# By using this file you agree to the legally binding terms of use found at # https://github.com/google-deepmind/alphafold3/blob/main/OUTPUT_TERMS_OF_USE.md. # To request access to the AlphaFold 3 model parameters, follow the process set # out at https://github.com/google-deepmind/alphafold3. You may only use these if # received directly from Google. Use is subject to terms of use available at # https://github.com/google-deepmind/alphafold3/blob/main/WEIGHTS_TERMS_OF_USE.md. data_spkb11572 # _entry.id spkb11572 # loop_ _atom_type.symbol C N O S # loop_ _audit_author.name _audit_author.pdbx_ordinal "Google DeepMind" 1 "Isomorphic Labs" 2 # _audit_conform.dict_location https://raw.githubusercontent.com/ihmwg/ModelCIF/master/dist/mmcif_ma.dic _audit_conform.dict_name mmcif_ma.dic _audit_conform.dict_version 1.4.5 # loop_ _chem_comp.formula _chem_comp.formula_weight _chem_comp.id _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_smiles _chem_comp.pdbx_synonyms _chem_comp.type "C6 H15 N4 O2" 175.209 ARG y ARGININE C(C[C@@H](C(=O)O)N)CNC(=[NH2+])N ? "L-PEPTIDE LINKING" "C3 H7 N O2 S" 121.158 CYS y CYSTEINE C([C@@H](C(=O)O)N)S ? "L-PEPTIDE LINKING" "C6 H13 N O2" 131.173 ILE y ISOLEUCINE CC[C@H](C)[C@@H](C(=O)O)N ? "L-PEPTIDE LINKING" "C6 H13 N O2" 131.173 LEU y LEUCINE CC(C)C[C@@H](C(=O)O)N ? "L-PEPTIDE LINKING" "C6 H15 N2 O2" 147.195 LYS y LYSINE C(CC[NH3+])C[C@@H](C(=O)O)N ? "L-PEPTIDE LINKING" "C5 H11 N O2 S" 149.211 MET y METHIONINE CSCC[C@@H](C(=O)O)N ? "L-PEPTIDE LINKING" "C9 H11 N O2" 165.189 PHE y PHENYLALANINE c1ccc(cc1)C[C@@H](C(=O)O)N ? "L-PEPTIDE LINKING" # _citation.book_publisher ? _citation.country UK _citation.id primary _citation.journal_full Nature _citation.journal_id_ASTM NATUAS _citation.journal_id_CSD 0006 _citation.journal_id_ISSN 0028-0836 _citation.journal_volume 630 _citation.page_first 493 _citation.page_last 500 _citation.pdbx_database_id_DOI 10.1038/s41586-024-07487-w _citation.pdbx_database_id_PubMed 38718835 _citation.title "Accurate structure prediction of biomolecular interactions with AlphaFold 3" _citation.year 2024 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary "Google DeepMind" 1 primary "Isomorphic Labs" 2 # _entity.id 1 _entity.pdbx_description . _entity.type polymer # _entity_poly.entity_id 1 _entity_poly.pdbx_strand_id A _entity_poly.type polypeptide(L) # loop_ _entity_poly_seq.entity_id _entity_poly_seq.hetero _entity_poly_seq.mon_id _entity_poly_seq.num 1 n MET 1 1 n ARG 2 1 n LYS 3 1 n MET 4 1 n LEU 5 1 n LEU 6 1 n PHE 7 1 n CYS 8 1 n ILE 9 1 n LEU 10 1 n LEU 11 1 n LEU 12 1 n PHE 13 # _ma_data.content_type "model coordinates" _ma_data.id 1 _ma_data.name Model # _ma_model_list.data_id 