# 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_spkb19956 # _entry.id spkb19956 # 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" "C2 H5 N O2" 75.067 GLY y GLYCINE C(C(=O)O)N ? "PEPTIDE LINKING" "C6 H13 N O2" 131.173 LEU y LEUCINE CC(C)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" "C5 H9 N O2" 115.130 PRO y PROLINE C1C[C@H](NC1)C(=O)O ? "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 MET 2 1 n LEU 3 1 n PRO 4 1 n LEU 5 1 n LEU 6 1 n ALA 7 1 n VAL 8 1 n SER 9 1 n ALA 10 1 n PHE 11 1 n ALA 12 1 n SER 13 1 n LEU 14 1 n GLY 15 1 n ALA 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 @ 2025-07-06 04:21:28)" _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 93.14 _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 84.58 1 1 A MET 2 2 89.93 1 2 A LEU 3 2 92.39 1 3 A PRO 4 2 96.49 1 4 A LEU 5 2 95.39 1 5 A LEU 6 2 94.45 1 6 A ALA 7 2 96.86 1 7 A VAL 8 2 96.80 1 8 A SER 9 2 94.98 1 9 A ALA 10 2 96.33 1 10 A PHE 11 2 93.99 1 11 A ALA 12 2 96.55 1 12 A SER 13 2 94.97 1 13 A LEU 14 2 93.04 1 14 A GLY 15 2 93.63 1 15 A ALA 16 2 90.76 1 16 A ALA 17 2 84.90 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 MET . 2 A 2 A 3 1 n LEU . 3 A 3 A 4 1 n PRO . 4 A 4 A 5 1 n LEU . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n ALA . 7 A 7 A 8 1 n VAL . 8 A 8 A 9 1 n SER . 9 A 9 A 10 1 n ALA . 10 A 10 A 11 1 n PHE . 11 A 11 A 12 1 n ALA . 12 A 12 A 13 1 n SER . 13 A 13 A 14 1 n LEU . 14 A 14 A 15 1 n GLY . 15 A 15 A 16 1 n ALA . 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 ? -13.954 -1.171 5.207 1.00 89.97 1 A 1 ATOM 2 C CA . MET A 1 1 ? -12.628 -0.577 5.464 1.00 90.02 1 A 1 ATOM 3 C C . MET A 1 1 ? -11.790 -0.562 4.189 1.00 90.90 1 A 1 ATOM 4 O O . MET A 1 1 ? -11.854 -1.498 3.402 1.00 89.32 1 A 1 ATOM 5 C CB . MET A 1 1 ? -11.901 -1.381 6.539 1.00 85.54 1 A 1 ATOM 6 C CG . MET A 1 1 ? -12.648 -1.361 7.864 1.00 81.18 1 A 1 ATOM 7 S SD . MET A 1 1 ? -11.841 -2.377 9.107 1.00 79.23 1 A 1 ATOM 8 C CE . MET A 1 1 ? -12.950 -2.119 10.482 1.00 70.50 1 A 1 ATOM 9 N N . MET A 1 2 ? -11.004 0.477 3.985 1.00 93.52 2 A 1 ATOM 10 C CA . MET A 1 2 ? -10.175 0.628 2.786 1.00 94.34 2 A 1 ATOM 11 C C . MET A 1 2 ? -8.753 0.099 3.022 1.00 95.53 2 A 1 ATOM 12 O O . MET