# 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_spkb18604 # _entry.id spkb18604 # 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 "C3 H7 N O2" 89.093 ALA y ALANINE 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" "C3 H7 N O3" 105.093 SER y SERINE C([C@@H](C(=O)O)N)O ? "L-PEPTIDE LINKING" "C5 H11 N O2" 117.146 VAL y VALINE CC(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 LYS 2 1 n PHE 3 1 n SER 4 1 n LEU 5 1 n SER 6 1 n ALA 7 1 n ALA 8 1 n VAL 9 1 n LEU 10 1 n ALA 11 1 n PHE 12 1 n ALA 13 1 n VAL 14 1 n SER 15 1 n VAL 16 1 n ALA 17 1 n ALA 18 # _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 @ 2025-07-04 07:59:55)" _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 93.37 _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 84.62 1 1 A LYS 2 2 86.52 1 2 A PHE 3 2 88.92 1 3 A SER 4 2 94.25 1 4 A LEU 5 2 92.07 1 5 A SER 6 2 95.34 1 6 A ALA 7 2 96.63 1 7 A ALA 8 2 97.15 1 8 A VAL 9 2 96.74 1 9 A LEU 10 2 94.79 1 10 A ALA 11 2 96.50 1 11 A PHE 12 2 94.83 1 12 A ALA 13 2 97.18 1 13 A VAL 14 2 96.29 1 14 A SER 15 2 96.14 1 15 A VAL 16 2 96.25 1 16 A ALA 17 2 96.31 1 17 A ALA 18 2 90.30 1 18 # _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 LYS . 2 A 2 A 3 1 n PHE . 3 A 3 A 4 1 n SER . 4 A 4 A 5 1 n LEU . 5 A 5 A 6 1 n SER . 6 A 6 A 7 1 n ALA . 7 A 7 A 8 1 n ALA . 8 A 8 A 9 1 n VAL . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n ALA . 11 A 11 A 12 1 n PHE . 12 A 12 A 13 1 n ALA . 13 A 13 A 14 1 n VAL . 14 A 14 A 15 1 n SER . 15 A 15 A 16 1 n VAL . 16 A 16 A 17 1 n ALA . 17 A 17 A 18 1 n ALA . 18 A 18 # _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 ? -12.826 5.245 3.949 1.00 89.05 1 A 1 ATOM 2 C CA . MET A 1 1 ? -12.391 3.843 3.770 1.00 90.33 1 A 1 ATOM 3 C C . MET A 1 1 ? -10.994 3.618 4.336 1.00 91.62 1 A 1 ATOM 4 O O . MET A 1 1 ? -10.185 4.542 4.380 1.00 89.00 1 A 1 ATOM 5 C CB . MET A 1 1 ? -12.379 3.492 2.289 1.00 85.78 1 A 1 ATOM 6 C CG . MET A 1 1 ? -13.772 3.359 1.720 1.00 83.83 1 A 1 ATOM 7 S SD . MET A 1 1 ? -13.727 2.570 0.109 1.00 79.02 1 A 1 ATOM 8 C CE . MET A 1 1 ? -14.938 3.551 -0.751 1.00 68.29 1 A 1 ATOM 9 N N . LYS A 1 2 ? -10.727 2.399 4.743 1.00 92.56 2 A 1 ATOM 10 C CA . LYS A 1 2 ? -9.427 2.063 5.318 1.00 93.66 2 A 1 ATOM 11 C C . LYS A 1 2 ? -8.357 1.977 4.230 1.00 94.19 2 A 1 ATOM 12 O O . LYS A 1 2 ? -7.175 2.177 4.504 1.00 93.85 2 A 1 ATOM 13 C CB . LYS A 1 2 ? -9.541 0.737 6.064 1.00 