1 _ma_model_list.model_group_id 1 _ma_model_list.model_group_name "AlphaFold-beta-20231127 (3.0.0 @ 2025-07-06 12:28:12)" _ma_model_list.model_id 1 _ma_model_list.model_name "Top ranked model" _ma_model_list.model_type "Ab initio model" _ma_model_list.ordinal_id 1 # loop_ _ma_protocol_step.method_type _ma_protocol_step.ordinal_id _ma_protocol_step.protocol_id _ma_protocol_step.step_id "coevolution MSA" 1 1 1 "template search" 2 1 2 modeling 3 1 3 # loop_ _ma_qa_metric.id _ma_qa_metric.mode _ma_qa_metric.name _ma_qa_metric.software_group_id _ma_qa_metric.type 1 global pLDDT 1 pLDDT 2 local pLDDT 1 pLDDT # _ma_qa_metric_global.metric_id 1 _ma_qa_metric_global.metric_value 91.30 _ma_qa_metric_global.model_id 1 _ma_qa_metric_global.ordinal_id 1 # loop_ _ma_qa_metric_local.label_asym_id _ma_qa_metric_local.label_comp_id _ma_qa_metric_local.label_seq_id _ma_qa_metric_local.metric_id _ma_qa_metric_local.metric_value _ma_qa_metric_local.model_id _ma_qa_metric_local.ordinal_id A MET 1 2 88.05 1 1 A ARG 2 2 82.63 1 2 A LYS 3 2 86.59 1 3 A MET 4 2 90.50 1 4 A LEU 5 2 92.20 1 5 A LEU 6 2 93.07 1 6 A PHE 7 2 92.04 1 7 A CYS 8 2 94.84 1 8 A ILE 9 2 94.26 1 9 A LEU 10 2 94.80 1 10 A LEU 11 2 94.89 1 11 A LEU 12 2 94.12 1 12 A PHE 13 2 92.70 1 13 # _ma_software_group.group_id 1 _ma_software_group.ordinal_id 1 _ma_software_group.software_id 1 # _ma_target_entity.data_id 1 _ma_target_entity.entity_id 1 _ma_target_entity.origin . # _ma_target_entity_instance.asym_id A _ma_target_entity_instance.details . _ma_target_entity_instance.entity_id 1 # loop_ _pdbx_data_usage.details _pdbx_data_usage.id _pdbx_data_usage.type _pdbx_data_usage.url ;Non-commercial use only, by using this file you agree to the terms of use found at https://github.com/google-deepmind/alphafold3/blob/main/OUTPUT_TERMS_OF_USE.md. To request access to the AlphaFold 3 model parameters, follow the process set out at https://github.com/google-deepmind/alphafold3. You may only use these if received directly from Google. Use is subject to terms of use available at https://github.com/google-deepmind/alphafold3/blob/main/WEIGHTS_TERMS_OF_USE.md. ; 1 license https://github.com/google-deepmind/alphafold3/blob/main/OUTPUT_TERMS_OF_USE.md ;AlphaFold 3 and its output are not intended for, have not been validated for, and are not approved for clinical use. They are provided "as-is" without any warranty of any kind, whether expressed or implied. No warranty is given that use shall not infringe the rights of any third party. ; 2 disclaimer ? # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.hetero _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.seq_id A 1 1 n MET . 1 A 1 A 2 1 n ARG . 