# 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_spkb28767 # _entry.id spkb28767 # 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 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" "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 LEU 2 1 n LYS 3 1 n SER 4 1 n PHE 5 1 n VAL 6 1 n ILE 7 1 n LEU 8 1 n PHE 9 1 n ALA 10 1 n PHE 11 1 n LEU 12 1 n ALA 13 1 n SER 14 1 n ALA 15 1 n SER 16 1 n ALA 17 # _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 @ 2025-07-03 00:43:14)" _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 92.80 _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 84.54 1 1 A LEU 2 2 91.50 1 2 A LYS 3 2 90.27 1 3 A SER 4 2 95.49 1 4 A PHE 5 2 91.85 1 5 A VAL 6 2 96.96 1 6 A ILE 7 2 96.07 1 7 A LEU 8 2 94.37 1 8 A PHE 9 2 93.22 1 9 A ALA 10 2 97.67 1 10 A PHE 11 2 93.72 1 11 A LEU 12 2 94.56 1 12 A ALA 13 2 97.55 1 13 A SER 14 2 94.53 1 14 A ALA 15 2 95.69 1 15 A SER 16 2 89.41 1 16 A ALA 17 2 83.55 1 17 # _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 LEU . 2 A 2 A 3 1 n LYS . 3 A 3 A 4 1 n SER . 4 A 4 A 5 1 n PHE . 5 A 5 A 6 1 n VAL . 6 A 6 A 7 1 n ILE . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n PHE . 9 A 9 A 10 1 n ALA . 10 A 10 A 11 1 n PHE . 11 A 11 A 12 1 n LEU . 12 A 12 A 13 1 n ALA . 13 A 13 A 14 1 n SER . 14 A 14 A 15 1 n ALA . 15 A 15 A 16 1 n SER . 16 A 16 A 17 1 n ALA . 17 A 17 # _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 ? -9.525 -1.351 9.487 1.00 90.26 1 A 1 ATOM 2 C CA . MET A 1 1 ? -9.147 -1.216 8.072 1.00 91.87 1 A 1 ATOM 3 C C . MET A 1 1 ? -7.665 -0.853 7.927 1.00 93.00 1 A 1 ATOM 4 O O . MET A 1 1 ? -7.328 0.300 7.654 1.00 90.43 1 A 1 ATOM 5 C CB . MET A 1 1 ? -10.023 -0.166 7.393 1.00 85.04 1 A 1 ATOM 6 C CG . MET A 1 1 ? -10.236 1.087 8.228 1.00 79.72 1 A 1 ATOM 7 S SD . MET A 1 1 ? -11.615 2.049 7.610 1.00 77.37 1 A 1 ATOM 8 C CE . MET A 1 1 ? -11.707 3.328 8.845 1.00 68.66 1 A 1 ATOM 9 N N . LEU A 1 2 ? -6.806 -1.836 8.110 1.00 94.14 2 A 1 ATOM 10 C CA . LEU A 1 2 ? -5.364 -1.632 8.008 1.00 96.08 2 A 1 ATOM 11 C C . LEU A 1 2 ? -4.818 -2.101 6.663 1.00 97.09 2 A 1 ATOM 12 O O . LEU A 1 2 ? -3.728 -1.693 6.257 1.00 95.90 2 A 1 ATOM 13 C CB . LEU A 1 2 ? -4.667 -2.367 9.148 1.00 94.58 2 A 1 ATOM 14 C CG . LEU A 1 2 ? -4.391 -1.489 10.360 1.00 88.06 2 A 1 ATOM 15 C CD1 . LEU A 1 2 ? -5.531 -1.572 11.360 1.00 84.46 2 A 1 ATOM 16 C CD2 . LEU A 1 2 ? -3.078 -1.895 