A 1 2 ? -7.769 0.747 2.665 1.00 94.24 2 A 1 ATOM 13 C CB . MET A 1 2 ? -10.137 2.096 2.369 1.00 91.55 2 A 1 ATOM 14 C CG . MET A 1 2 ? -11.499 2.652 2.007 1.00 88.23 2 A 1 ATOM 15 S SD . MET A 1 2 ? -11.400 4.383 1.520 1.00 85.27 2 A 1 ATOM 16 C CE . MET A 1 2 ? -13.122 4.721 1.212 1.00 76.75 2 A 1 ATOM 17 N N . LEU A 1 3 ? -8.656 -1.078 3.615 1.00 94.13 3 A 1 ATOM 18 C CA . LEU A 1 3 ? -7.359 -1.704 3.883 1.00 95.28 3 A 1 ATOM 19 C C . LEU A 1 3 ? -6.612 -2.055 2.595 1.00 96.46 3 A 1 ATOM 20 O O . LEU A 1 3 ? -5.405 -1.817 2.502 1.00 95.69 3 A 1 ATOM 21 C CB . LEU A 1 3 ? -7.561 -2.959 4.739 1.00 93.69 3 A 1 ATOM 22 C CG . LEU A 1 3 ? -7.701 -2.668 6.228 1.00 90.57 3 A 1 ATOM 23 C CD1 . LEU A 1 3 ? -8.271 -3.877 6.950 1.00 87.78 3 A 1 ATOM 24 C CD2 . LEU A 1 3 ? -6.347 -2.294 6.816 1.00 85.53 3 A 1 ATOM 25 N N . PRO A 1 4 ? -7.301 -2.620 1.590 1.00 96.96 4 A 1 ATOM 26 C CA . PRO A 1 4 ? -6.639 -2.987 0.331 1.00 97.25 4 A 1 ATOM 27 C C . PRO A 1 4 ? -6.057 -1.785 -0.397 1.00 97.69 4 A 1 ATOM 28 O O . PRO A 1 4 ? -4.961 -1.862 -0.954 1.00 96.99 4 A 1 ATOM 29 C CB . PRO A 1 4 ? -7.758 -3.647 -0.489 1.00 96.01 4 A 1 ATOM 30 C CG . PRO A 1 4 ? -9.025 -3.127 0.100 1.00 94.36 4 A 1 ATOM 31 C CD . PRO A 1 4 ? -8.730 -2.944 1.568 1.00 96.18 4 A 1 ATOM 32 N N . LEU A 1 5 ? -6.774 -0.672 -0.396 1.00 96.63 5 A 1 ATOM 33 C CA . LEU A 1 5 ? -6.300 0.548 -1.048 1.00 96.94 5 A 1 ATOM 34 C C . LEU A 1 5 ? -5.049 1.085 -0.360 1.00 97.36 5 A 1 ATOM 35 O O . LEU A 1 5 ? -4.119 1.563 -1.012 1.00 96.91 5 A 1 ATOM 36 C CB . LEU A 1 5 ? -7.410 1.603 -1.032 1.00 96.32 5 A 1 ATOM 37 C CG . LEU A 1 5 ? -8.232 1.640 -2.318 1.00 94.16 5 A 1 ATOM 38 C CD1 . LEU A 1 5 ? -9.499 2.460 -2.117 1.00 92.96 5 A 1 ATOM 39 C CD2 . LEU A 1 5 ? -7.408 2.240 -3.447 1.00 91.81 5 A 1 ATOM 40 N N . LEU A 1 6 ? -5.025 0.986 0.959 1.00 96.64 6 A 1 ATOM 41 C CA . LEU A 1 6 ? -3.882 1.448 1.744 1.00 96.61 6 A 1 ATOM 42 C C . LEU A 1 6 ? -2.633 0.640 1.402 1.00 97.12 6 A 1 ATOM 43 O O . LEU A 1 6 ? -1.538 1.189 1.263 1.00 96.89 6 A 1 ATOM 44 C CB . LEU A 1 6 ? -4.213 1.330 3.235 1.00 96.14 6 A 1 ATOM 45 C CG . LEU A 1 6 ? -3.881 2.584 4.037 1.00 92.00 6 A 1 ATOM 46 C CD1 . LEU A 1 6 ? -4.532 2.522 5.414 1.00 90.41 6 A 1 ATOM 47 C CD2 . LEU A 1 6 ? -2.388 2.764 4.175 1.00 89.82 6 A 1 ATOM 48 N N . ALA A 1 7 ? -2.803 -0.665 1.248 1.00 96.97 7 A 1 ATOM 49 C CA . ALA A 1 7 ? -1.692 -1.553 0.900 1.00 96.94 7 A 1 ATOM 50 C C . ALA A 1 7 ? -1.127 -1.214 -0.477 1.00 97.33 7 A 1 ATOM 51 O O . ALA A 1 7 ? 