2 A 2 A 3 1 n LYS . 3 A 3 A 4 1 n MET . 4 A 4 A 5 1 n LEU . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n PHE . 7 A 7 A 8 1 n CYS . 8 A 8 A 9 1 n ILE . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n LEU . 11 A 11 A 12 1 n LEU . 12 A 12 A 13 1 n PHE . 13 A 13 # _software.classification other _software.date ? _software.description "Structure prediction" _software.name AlphaFold _software.pdbx_ordinal 1 _software.type package _software.version "AlphaFold-beta-20231127 (9ceee3b5f7825b611ab42eaad843248507ced2da1e745fa3b3d93c6c4ad3ca74)" # _struct_asym.entity_id 1 _struct_asym.id A # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_alt_id _atom_site.label_comp_id _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.label_seq_id _atom_site.pdbx_PDB_ins_code _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num ATOM 1 N N . MET A 1 1 ? -7.858 8.958 -2.200 1.00 91.54 1 A 1 ATOM 2 C CA . MET A 1 1 ? -7.128 8.621 -0.985 1.00 93.60 1 A 1 ATOM 3 C C . MET A 1 1 ? -6.527 7.217 -1.044 1.00 94.20 1 A 1 ATOM 4 O O . MET A 1 1 ? -6.558 6.473 -0.071 1.00 91.85 1 A 1 ATOM 5 C CB . MET A 1 1 ? -8.050 8.730 0.229 1.00 91.79 1 A 1 ATOM 6 C CG . MET A 1 1 ? -8.642 10.123 0.405 1.00 84.71 1 A 1 ATOM 7 S SD . MET A 1 1 ? -7.375 11.359 0.624 1.00 82.08 1 A 1 ATOM 8 C CE . MET A 1 1 ? -8.378 12.811 0.871 1.00 74.66 1 A 1 ATOM 9 N N . ARG A 1 2 ? -5.980 6.870 -2.200 1.00 90.72 2 A 1 ATOM 10 C CA . ARG A 1 2 ? -5.375 5.555 -2.388 1.00 92.84 2 A 1 ATOM 11 C C . ARG A 1 2 ? -4.009 5.475 -1.715 1.00 93.94 2 A 1 ATOM 12 O O . ARG A 1 2 ? -3.449 4.392 -1.579 1.00 91.24 2 A 1 ATOM 13 C CB . ARG A 1 2 ? -5.232 5.235 -3.885 1.00 90.76 2 A 1 ATOM 14 C CG . ARG A 1 2 ? -6.552 4.954 -4.587 1.00 83.37 2 A 1 ATOM 15 C CD . ARG A 1 2 ? -7.238 6.226 -5.044 1.00 82.49 2 A 1 ATOM 16 N NE . ARG A 1 2 ? -6.494 6.902 -6.112 1.00 76.79 2 A 1 ATOM 17 C CZ . ARG A 1 2 ? -6.675 6.684 -7.410 1.00 73.52 2 A 1 ATOM 18 N NH1 . ARG A 1 2 ? -7.565 5.810 -7.833 1.00 68.66 2 A 1 ATOM 19 N NH2 . ARG A 1 2 ? -5.958 7.351 -8.301 1.00 64.61 2 A 1 ATOM 20 N N . LYS A 1 3 ? -3.489 6.614 -1.302 1.00 91.67 3 A 1 ATOM 21 C CA . LYS A 1 3 ? -2.177 6.677 -0.669 1.00 91.88 3 A 1 ATOM 22 C C . LYS A 1 3 ? -2.154 5.944 0.668 1.00 93.50 3 A 1 ATOM 23 O O . LYS A 1 3 ? -1.095 5.522 1.121 1.00 91.46 3 A 1 ATOM 24 C CB . LYS A 1 3 ? -1.756 8.136 -0.470 1.00 89.97 3 A 1 ATOM 25 C CG . LYS A 1 3 ? -1.667 8.930 -1.768 1.00 85.43 3 A 1 ATOM 26 C CD . LYS A 1 3 ? -0.602 8.374 -2.697 1.00 83.52 3 A 1 ATOM 27 C CE . LYS A 1 3 ? -0.486 9.173 -3.982 1.00 79.32 3 A 1 ATOM 28 N NZ . LYS A 1 3 ? 