11.008 1.00 81.69 2 A 1 ATOM 17 N N . LYS A 1 3 ? -5.592 -2.955 5.986 1.00 97.11 3 A 1 ATOM 18 C CA . LYS A 1 3 ? -5.182 -3.490 4.688 1.00 97.18 3 A 1 ATOM 19 C C . LYS A 1 3 ? -4.987 -2.366 3.674 1.00 97.40 3 A 1 ATOM 20 O O . LYS A 1 3 ? -3.993 -2.347 2.950 1.00 96.95 3 A 1 ATOM 21 C CB . LYS A 1 3 ? -6.231 -4.489 4.194 1.00 96.18 3 A 1 ATOM 22 C CG . LYS A 1 3 ? -5.738 -5.358 3.054 1.00 89.90 3 A 1 ATOM 23 C CD . LYS A 1 3 ? -5.098 -6.634 3.578 1.00 85.66 3 A 1 ATOM 24 C CE . LYS A 1 3 ? -4.791 -7.596 2.449 1.00 79.57 3 A 1 ATOM 25 N NZ . LYS A 1 3 ? -4.161 -8.840 2.964 1.00 72.48 3 A 1 ATOM 26 N N . SER A 1 4 ? -5.929 -1.444 3.630 1.00 96.67 4 A 1 ATOM 27 C CA . SER A 1 4 ? -5.859 -0.314 2.709 1.00 97.27 4 A 1 ATOM 28 C C . SER A 1 4 ? -4.701 0.615 3.068 1.00 97.65 4 A 1 ATOM 29 O O . SER A 1 4 ? -4.050 1.180 2.193 1.00 96.74 4 A 1 ATOM 30 C CB . SER A 1 4 ? -7.175 0.461 2.721 1.00 96.36 4 A 1 ATOM 31 O OG . SER A 1 4 ? -7.983 0.112 1.623 1.00 88.26 4 A 1 ATOM 32 N N . PHE A 1 5 ? -4.440 0.750 4.354 1.00 95.50 5 A 1 ATOM 33 C CA . PHE A 1 5 ? -3.350 1.594 4.829 1.00 95.69 5 A 1 ATOM 34 C C . PHE A 1 5 ? -1.997 1.018 4.433 1.00 96.81 5 A 1 ATOM 35 O O . PHE A 1 5 ? -1.081 1.760 4.073 1.00 96.08 5 A 1 ATOM 36 C CB . PHE A 1 5 ? -3.432 1.740 6.348 1.00 95.03 5 A 1 ATOM 37 C CG . PHE A 1 5 ? -4.205 2.966 6.774 1.00 92.26 5 A 1 ATOM 38 C CD1 . PHE A 1 5 ? -3.726 4.233 6.477 1.00 88.38 5 A 1 ATOM 39 C CD2 . PHE A 1 5 ? -5.396 2.838 7.467 1.00 89.31 5 A 1 ATOM 40 C CE1 . PHE A 1 5 ? -4.425 5.367 6.864 1.00 87.01 5 A 1 ATOM 41 C CE2 . PHE A 1 5 ? -6.103 3.972 7.860 1.00 87.43 5 A 1 ATOM 42 C CZ . PHE A 1 5 ? -5.617 5.234 7.560 1.00 86.84 5 A 1 ATOM 43 N N . VAL A 1 6 ? -1.880 -0.294 4.496 1.00 97.49 6 A 1 ATOM 44 C CA . VAL A 1 6 ? -0.632 -0.969 4.138 1.00 97.74 6 A 1 ATOM 45 C C . VAL A 1 6 ? -0.317 -0.748 2.661 1.00 97.97 6 A 1 ATOM 46 O O . VAL A 1 6 ? 0.837 -0.520 2.287 1.00 97.63 6 A 1 ATOM 47 C CB . VAL A 1 6 ? -0.716 -2.476 4.442 1.00 97.37 6 A 1 ATOM 48 C CG1 . VAL A 1 6 ? 0.562 -3.185 4.025 1.00 95.42 6 A 1 ATOM 49 C CG2 . VAL A 1 6 ? -0.975 -2.705 5.921 1.00 95.09 6 A 1 ATOM 50 N N . ILE A 1 7 ? -1.349 -0.814 1.838 1.00 97.63 7 A 1 ATOM 51 C CA . ILE A 1 7 ? -1.193 -0.618 0.399 1.00 97.46 7 A 1 ATOM 52 C C . ILE A 1 7 ? -0.769 0.820 0.104 1.00 97.59 7 A 1 ATOM 53 O O . ILE A 1 7 ? 