3 ? C2A 5PA 500 A 1 HETATM 14 C C3 5PA . . . D 4 16.129 52.893 15.864 1 35.54 ? C3 5PA 500 A 1 HETATM 15 O O3 5PA . . . D 4 14.932 53.147 16.449 1 32.97 ? O3 5PA 500 A 1 HETATM 16 N N 5PA . . . D 4 16.928 52.125 18.818 1 100 ? N 5PA 500 A 1 HETATM 17 C C8 5PA . . . D 4 16.42 51.77 20.192 1 100 ? C8 5PA 500 A 1 HETATM 18 C C7 5PA . . . D 4 15.135 52.328 20.721 1 57.88 ? C7 5PA 500 A 1 HETATM 19 O O7 5PA . . . D 4 14.025 51.664 20.539 1 41.52 ? O7 5PA 500 A 1 HETATM 20 O O8 5PA . . . D 4 15.144 53.389 21.348 1 72.83 ? O8 5PA 500 A 1 HETATM 21 C C9 5PA . . . D 4 16.843 50.328 20.509 1 34.11 ? C9 5PA 500 A 1 HETATM 22 C C10 5PA . . . D 4 17.414 51.405 21.312 1 100 ? C10 5PA 500 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 329 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 22 #