90.52 2 A 1 ATOM 14 C CG . LYS A 1 2 ? -8.484 0.577 7.136 1.00 84.87 2 A 1 ATOM 15 C CD . LYS A 1 2 ? -8.860 1.347 8.396 1.00 82.80 2 A 1 ATOM 16 C CE . LYS A 1 2 ? -7.734 1.325 9.403 1.00 76.17 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? -8.063 0.469 10.564 1.00 70.09 2 A 1 ATOM 18 N N . PHE A 1 3 ? -8.767 1.662 3.002 1.00 91.99 3 A 1 ATOM 19 C CA . PHE A 1 3 ? -7.838 1.552 1.881 1.00 93.02 3 A 1 ATOM 20 C C . PHE A 1 3 ? -7.147 2.880 1.599 1.00 95.15 3 A 1 ATOM 21 O O . PHE A 1 3 ? -5.965 2.911 1.247 1.00 93.92 3 A 1 ATOM 22 C CB . PHE A 1 3 ? -8.592 1.088 0.640 1.00 91.70 3 A 1 ATOM 23 C CG . PHE A 1 3 ? -8.689 -0.417 0.558 1.00 89.05 3 A 1 ATOM 24 C CD1 . PHE A 1 3 ? -7.543 -1.177 0.399 1.00 86.17 3 A 1 ATOM 25 C CD2 . PHE A 1 3 ? -9.914 -1.053 0.632 1.00 85.62 3 A 1 ATOM 26 C CE1 . PHE A 1 3 ? -7.611 -2.558 0.321 1.00 84.05 3 A 1 ATOM 27 C CE2 . PHE A 1 3 ? -9.994 -2.438 0.556 1.00 84.43 3 A 1 ATOM 28 C CZ . PHE A 1 3 ? -8.840 -3.192 0.401 1.00 83.04 3 A 1 ATOM 29 N N . SER A 1 4 ? -7.876 3.967 1.761 1.00 95.60 4 A 1 ATOM 30 C CA . SER A 1 4 ? -7.314 5.298 1.538 1.00 96.23 4 A 1 ATOM 31 C C . SER A 1 4 ? -6.192 5.578 2.529 1.00 96.91 4 A 1 ATOM 32 O O . SER A 1 4 ? -5.167 6.161 2.181 1.00 96.14 4 A 1 ATOM 33 C CB . SER A 1 4 ? -8.400 6.364 1.670 1.00 94.97 4 A 1 ATOM 34 O OG . SER A 1 4 ? -8.894 6.721 0.396 1.00 85.63 4 A 1 ATOM 35 N N . LEU A 1 5 ? -6.396 5.148 3.769 1.00 94.43 5 A 1 ATOM 36 C CA . LEU A 1 5 ? -5.396 5.334 4.812 1.00 95.33 5 A 1 ATOM 37 C C . LEU A 1 5 ? -4.203 4.415 4.583 1.00 96.54 5 A 1 ATOM 38 O O . LEU A 1 5 ? -3.051 4.818 4.753 1.00 95.66 5 A 1 ATOM 39 C CB . LEU A 1 5 ? -6.017 5.056 6.183 1.00 94.07 5 A 1 ATOM 40 C CG . LEU A 1 5 ? -5.812 6.193 7.177 1.00 89.07 5 A 1 ATOM 41 C CD1 . LEU A 1 5 ? -6.919 7.223 7.038 1.00 86.15 5 A 1 ATOM 42 C CD2 . LEU A 1 5 ? -5.764 5.647 8.593 1.00 85.30 5 A 1 ATOM 43 N N . SER A 1 6 ? -4.486 3.186 4.188 1.00 96.49 6 A 1 ATOM 44 C CA . SER A 1 6 ? -3.445 2.195 3.933 1.00 96.89 6 A 1 ATOM 45 C C . SER A 1 6 ? -2.628 2.544 2.697 1.00 97.55 6 A 1 ATOM 46 O O . SER A 1 6 ? -1.507 2.069 2.528 1.00 97.11 6 A 1 ATOM 47 C CB . SER A 1 6 ? -4.071 0.816 3.762 1.00 95.93 6 A 1 ATOM 48 O OG . SER A 1 6 ? -4.209 0.183 5.018 1.00 88.06 6 A 1 ATOM 49 N N . ALA A 1 7 ? -3.196 3.372 1.832 1.00 96.37 7 A 1 ATOM 50 C CA . ALA A 1 7 ? -2.510 3.785 0.608 1.00 96.69 7 A 1 ATOM 51 C C . ALA A 1 7 ? -1.159 4.412 0.930 1.00 97.53 7 A 1 ATOM 52 O O . ALA A 1 7 ? -0.181 4.217 0.206 1.00 96.99 7 A 1 ATOM 53 C CB . ALA A 1 7 ? -3.377 4.775 -0.157 1.00 95.58 7 A 1 ATOM 54 N N . ALA A 1 8 ? -1.107 5.155 2.019 1.00 96.99 8 A 1 ATOM 55 C CA . ALA A 1 8 ? 