data_4KN1 # _model_server_result.job_id xQzd4cQyrD4gYuXHuGwdeg _model_server_result.datetime_utc '2024-10-28 13:14:20' _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 4kn1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":301}' # _entry.id 4KN1 # _exptl.entry_id 4KN1 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 440.413 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description Aminopterin _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 4KN1 _cell.length_a 97.075 _cell.length_b 97.075 _cell.length_c 98.955 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4KN1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 2 3 2 BMA NAG C1 O1 . O4 HO4 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n B NAG 1 B 1 NAG A 301 NAG 2 n B NAG 2 B 2 NAG A 302 NAG 2 n B BMA 3 B 3 BMA A 303 BMA # 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 disulf ? disulf1 A SG CYS 10 A CYS 31 1_555 A SG CYS 38 A CYS 59 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf2 A SG CYS 30 A CYS 51 1_555 A SG CYS 78 A CYS 99 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf3 A SG CYS 39 A CYS 60 1_555 A SG CYS 82 A CYS 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf4 A SG CYS 62 A CYS 83 1_555 A SG CYS 148 A CYS 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf5 A SG CYS 69 A CYS 90 1_555 A SG CYS 119 A CYS 140 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf6 A SG CYS 108 A CYS 129 1_555 A SG CYS 182 A CYS 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf7 A SG CYS 112 A CYS 133 1_555 A SG CYS 162 A CYS 183 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf8 A SG CYS 125 A CYS 146 1_555 A SG CYS 142 A CYS 163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? covale ? covale1 A ND2 ASN 174 A ASN 195 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale2 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.42 ? covale ? covale3 B O4 NAG . B NAG 2 1_555 B C1 BMA . B BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.419 ? metalc ? metalc1 A OG SER 83 A SER 104 1_555 D K K . A K 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.263 ? # _chem_comp.formula 'C19 H20 N8 O5' _chem_comp.formula_weight 440.413 _chem_comp.id 04J _chem_comp.mon_nstd_flag . _chem_comp.name Aminopterin _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'N-(4-{[(2,4-diaminopteridin-6-yl)methyl]amino}benzoyl)-L-glutamic acid' # 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 N C 04J sing 1 n n C11 C 04J sing 2 n n C O 04J doub 3 n n N CA 04J sing 4 n n N HN 04J sing 5 n n C2 N1 04J doub 6 n y N1 C8A 04J sing 7 n y O1 CT 04J doub 8 n n NA2 C2 04J sing 9 n n C2 N3 04J sing 10 n y CT O2 04J sing 11 n n O2 HO2 04J sing 12 n n N3 C4 04J doub 13 n y C4 NA4 04J sing 14 n n C4 C4A 04J sing 15 n y C4A N5 04J sing 16 n y N5 C6 04J doub 17 n y C7 C6 04J sing 18 n y C6 C9 04J sing 19 n n N8 C7 04J doub 20 n y C7 H7 04J sing 21 n n C8A N8 04J sing 22 n y C9 N10 04J sing 23 n n C9 H9 04J sing 24 n n C9 H9A 04J sing 25 n n CB CA 04J sing 26 n n CA CT 04J sing 27 n n CA HA 04J sing 28 n n CB CG 04J sing 29 n n CB HB 04J sing 30 n n CB HBA 04J sing 31 n n OE1 CD 04J doub 32 n n CD CG 04J sing 33 n n CD OE2 04J sing 34 n n CG HG 04J sing 35 n n CG HGA 04J sing 36 n n N10 C14 04J sing 37 n n N10 HN10 04J sing 38 n n C16 C11 04J doub 39 n y C12 C11 04J sing 40 n