0.090 -1.204 -0.671 1.00 96.89 7 A 1 ATOM 52 C CB . ALA A 1 7 ? -2.169 -3.001 0.936 1.00 96.19 7 A 1 ATOM 53 N N . VAL A 1 8 ? -2.003 -0.924 -1.428 1.00 97.27 8 A 1 ATOM 54 C CA . VAL A 1 8 ? -1.590 -0.565 -2.788 1.00 97.45 8 A 1 ATOM 55 C C . VAL A 1 8 ? -0.772 0.724 -2.775 1.00 97.61 8 A 1 ATOM 56 O O . VAL A 1 8 ? 0.252 0.832 -3.454 1.00 97.24 8 A 1 ATOM 57 C CB . VAL A 1 8 ? -2.817 -0.407 -3.703 1.00 97.00 8 A 1 ATOM 58 C CG1 . VAL A 1 8 ? -2.403 0.088 -5.085 1.00 95.48 8 A 1 ATOM 59 C CG2 . VAL A 1 8 ? -3.551 -1.732 -3.838 1.00 95.52 8 A 1 ATOM 60 N N . SER A 1 9 ? -1.218 1.690 -2.000 1.00 96.71 9 A 1 ATOM 61 C CA . SER A 1 9 ? -0.528 2.974 -1.890 1.00 96.53 9 A 1 ATOM 62 C C . SER A 1 9 ? 0.872 2.794 -1.310 1.00 96.82 9 A 1 ATOM 63 O O . SER A 1 9 ? 1.840 3.380 -1.797 1.00 96.37 9 A 1 ATOM 64 C CB . SER A 1 9 ? -1.339 3.928 -1.015 1.00 95.72 9 A 1 ATOM 65 O OG . SER A 1 9 ? -0.730 5.192 -0.977 1.00 87.73 9 A 1 ATOM 66 N N . ALA A 1 10 ? 0.982 1.965 -0.283 1.00 96.58 10 A 1 ATOM 67 C CA . ALA A 1 10 ? 2.271 1.693 0.353 1.00 96.28 10 A 1 ATOM 68 C C . ALA A 1 10 ? 3.218 0.974 -0.604 1.00 96.97 10 A 1 ATOM 69 O O . ALA A 1 10 ? 4.405 1.296 -0.675 1.00 96.32 10 A 1 ATOM 70 C CB . ALA A 1 10 ? 2.054 0.859 1.610 1.00 95.48 10 A 1 ATOM 71 N N . PHE A 1 11 ? 2.688 0.001 -1.342 1.00 96.17 11 A 1 ATOM 72 C CA . PHE A 1 11 ? 3.486 -0.762 -2.300 1.00 96.13 11 A 1 ATOM 73 C C . PHE A 1 11 ? 3.993 0.134 -3.424 1.00 96.75 11 A 1 ATOM 74 O O . PHE A 1 11 ? 5.151 0.034 -3.841 1.00 96.20 11 A 1 ATOM 75 C CB . PHE A 1 11 ? 2.646 -1.899 -2.879 1.00 95.44 11 A 1 ATOM 76 C CG . PHE A 1 11 ? 3.498 -3.038 -3.381 1.00 93.79 11 A 1 ATOM 77 C CD1 . PHE A 1 11 ? 4.064 -2.994 -4.644 1.00 92.22 11 A 1 ATOM 78 C CD2 . PHE A 1 11 ? 3.725 -4.147 -2.575 1.00 92.78 11 A 1 ATOM 79 C CE1 . PHE A 1 11 ? 4.857 -4.035 -5.106 1.00 91.50 11 A 1 ATOM 80 C CE2 . PHE A 1 11 ? 4.513 -5.195 -3.032 1.00 91.47 11 A 1 ATOM 81 C CZ . PHE A 1 11 ? 