0.572 8.621 -4.858 1.00 72.58 3 A 1 ATOM 29 N N . MET A 1 4 ? -3.321 5.816 1.263 1.00 94.26 4 A 1 ATOM 30 C CA . MET A 1 4 ? -3.437 5.099 2.528 1.00 95.07 4 A 1 ATOM 31 C C . MET A 1 4 ? -3.034 3.639 2.353 1.00 96.01 4 A 1 ATOM 32 O O . MET A 1 4 ? -2.395 3.050 3.219 1.00 94.22 4 A 1 ATOM 33 C CB . MET A 1 4 ? -4.872 5.182 3.056 1.00 94.04 4 A 1 ATOM 34 C CG . MET A 1 4 ? -5.292 6.595 3.432 1.00 89.33 4 A 1 ATOM 35 S SD . MET A 1 4 ? -4.301 7.249 4.772 1.00 84.30 4 A 1 ATOM 36 C CE . MET A 1 4 ? -5.144 8.801 5.070 1.00 76.81 4 A 1 ATOM 37 N N . LEU A 1 5 ? -3.400 3.086 1.208 1.00 94.15 5 A 1 ATOM 38 C CA . LEU A 1 5 ? -3.060 1.707 0.891 1.00 94.78 5 A 1 ATOM 39 C C . LEU A 1 5 ? -1.555 1.584 0.695 1.00 95.54 5 A 1 ATOM 40 O O . LEU A 1 5 ? -0.930 0.636 1.172 1.00 94.46 5 A 1 ATOM 41 C CB . LEU A 1 5 ? -3.830 1.271 -0.359 1.00 94.45 5 A 1 ATOM 42 C CG . LEU A 1 5 ? -4.104 -0.226 -0.422 1.00 89.66 5 A 1 ATOM 43 C CD1 . LEU A 1 5 ? -5.227 -0.517 -1.393 1.00 86.84 5 A 1 ATOM 44 C CD2 . LEU A 1 5 ? -2.858 -0.984 -0.840 1.00 87.71 5 A 1 ATOM 45 N N . LEU A 1 6 ? -0.983 2.548 0.008 1.00 95.35 6 A 1 ATOM 46 C CA . LEU A 1 6 ? 0.457 2.594 -0.216 1.00 95.68 6 A 1 ATOM 47 C C . LEU A 1 6 ? 1.209 2.698 1.104 1.00 96.18 6 A 1 ATOM 48 O O . LEU A 1 6 ? 2.271 2.097 1.268 1.00 95.68 6 A 1 ATOM 49 C CB . LEU A 1 6 ? 0.801 3.788 -1.106 1.00 95.32 6 A 1 ATOM 50 C CG . LEU A 1 6 ? 2.274 3.858 -1.501 1.00 89.01 6 A 1 ATOM 51 C CD1 . LEU A 1 6 ? 2.639 2.705 -2.422 1.00 87.90 6 A 1 ATOM 52 C CD2 . LEU A 1 6 ? 2.577 5.179 -2.171 1.00 89.45 6 A 1 ATOM 53 N N . PHE A 1 7 ? 0.652 3.447 2.015 1.00 95.26 7 A 1 ATOM 54 C CA . PHE A 1 7 ? 1.231 3.610 3.343 1.00 95.38 7 A 1 ATOM 55 C C . PHE A 1 7 ? 1.328 2.268 4.059 1.00 95.81 7 A 1 ATOM 56 O O . PHE A 1 7 ? 2.331 1.967 4.700 1.00 94.67 7 A 1 ATOM 57 C CB . PHE A 1 7 ? 0.380 4.589 4.155 1.00 94.75 7 A 1 ATOM 58 C CG . PHE A 1 7 ? 0.849 4.755 5.575 1.00 92.30 7 A 1 ATOM 59 C CD1 . PHE A 1 7 ? 2.062 5.365 5.858 1.00 89.78 7 A 1 ATOM 60 C CD2 . PHE A 1 7 ? 0.073 4.300 6.625 1.00 90.30 7 A 1 ATOM 61 C CE1 . PHE A 1 7 ? 2.491 5.514 7.167 1.00 88.83 7 A 1 ATOM 62 C CE2 . PHE A 1 7 ? 0.499 4.449 7.940 1.00 87.79 7 A 1 ATOM 63 C CZ . PHE A 1 7 ? 1.710 5.056 8.207 1.00 87.53 7 A 1 ATOM 64 N N . CYS A 1 8 ? 0.288 1.475 3.920 1.00 95.71 8 A 1 ATOM 65 C CA . CYS A 1 8 ? 0.254 0.157 4.533 1.00 95.75 8 A 1 ATOM 66 C C . CYS A 1 8 ? 1.306 -0.758 3.910 1.00 96.21 8 A 1 ATOM 67 O O . CYS A 1 8 ? 2.005 -1.485 4.612 1.00 95.16 8 A 1 ATOM 68 C CB . CYS A 1 8 ? -1.138 -0.461 4.383 1.00 95.18 8 A 1 ATOM 69 S SG . CYS A 1 8 ? -1.363 -1.862 5.493 1.00 91.03 8 A 1 ATOM 70 N N . ILE A 1 9 ? 1.423 -0.700 2.595 1.00 95.67 9 A 1 ATOM 71 C CA . ILE A 1 9 ? 2.411 -1.492 1.866 1.00 95.65 9 A 1 ATOM 72 C C . ILE A 1 9 ? 