y C13 C12 04J doub 41 n y C12 H12 04J sing 42 n n C14 C13 04J sing 43 n y C13 H13 04J sing 44 n n C14 C15 04J doub 45 n y C15 C16 04J sing 46 n y C15 H15 04J sing 47 n n C16 H16 04J sing 48 n n C8A C4A 04J doub 49 n y NA2 HNA2 04J sing 50 n n NA2 HNAA 04J sing 51 n n NA4 HNA4 04J sing 52 n n NA4 HNAB 04J sing 53 n n OE2 HOE2 04J sing 54 n n # _atom_sites.entry_id 4KN1 _atom_sites.fract_transf_matrix[1][1] 0.010301 _atom_sites.fract_transf_matrix[1][2] 0.005947 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011895 _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] 0.010106 _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 3 04J A 1 301 241 04J AMT . D 4 K A 1 302 251 K K . E 5 CL A 1 303 261 CL CL . F 5 CL A 1 304 262 CL CL . G 5 CL A 1 305 263 CL CL . H 6 HOH A 1 401 1 HOH HOH . H 6 HOH A 2 402 2 HOH HOH . H 6 HOH A 3 403 3 HOH HOH . H 6 HOH A 4 404 4 HOH HOH . H 6 HOH A 5 405 5 HOH HOH . H 6 HOH A 6 406 6 HOH HOH . H 6 HOH A 7 407 7 HOH HOH . H 6 HOH A 8 408 8 HOH HOH . H 6 HOH A 9 409 9 HOH HOH . H 6 HOH A 10 410 10 HOH HOH . H 6 HOH A 11 411 11 HOH HOH . H 6 HOH A 12 412 12 HOH HOH . H 6 HOH A 13 413 13 HOH HOH . H 6 HOH A 14 414 14 HOH HOH . H 6 HOH A 15 415 15 HOH HOH . H 6 HOH A 16 416 16 HOH HOH . H 6 HOH A 17 417 17 HOH HOH . H 6 HOH A 18 418 18 HOH HOH . H 6 HOH A 19 419 19 HOH HOH . H 6 HOH A 20 420 20 HOH HOH . H 6 HOH A 21 421 21 HOH HOH . H 6 HOH A 22 422 22 HOH HOH . H 6 HOH A 23 423 23 HOH HOH . H 6 HOH A 24 424 24 HOH HOH . H 6 HOH A 25 425 25 HOH HOH . H 6 HOH A 26 426 26 HOH HOH . H 6 HOH A 27 427 27 HOH HOH . H 6 HOH A 28 428 28 HOH HOH . H 6 HOH A 29 429 29 HOH HOH . H 6 HOH A 30 430 30 HOH HOH . H 6 HOH A 31 431 31 HOH HOH . H 6 HOH A 32 432 32 HOH HOH . H 6 HOH A 33 433 33 HOH HOH . H 6 HOH A 34 434 34 HOH HOH . H 6 HOH A 35 435 35 HOH HOH . H 6 HOH A 36 436 36 HOH HOH . H 6 HOH A 37 437 37 HOH HOH . H 6 HOH A 38 438 38 HOH HOH . H 6 HOH A 39 439 39 HOH HOH . H 6 HOH A 40 440 40 HOH HOH . H 6 HOH A 41 441 41 HOH HOH . H 6 HOH A 42 442 42 HOH HOH . H 6 HOH A 43 443 43 HOH HOH . H 6 HOH A 44 444 44 HOH HOH . H 6 HOH A 45 445 45 HOH HOH . H 6 HOH A 46 446 46 HOH HOH . H 6 HOH A 47 447 47 HOH HOH . H 6 HOH A 48 448 48 HOH HOH . H 6 HOH A 49 449 49 HOH HOH . H 6 HOH A 50 450 50 HOH HOH . H 6 HOH A 51 451 51 HOH HOH . H 6 HOH A 52 452 52 HOH HOH . H 6 HOH A 53 453 53 HOH HOH . H 6 HOH A 54 454 54 HOH HOH . H 6 HOH A 55 455 55 HOH HOH . H 6 HOH A 56 456 56 HOH HOH . H 6 HOH A 57 457 57 HOH HOH . H 6 HOH A 58 458 458 HOH HOH . H 6 HOH A 59 459 59 HOH HOH . H 6 HOH A 60 460 60 HOH HOH . H 6 HOH A 61 461 61 HOH HOH . H 6 HOH A 62 462 62 HOH HOH . H 6 HOH A 63 463 63 HOH HOH . H 6 HOH A 64 464 64 HOH HOH . H 6 HOH A 65 465 65 HOH HOH . H 6 HOH A 66 466 66 HOH HOH . H 6 HOH A 67 467 67 HOH HOH . H 6 HOH A 68 468 68 HOH HOH . H 6 HOH A 69 469 69 HOH HOH . H 6 HOH A 70 470 70 HOH HOH . H 6 HOH A 71 471 71 HOH HOH . H 6 HOH A 72 472 72 HOH HOH . H 6 HOH A 73 473 73 HOH HOH . H 6 HOH A 74 474 74 HOH HOH . H 6 HOH A 75 475 75 HOH HOH . H 6 HOH A 76 476 76 HOH HOH . H 6 HOH A 77 477 77 HOH HOH . H 6 HOH A 78 478 78 HOH HOH . H 6 HOH A 79 479 79 HOH HOH . H 6 HOH A 80 480 80 HOH HOH . H 6 HOH A 81 481 81 HOH HOH . H 6 HOH A 82 482 82 HOH HOH . H 6 HOH A 83 483 83 HOH HOH . H 6 HOH A 84 484 84 HOH HOH . H 6 HOH A 85 485 85 HOH HOH . H 6 HOH A 86 486 86 HOH