5.080 -5.139 -4.295 1.00 91.41 11 A 1 ATOM 82 N N . ALA A 1 12 ? 3.130 1.021 -3.904 1.00 96.92 12 A 1 ATOM 83 C CA . ALA A 1 12 ? 3.501 1.950 -4.971 1.00 96.67 12 A 1 ATOM 84 C C . ALA A 1 12 ? 4.597 2.906 -4.508 1.00 97.19 12 A 1 ATOM 85 O O . ALA A 1 12 ? 5.540 3.183 -5.250 1.00 96.22 12 A 1 ATOM 86 C CB . ALA A 1 12 ? 2.273 2.730 -5.421 1.00 95.77 12 A 1 ATOM 87 N N . SER A 1 13 ? 4.476 3.391 -3.291 1.00 96.60 13 A 1 ATOM 88 C CA . SER A 1 13 ? 5.456 4.313 -2.724 1.00 96.56 13 A 1 ATOM 89 C C . SER A 1 13 ? 6.806 3.638 -2.528 1.00 96.99 13 A 1 ATOM 90 O O . SER A 1 13 ? 7.851 4.203 -2.851 1.00 95.67 13 A 1 ATOM 91 C CB . SER A 1 13 ? 4.955 4.864 -1.392 1.00 95.27 13 A 1 ATOM 92 O OG . SER A 1 13 ? 5.842 5.843 -0.908 1.00 88.74 13 A 1 ATOM 93 N N . LEU A 1 14 ? 6.783 2.416 -2.007 1.00 95.66 14 A 1 ATOM 94 C CA . LEU A 1 14 ? 8.013 1.659 -1.769 1.00 95.62 14 A 1 ATOM 95 C C . LEU A 1 14 ? 8.672 1.246 -3.078 1.00 96.35 14 A 1 ATOM 96 O O . LEU A 1 14 ? 9.898 1.302 -3.210 1.00 95.47 14 A 1 ATOM 97 C CB . LEU A 1 14 ? 7.700 0.420 -0.930 1.00 94.36 14 A 1 ATOM 98 C CG . LEU A 1 14 ? 8.939 -0.327 -0.447 1.00 91.01 14 A 1 ATOM 99 C CD1 . LEU A 1 14 ? 9.678 0.480 0.608 1.00 88.77 14 A 1 ATOM 100 C CD2 . LEU A 1 14 ? 8.546 -1.685 0.116 1.00 87.06 14 A 1 ATOM 101 N N . GLY A 1 15 ? 7.870 0.827 -4.038 1.00 94.54 15 A 1 ATOM 102 C CA . GLY A 1 15 ? 8.389 0.404 -5.336 1.00 93.59 15 A 1 ATOM 103 C C . GLY A 1 15 ? 8.909 1.563 -6.161 1.00 93.75 15 A 1 ATOM 104 O O . GLY A 1 15 ? 9.891 1.425 -6.892 1.00 92.66 15 A 1 ATOM 105 N N . ALA A 1 16 ? 8.260 2.715 -6.055 1.00 91.49 16 A 1 ATOM 106 C CA . ALA A 1 16 ? 8.665 3.912 -6.793 1.00 91.21 16 A 1 ATOM 107 C C . ALA A 1 16 ? 9.850 4.611 -6.142 1.00 92.52 16 A 1 ATOM 108 O O . ALA A 1 16 ? 10.617 5.296 -6.816 1.00 89.88 16 A 1 ATOM 109 C CB . ALA A 1 16 ? 7.486 4.874 -6.903 1.00 88.69 16 A 1 ATOM 110 N N . ALA A 1 17 ? 9.999 4.445 -4.829 1.00 90.97 17 A 1 ATOM 111 C CA . ALA A 1 17 ? 11.075 5.092 -4.087 1.00 88.83 17 A 1 ATOM 112 C C . ALA A 1 17 ? 12.443 4.614 -4.559 1.00 86.96 17 A 1 ATOM 113 O O . ALA A 1 17 ? 12.606 3.416 -4.805 1.00 82.87 17 A 1 ATOM 114 C CB . ALA A 1 17 ? 10.905 4.847 -2.594 1.00 82.96 17 A 1 ATOM 115 O OXT . ALA A 1 17 ? 13.358 5.442 -4.676 1.00 76.80 17 A 1 #