0.131 5.799 2.444 1.00 97.17 8 A 1 ATOM 56 C C . ALA A 1 8 ? 1.165 4.761 2.863 1.00 97.86 8 A 1 ATOM 57 O O . ALA A 1 8 ? 2.354 4.898 2.574 1.00 97.26 8 A 1 ATOM 58 C CB . ALA A 1 8 ? -0.157 6.750 3.599 1.00 96.46 8 A 1 ATOM 59 N N . VAL A 1 9 ? 0.698 3.719 3.535 1.00 97.03 9 A 1 ATOM 60 C CA . VAL A 1 9 ? 1.574 2.640 3.988 1.00 97.54 9 A 1 ATOM 61 C C . VAL A 1 9 ? 2.089 1.844 2.796 1.00 97.96 9 A 1 ATOM 62 O O . VAL A 1 9 ? 3.241 1.408 2.775 1.00 97.56 9 A 1 ATOM 63 C CB . VAL A 1 9 ? 0.831 1.704 4.954 1.00 97.10 9 A 1 ATOM 64 C CG1 . VAL A 1 9 ? 1.768 0.618 5.465 1.00 95.27 9 A 1 ATOM 65 C CG2 . VAL A 1 9 ? 0.251 2.493 6.117 1.00 94.75 9 A 1 ATOM 66 N N . LEU A 1 10 ? 1.220 1.652 1.810 1.00 97.10 10 A 1 ATOM 67 C CA . LEU A 1 10 ? 1.586 0.908 0.608 1.00 96.82 10 A 1 ATOM 68 C C . LEU A 1 10 ? 2.673 1.648 -0.164 1.00 97.39 10 A 1 ATOM 69 O O . LEU A 1 10 ? 3.636 1.048 -0.636 1.00 97.28 10 A 1 ATOM 70 C CB . LEU A 1 10 ? 0.352 0.710 -0.273 1.00 96.30 10 A 1 ATOM 71 C CG . LEU A 1 10 ? 0.358 -0.619 -1.030 1.00 91.85 10 A 1 ATOM 72 C CD1 . LEU A 1 10 ? 0.070 -1.770 -0.079 1.00 90.50 10 A 1 ATOM 73 C CD2 . LEU A 1 10 ? -0.651 -0.595 -2.161 1.00 91.09 10 A 1 ATOM 74 N N . ALA A 1 11 ? 2.499 2.943 -0.292 1.00 96.70 11 A 1 ATOM 75 C CA . ALA A 1 11 ? 3.471 3.773 -0.998 1.00 96.46 11 A 1 ATOM 76 C C . ALA A 1 11 ? 4.816 3.762 -0.276 1.00 97.30 11 A 1 ATOM 77 O O . ALA A 1 11 ? 5.875 3.771 -0.906 1.00 96.63 11 A 1 ATOM 78 C CB . ALA A 1 11 ? 2.943 5.197 -1.108 1.00 95.39 11 A 1 ATOM 79 N N . PHE A 1 12 ? 4.753 3.747 1.038 1.00 96.87 12 A 1 ATOM 80 C CA . PHE A 1 12 ? 5.968 3.717 1.850 1.00 96.80 12 A 1 ATOM 81 C C . PHE A 1 12 ? 6.720 2.406 1.646 1.00 97.46 12 A 1 ATOM 82 O O . PHE A 1 12 ? 7.947 2.395 1.516 1.00 97.11 12 A 1 ATOM 83 C CB . PHE A 1 12 ? 5.602 3.882 3.326 1.00 96.38 12 A 1 ATOM 84 C CG . PHE A 1 12 ? 6.803 3.779 4.236 1.00 95.03 12 A 1 ATOM 85 C CD1 . PHE A 1 12 ? 7.736 4.804 4.285 1.00 93.19 12 A 1 ATOM 86 C CD2 . PHE A 1 12 ? 6.990 2.663 5.035 1.00 93.64 12 A 1 ATOM 87 C CE1 . PHE A 1 12 ? 8.846 4.722 5.116 1.00 92.26 12 A 1 ATOM 88 C CE2 . PHE A 1 12 ? 8.102 2.568 5.873 1.00 92.24 12 A 1 ATOM 89 C CZ . PHE A 1 12 ? 