3.822 -1.060 2.237 1.00 96.14 9 A 1 ATOM 73 O O . ILE A 1 9 ? 4.725 -1.889 2.350 1.00 95.25 9 A 1 ATOM 74 C CB . ILE A 1 9 ? 2.199 -1.362 0.351 1.00 95.37 9 A 1 ATOM 75 C CG1 . ILE A 1 9 ? 0.838 -1.936 -0.038 1.00 93.43 9 A 1 ATOM 76 C CG2 . ILE A 1 9 ? 3.305 -2.073 -0.413 1.00 93.24 9 A 1 ATOM 77 C CD1 . ILE A 1 9 ? 0.409 -1.564 -1.434 1.00 89.32 9 A 1 ATOM 78 N N . LEU A 1 10 ? 3.994 0.223 2.417 1.00 96.38 10 A 1 ATOM 79 C CA . LEU A 1 10 ? 5.288 0.785 2.788 1.00 96.24 10 A 1 ATOM 80 C C . LEU A 1 10 ? 5.760 0.213 4.119 1.00 96.53 10 A 1 ATOM 81 O O . LEU A 1 10 ? 6.939 -0.101 4.286 1.00 95.75 10 A 1 ATOM 82 C CB . LEU A 1 10 ? 5.185 2.311 2.852 1.00 95.88 10 A 1 ATOM 83 C CG . LEU A 1 10 ? 6.519 3.030 3.059 1.00 93.46 10 A 1 ATOM 84 C CD1 . LEU A 1 10 ? 6.484 4.389 2.386 1.00 91.81 10 A 1 ATOM 85 C CD2 . LEU A 1 10 ? 6.844 3.204 4.529 1.00 92.37 10 A 1 ATOM 86 N N . LEU A 1 11 ? 4.843 0.064 5.050 1.00 96.61 11 A 1 ATOM 87 C CA . LEU A 1 11 ? 5.155 -0.510 6.353 1.00 96.46 11 A 1 ATOM 88 C C . LEU A 1 11 ? 5.473 -1.989 6.229 1.00 96.62 11 A 1 ATOM 89 O O . LEU A 1 11 ? 6.307 -2.515 6.965 1.00 95.61 11 A 1 ATOM 90 C CB . LEU A 1 11 ? 3.971 -0.320 7.301 1.00 95.97 11 A 1 ATOM 91 C CG . LEU A 1 11 ? 3.719 1.127 7.698 1.00 93.93 11 A 1 ATOM 92 C CD1 . LEU A 1 11 ? 2.340 1.255 8.331 1.00 92.00 11 A 1 ATOM 93 C CD2 . LEU A 1 11 ? 4.780 1.612 8.676 1.00 91.90 11 A 1 ATOM 94 N N . LEU A 1 12 ? 4.798 -2.643 5.316 1.00 96.32 12 A 1 ATOM 95 C CA . LEU A 1 12 ? 5.006 -4.062 5.069 1.00 96.30 12 A 1 ATOM 96 C C . LEU A 1 12 ? 6.376 -4.309 4.454 1.00 96.54 12 A 1 ATOM 97 O O . LEU A 1 12 ? 7.063 -5.264 4.819 1.00 95.54 12 A 1 ATOM 98 C CB . LEU A 1 12 ? 3.909 -4.587 4.143 1.00 95.59 12 A 1 ATOM 99 C CG . LEU A 1 12 ? 4.055 -6.058 3.757 1.00 93.04 12 A 1 ATOM 100 C CD1 . LEU A 1 12 ? 3.863 -6.953 4.977 1.00 90.03 12 A 1 ATOM 101 C CD2 . LEU A 1 12 ? 3.056 -6.415 2.678 1.00 89.63 12 A 1 ATOM 102 N N . PHE A 1 13 ? 6.731 -3.471 3.510 1.00 96.78 13 A 1 ATOM 103 C CA . PHE A 1 13 ? 7.998 -3.566 2.800 1.00 96.24 13 A 1 ATOM 104 C C . PHE A 1 13 ? 9.163 -3.300 3.745 1.00 95.67 13 A 1 ATOM 105 O O . PHE A 1 13 ? 10.076 -4.141 3.821 1.00 93.03 13 A 1 ATOM 106 C CB . PHE A 1 13 ? 8.023 -2.570 1.638 1.00 94.94 13 A 1 ATOM 107 C CG . PHE A 1 13 ? 9.178 -2.789 0.710 1.00 93.81 13 A 1 ATOM 108 C CD1 . PHE A 1 13 ? 10.414 -2.200 0.950 1.00 91.33 13 A 1 ATOM 109 C CD2 . PHE A 1 13 ? 9.039 -3.601 -0.400 1.00 90.88 13 A 1 ATOM 110 C CE1 . PHE A 1 13 ? 11.487 -2.406 0.104 1.00 90.59 13 A 1 ATOM 111 C CE2 . PHE A 1 13 ? 10.110 -3.810 -1.256 1.00 91.68 13 A 1 ATOM 112 C CZ . PHE A 1 13 ? 11.332 -3.213 -1.002 1.00 90.78 13 A 1 ATOM 113 O OXT . PHE A 1 13 ? 9.164 -2.256 4.382 1.00 86.69 13 A 1 #