0.122 1.062 -0.719 1.00 97.33 7 A 1 ATOM 54 C CB . ILE A 1 7 ? -2.505 -0.955 -0.343 1.00 97.34 7 A 1 ATOM 55 C CG1 . ILE A 1 7 ? -2.904 -2.415 -0.116 1.00 95.82 7 A 1 ATOM 56 C CG2 . ILE A 1 7 ? -2.343 -0.691 -1.845 1.00 95.42 7 A 1 ATOM 57 C CD1 . ILE A 1 7 ? -4.385 -2.662 -0.315 1.00 89.95 7 A 1 ATOM 58 N N . LEU A 1 8 ? -1.408 1.742 0.768 1.00 96.97 8 A 1 ATOM 59 C CA . LEU A 1 8 ? -1.098 3.160 0.588 1.00 96.98 8 A 1 ATOM 60 C C . LEU A 1 8 ? 0.323 3.466 1.057 1.00 97.48 8 A 1 ATOM 61 O O . LEU A 1 8 ? 1.047 4.235 0.425 1.00 97.63 8 A 1 ATOM 62 C CB . LEU A 1 8 ? -2.106 4.016 1.360 1.00 96.87 8 A 1 ATOM 63 C CG . LEU A 1 8 ? -2.520 5.294 0.632 1.00 91.05 8 A 1 ATOM 64 C CD1 . LEU A 1 8 ? -3.586 4.994 -0.416 1.00 88.44 8 A 1 ATOM 65 C CD2 . LEU A 1 8 ? -3.027 6.324 1.623 1.00 89.53 8 A 1 ATOM 66 N N . PHE A 1 9 ? 0.705 2.854 2.161 1.00 96.94 9 A 1 ATOM 67 C CA . PHE A 1 9 ? 2.035 3.049 2.726 1.00 96.83 9 A 1 ATOM 68 C C . PHE A 1 9 ? 3.102 2.490 1.799 1.00 97.39 9 A 1 ATOM 69 O O . PHE A 1 9 ? 4.166 3.091 1.627 1.00 97.28 9 A 1 ATOM 70 C CB . PHE A 1 9 ? 2.112 2.369 4.092 1.00 96.30 9 A 1 ATOM 71 C CG . PHE A 1 9 ? 3.186 2.955 4.969 1.00 93.26 9 A 1 ATOM 72 C CD1 . PHE A 1 9 ? 3.041 4.223 5.512 1.00 90.01 9 A 1 ATOM 73 C CD2 . PHE A 1 9 ? 4.331 2.227 5.249 1.00 90.43 9 A 1 ATOM 74 C CE1 . PHE A 1 9 ? 4.029 4.765 6.318 1.00 89.26 9 A 1 ATOM 75 C CE2 . PHE A 1 9 ? 5.326 2.767 6.057 1.00 89.26 9 A 1 ATOM 76 C CZ . PHE A 1 9 ? 5.175 4.036 6.591 1.00 88.46 9 A 1 ATOM 77 N N . ALA A 1 10 ? 2.807 1.339 1.207 1.00 97.68 10 A 1 ATOM 78 C CA . ALA A 1 10 ? 3.740 0.698 0.283 1.00 97.72 10 A 1 ATOM 79 C C . ALA A 1 10 ? 3.930 1.543 -0.974 1.00 97.96 10 A 1 ATOM 80 O O . ALA A 1 10 ? 5.041 1.652 -1.495 1.00 97.57 10 A 1 ATOM 81 C CB . ALA A 1 10 ? 3.225 -0.688 -0.084 1.00 97.43 10 A 1 ATOM 82 N N . PHE A 1 11 ? 2.846 2.128 -1.452 1.00 97.24 11 A 1 ATOM 83 C CA . PHE A 1 11 ? 2.884 2.966 -2.649 1.00 97.14 11 A 1 ATOM 84 C C . PHE A 1 11 ? 3.687 4.238 -2.391 1.00 97.56 11 A 1 ATOM 85 O O . PHE A 1 11 ? 4.498 4.650 -3.224 1.00 97.13 11 A 1 ATOM 86 C CB . PHE A 1 11 ? 1.459 3.321 -3.073 1.00 96.77 11 A 1 ATOM 87 C CG . PHE A 1 11 ? 1.315 3.461 -4.573 1.00 93.58 11 A 1 ATOM 88 C CD1 . PHE A 1 11 ? 1.648 4.644 -5.211 1.00 90.66 11 A 1 ATOM 89 C CD2 . PHE A 1 11 ? 0.841 2.397 -5.330 1.00 91.25 11 A 1 ATOM 90 C CE1 . PHE A 1 11 ? 1.520 4.773 -6.589 1.00 89.80 11 A 1 ATOM 91 C CE2 . PHE A 1 11 ? 0.709 2.522 -6.710 1.00 90.06 11 A 1 ATOM 92 C CZ . PHE A 1 11 ? 