9.031 3.598 5.912 1.00 92.18 12 A 1 ATOM 90 N N . ALA A 1 13 ? 5.966 1.307 1.627 1.00 97.19 13 A 1 ATOM 91 C CA . ALA A 1 13 ? 6.562 -0.014 1.440 1.00 97.24 13 A 1 ATOM 92 C C . ALA A 1 13 ? 7.264 -0.105 0.087 1.00 97.69 13 A 1 ATOM 93 O O . ALA A 1 13 ? 8.339 -0.695 -0.027 1.00 97.07 13 A 1 ATOM 94 C CB . ALA A 1 13 ? 5.480 -1.086 1.546 1.00 96.69 13 A 1 ATOM 95 N N . VAL A 1 14 ? 6.650 0.471 -0.930 1.00 97.68 14 A 1 ATOM 96 C CA . VAL A 1 14 ? 7.221 0.459 -2.278 1.00 97.46 14 A 1 ATOM 97 C C . VAL A 1 14 ? 8.511 1.272 -2.314 1.00 97.82 14 A 1 ATOM 98 O O . VAL A 1 14 ? 9.487 0.888 -2.966 1.00 97.13 14 A 1 ATOM 99 C CB . VAL A 1 14 ? 6.214 1.019 -3.293 1.00 96.57 14 A 1 ATOM 100 C CG1 . VAL A 1 14 ? 6.839 1.087 -4.681 1.00 93.43 14 A 1 ATOM 101 C CG2 . VAL A 1 14 ? 4.963 0.152 -3.327 1.00 93.95 14 A 1 ATOM 102 N N . SER A 1 15 ? 8.511 2.380 -1.624 1.00 97.99 15 A 1 ATOM 103 C CA . SER A 1 15 ? 9.682 3.252 -1.570 1.00 97.94 15 A 1 ATOM 104 C C . SER A 1 15 ? 10.844 2.570 -0.848 1.00 98.18 15 A 1 ATOM 105 O O . SER A 1 15 ? 12.003 2.709 -1.247 1.00 97.48 15 A 1 ATOM 106 C CB . SER A 1 15 ? 9.325 4.558 -0.864 1.00 97.23 15 A 1 ATOM 107 O OG . SER A 1 15 ? 10.313 5.535 -1.097 1.00 88.00 15 A 1 ATOM 108 N N . VAL A 1 16 ? 10.523 1.846 0.206 1.00 97.90 16 A 1 ATOM 109 C CA . VAL A 1 16 ? 11.539 1.132 0.987 1.00 97.68 16 A 1 ATOM 110 C C . VAL A 1 16 ? 12.076 -0.067 0.218 1.00 97.90 16 A 1 ATOM 111 O O . VAL A 1 16 ? 13.279 -0.355 0.256 1.00 97.35 16 A 1 ATOM 112 C CB . VAL A 1 16 ? 10.958 0.665 2.335 1.00 96.63 16 A 1 ATOM 113 C CG1 . VAL A 1 16 ? 11.990 -0.152 3.105 1.00 93.05 16 A 1 ATOM 114 C CG2 . VAL A 1 16 ? 10.519 1.853 3.170 1.00 93.23 16 A 1 ATOM 115 N N . ALA A 1 17 ? 11.180 -0.776 -0.462 1.00 97.04 17 A 1 ATOM 116 C CA . ALA A 1 17 ? 11.561 -1.961 -1.231 1.00 96.62 17 A 1 ATOM 117 C C . ALA A 1 17 ? 12.226 -1.588 -2.552 1.00 96.86 17 A 1 ATOM 118 O O . ALA A 1 17 ? 13.004 -2.367 -3.106 1.00 95.75 17 A 1 ATOM 119 C CB . ALA A 1 17 ? 10.329 -2.831 -1.487 1.00 95.27 17 A 1 ATOM 120 N N . ALA A 1 18 ? 11.912 -0.410 -3.074 1.00 95.84 18 A 1 ATOM 121 C CA . ALA A 1 18 ? 12.442 0.052 -4.349 1.00 94.23 18 A 1 ATOM 122 C C . ALA A 1 18 ? 13.966 0.163 -4.308 1.00 91.79 18 A 1 ATOM 123 O O . ALA A 1 18 ? 14.513 0.554 -3.272 1.00 87.63 18 A 1 ATOM 124 C CB . ALA A 1 18 ? 11.823 1.389 -4.725 1.00 90.80 18 A 1 ATOM 125 O OXT . ALA A 1 18 ? 14.607 -0.117 -5.336 1.00 81.50 18 A 1 #