HOH . H 6 HOH A 87 487 87 HOH HOH . H 6 HOH A 88 488 88 HOH HOH . H 6 HOH A 89 489 89 HOH HOH . H 6 HOH A 90 490 90 HOH HOH . H 6 HOH A 91 491 91 HOH HOH . H 6 HOH A 92 492 92 HOH HOH . H 6 HOH A 93 493 93 HOH HOH . H 6 HOH A 94 494 94 HOH HOH . H 6 HOH A 95 495 95 HOH HOH . H 6 HOH A 96 496 96 HOH HOH . H 6 HOH A 97 497 97 HOH HOH . H 6 HOH A 98 498 98 HOH HOH . H 6 HOH A 99 499 99 HOH HOH . H 6 HOH A 100 500 100 HOH HOH . H 6 HOH A 101 501 101 HOH HOH . H 6 HOH A 102 502 102 HOH HOH . H 6 HOH A 103 503 103 HOH HOH . H 6 HOH A 104 504 104 HOH HOH . H 6 HOH A 105 505 105 HOH HOH . H 6 HOH A 106 506 106 HOH HOH . H 6 HOH A 107 507 107 HOH HOH . H 6 HOH A 108 508 108 HOH HOH . H 6 HOH A 109 509 109 HOH HOH . H 6 HOH A 110 510 110 HOH HOH . H 6 HOH A 111 511 111 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 C C 04J . . . C 3 19.856 -36.778 4.379 1 38.78 ? C 04J 301 A 1 HETATM 2 N N 04J . . . C 3 20.571 -35.725 4.008 1 42.39 ? N 04J 301 A 1 HETATM 3 O O 04J . . . C 3 20.461 -37.839 5.078 1 39.72 ? O 04J 301 A 1 HETATM 4 N N1 04J . . . C 3 14.076 -35.708 -3.012 1 27.08 ? N1 04J 301 A 1 HETATM 5 O O1 04J . . . C 3 23.581 -33.976 4.825 1 45.61 ? O1 04J 301 A 1 HETATM 6 C C2 04J . . . C 3 13.013 -35.278 -3.776 1 26.9 ? C2 04J 301 A 1 HETATM 7 O O2 04J . . . C 3 21.603 -33.757 5.639 1 40.46 ? O2 04J 301 A 1 HETATM 8 N N3 04J . . . C 3 11.799 -34.999 -3.184 1 29.88 ? N3 04J 301 A 1 HETATM 9 C C4 04J . . . C 3 11.63 -35.149 -1.821 1 30.34 ? C4 04J 301 A 1 HETATM 10 N N5 04J . . . C 3 12.543 -35.718 0.32 1 32.74 ? N5 04J 301 A 1 HETATM 11 C C6 04J . . . C 3 13.607 -36.146 1.092 1 33.46 ? C6 04J 301 A 1 HETATM 12 C C7 04J . . . C 3 14.825 -36.43 0.486 1 33.42 ? C7 04J 301 A 1 HETATM 13 N N8 04J . . . C 3 14.978 -36.28 -0.879 1 29.12 ? N8 04J 301 A 1 HETATM 14 C C9 04J . . . C 3 13.436 -36.302 2.587 1 36.37 ? C9 04J 301 A 1 HETATM 15 C CA 04J . . . C 3 21.994 -35.697 4.289 1 47.82 ? CA 04J 301 A 1 HETATM 16 C CB 04J . . . C 3 22.784 -35.93 3.001 1 54.38 ? CB 04J 301 A 1 HETATM 17 C CD 04J . . . C 3 23.295 -38.376 2.869 1 60.44 ? CD 04J 301 A 1 HETATM 18 C CG 04J . . . C 3 23.848 -37.008 3.193 1 61.76 ? CG 04J 301 A 1 HETATM 19 C CT 04J . . . C 3 22.416 -34.412 4.951 1 43.86 ? CT 04J 301 A 1 HETATM 20 N N10 04J . . . C 3 14.309 -37.332 3.121 1 38.63 ? N10 04J 301 A 1 HETATM 21 C C11 04J . . . C 3 18.394 -36.866 4.045 1 37.63 ? C11 04J 301 A 1 HETATM 22 C C12 04J . . . C 3 17.815 -38.127 3.967 1 36.48 ? C12 04J 301 A 1 HETATM 23 C C13 04J . . . C 3 16.466 -38.26 3.663 1 34.51 ? C13 04J 301 A 1 HETATM 24 C C14 04J . . . C 3 15.684 -37.135 3.427 1 34.76 ? C14 04J 301 A 1 HETATM 25 C C15 04J . . . C 3 16.258 -35.867 3.51 1 34.28 ? C15 04J 301 A 1 HETATM 26 C C16 04J . . . C 3 17.614 -35.73 3.817 1 35.23 ? C16 04J 301 A 1 HETATM 27 C C4A 04J . . . C 3 12.698 -35.575 -1.045 1 30.56 ? C4A 04J 301 A 1 HETATM 28 C C8A 04J . . . C 3 13.918 -35.855 -1.649 1 28.72 ? C8A 04J 301 A 1 HETATM 29 N NA2 04J . . . C 3 13.153 -35.135 -5.089 1 25.82 ? NA2 04J 301 A 1 HETATM 30 N NA4 04J . . . C 3 10.456 -34.88 -1.252 1 27.9 ? NA4 04J 301 A 1 HETATM 31 O OE1 04J . . . C 3 22.982 -38.668 1.695 1 60.13 ? OE1 04J 301 A 1 HETATM 32 O OE2 04J . . . C 3 23.141 -39.23 3.769 1 59.95 ? OE2 04J 301 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 346 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 32 #