1.048 3.708 -7.338 1.00 89.70 11 A 1 ATOM 93 N N . LEU A 1 12 ? 3.458 4.830 -1.246 1.00 97.60 12 A 1 ATOM 94 C CA . LEU A 1 12 ? 4.166 6.052 -0.872 1.00 97.39 12 A 1 ATOM 95 C C . LEU A 1 12 ? 5.641 5.775 -0.625 1.00 97.57 12 A 1 ATOM 96 O O . LEU A 1 12 ? 6.505 6.565 -1.010 1.00 97.05 12 A 1 ATOM 97 C CB . LEU A 1 12 ? 3.519 6.663 0.373 1.00 96.80 12 A 1 ATOM 98 C CG . LEU A 1 12 ? 2.943 8.059 0.141 1.00 92.74 12 A 1 ATOM 99 C CD1 . LEU A 1 12 ? 1.798 8.333 1.101 1.00 88.55 12 A 1 ATOM 100 C CD2 . LEU A 1 12 ? 4.028 9.109 0.297 1.00 88.75 12 A 1 ATOM 101 N N . ALA A 1 13 ? 5.922 4.651 0.006 1.00 97.95 13 A 1 ATOM 102 C CA . ALA A 1 13 ? 7.299 4.259 0.296 1.00 97.70 13 A 1 ATOM 103 C C . ALA A 1 13 ? 8.072 3.988 -0.989 1.00 97.87 13 A 1 ATOM 104 O O . ALA A 1 13 ? 9.246 4.341 -1.099 1.00 97.22 13 A 1 ATOM 105 C CB . ALA A 1 13 ? 7.303 3.025 1.186 1.00 97.01 13 A 1 ATOM 106 N N . SER A 1 14 ? 7.415 3.364 -1.959 1.00 97.51 14 A 1 ATOM 107 C CA . SER A 1 14 ? 8.032 3.047 -3.243 1.00 97.20 14 A 1 ATOM 108 C C . SER A 1 14 ? 8.262 4.308 -4.067 1.00 97.13 14 A 1 ATOM 109 O O . SER A 1 14 ? 9.296 4.456 -4.723 1.00 94.80 14 A 1 ATOM 110 C CB . SER A 1 14 ? 7.158 2.063 -4.015 1.00 95.75 14 A 1 ATOM 111 O OG . SER A 1 14 ? 7.927 1.313 -4.919 1.00 84.79 14 A 1 ATOM 112 N N . ALA A 1 15 ? 7.297 5.202 -4.032 1.00 96.91 15 A 1 ATOM 113 C CA . ALA A 1 15 ? 7.382 6.459 -4.772 1.00 96.10 15 A 1 ATOM 114 C C . ALA A 1 15 ? 8.356 7.433 -4.119 1.00 96.40 15 A 1 ATOM 115 O O . ALA A 1 15 ? 8.978 8.249 -4.801 1.00 94.83 15 A 1 ATOM 116 C CB . ALA A 1 15 ? 5.995 7.088 -4.877 1.00 94.21 15 A 1 ATOM 117 N N . SER A 1 16 ? 8.482 7.341 -2.814 1.00 93.61 16 A 1 ATOM 118 C CA . SER A 1 16 ? 9.367 8.215 -2.049 1.00 92.83 16 A 1 ATOM 119 C C . SER A 1 16 ? 10.723 7.564 -1.765 1.00 91.57 16 A 1 ATOM 120 O O . SER A 1 16 ? 11.577 8.148 -1.098 1.00 87.96 16 A 1 ATOM 121 C CB . SER A 1 16 ? 8.706 8.617 -0.730 1.00 90.26 16 A 1 ATOM 122 O OG . SER A 1 16 ? 9.172 9.872 -0.291 1.00 80.23 16 A 1 ATOM 123 N N . ALA A 1 17 ? 10.919 6.364 -2.273 1.00 90.42 17 A 1 ATOM 124 C CA . ALA A 1 17 ? 12.144 5.616 -2.036 1.00 88.00 17 A 1 ATOM 125 C C . ALA A 1 17 ? 13.272 6.093 -2.953 1.00 86.47 17 A 1 ATOM 126 O O . ALA A 1 17 ? 12.999 6.452 -4.110 1.00 80.10 17 A 1 ATOM 127 C CB . ALA A 1 17 ? 11.898 4.125 -2.217 1.00 81.72 17 A 1 ATOM 128 O OXT . ALA A 1 17 ? 14.440 6.083 -2.517 1.00 74.57 17 A 1 #