# 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_spkb16866 # _entry.id spkb16866 # 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" "C4 H8 N2 O3" 132.118 ASN y ASPARAGINE C([C@@H](C(=O)O)N)C(=O)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 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" "C4 H9 N O3" 119.119 THR y THREONINE C[C@H]([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 ASN 2 1 n LEU 3 1 n THR 4 1 n LYS 5 1 n MET 6 1 n ALA 7 1 n VAL 8 1 n PHE 9 1 n ALA 10 1 n ALA 11 1 n SER 12 1 n LEU 13 1 n PHE 14 1 n CYS 15 1 n LEU 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 @ 2025-07-10 13:24:18)" _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 92.75 _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 81.91 1 1 A ASN 2 2 88.97 1 2 A LEU 3 2 93.36 1 3 A THR 4 2 93.40 1 4 A LYS 5 2 91.70 1 5 A MET 6 2 91.00 1 6 A ALA 7 2 96.71 1 7 A VAL 8 2 96.24 1 8 A PHE 9 2 94.50 1 9 A ALA 10 2 97.11 1 10 A ALA 11 2 97.13 1 11 A SER 12 2 96.24 1 12 A LEU 13 2 94.76 1 13 A PHE 14 2 94.22 1 14 A CYS 15 2 94.83 1 15 A LEU 16 2 90.65 1 16 A ALA 17 2 88.58 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 ASN . 2 A 2 A 3 1 n LEU . 3 A 3 A 4 1 n THR . 4 A 4 A 5 1 n LYS . 5 A 5 A 6 1 n MET . 6 A 6 A 7 1 n ALA . 7 A 7 A 8 1 n VAL . 8 A 8 A 9 1 n PHE . 9 A 9 A 10 1 n ALA . 10 A 10 A 11 1 n ALA . 11 A 11 A 12 1 n SER . 12 A 12 A 13 1 n LEU . 13 A 13 A 14 1 n PHE . 14 A 14 A 15 1 n CYS . 15 A 15 A 16 1 n LEU . 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 ? -13.822 -4.988 -3.104 1.00 88.48 1 A 1 ATOM 2 C CA . MET A 1 1 ? -12.979 -4.012 -2.388 1.00 89.73 1 A 1 ATOM 3 C C . MET A 1 1 ? -11.568 -3.959 -2.973 1.00 91.37 1 A 1 ATOM 4 O O . MET A 1 1 ? -10.620 -4.456 -2.382 1.00 88.50 1 A 1 ATOM 5 C CB . MET A 1 1 ? -12.909 -4.378 -0.909 1.00 83.15 1 A 1 ATOM 6 C CG . MET A 1 1 ? -13.756 -3.476 -0.043 1.00 78.33 1 A 1 ATOM 7 S SD . MET A 1 1 ? -13.471 -3.779 1.707 1.00 72.56 1 A 1 ATOM 8 C CE . MET A 1 1 ? -14.963 -3.104 2.411 1.00 63.14 1 A 1 ATOM 9 N N . ASN A 1 2 ? -11.460 -3.370 -4.139 1.00 90.00 2 A 1 ATOM 10 C CA . ASN A 1 2 ? -10.168 -3.225 -4.795 1.00 92.82 2 A 1 ATOM 11 C C . ASN A 1 2 ? -9.518 -1.892 -4.446 1.00 94.38 2 A 1 ATOM 12 O O . ASN A 1 2 ? -8.295 -1.791 -4.361 1.00 93.64 2 A 1 ATOM 13 C CB . ASN A 1 2 ? -10.348 -3.339 -6.304 1.00 90.62 2 A 1 ATOM 14 C CG . ASN A 1 2 ? -11.499 -2.495 -6.816 1.00 86.12 2 A 1 ATOM 15 O OD1 . ASN A 1 2 ? -11.542 -1.296 -6.600 1.00 83.15 2 A 1 ATOM 16 N ND2 . ASN A 1 2 ? -12.423 -3.131 -7.501 1.00 81.07 2 A 1 ATOM 17 N N . LEU A 1 3 ? -10.350 -0.879 -4.245 1.00 95.65 3 A 1 ATOM 18 C CA . LEU A 1 3 ? -9.863 0.453 -3.895 1.00 95.90 3 A 1 ATOM 19 C C . LEU A 1 3 ? -9.250 0.450 -2.503 1.00 96.71 3 A 1 ATOM 20 O O . LEU A 1 3 ? -8.220 1.075 -2.260 1.00 95.92 3 A 1 ATOM 21 C CB . LEU A 1 3 ? -11.008 1.471 -3.959 1.00 95.04 3 A 1 ATOM 22 C CG . LEU A 1 3 ? -10.651 2.759 -4.691 1.00 91.64 3 A 1 ATOM 23 C CD1 . LEU A 1 3 ? -10.975 2.639 -6.171 1.00 88.41 3 A 1 ATOM 24 C CD2 . LEU A 1 3 ? -11.384 3.938 -4.083 1.00 87.61 3 A 1 ATOM 25 N N . THR A 1 4 ? -9.888 -0.264 -1.596 1.00 95.30 4 A 1 ATOM 26 C CA . THR A 1 4 ? -9.420 -0.347 -0.214 1.00 95.58 4 A 1 ATOM 27 C C . THR A 1 4 ? -8.082 -1.070 -0.148 1.00 96.15 4 A 1 ATOM 28 O O . THR A 1 4 ? -7.180 -0.668 0.588 1.00 95.31 4 A 1 ATOM 29 C CB . THR A 1 4 ? -10.440 -1.080 0.663 1.00 94.62 4 A 1 ATOM 30 O OG1 . THR A 1 4 ? -11.724 -0.472 0.521 1.00 89.23 4 A 1 ATOM 31 C CG2 . THR A 1 4 ? -10.033 -1.027 2.128 1.00 87.63 4 A 1 ATOM 32 N N . LYS A 1 5 ? -7.949 -2.127 -0.938 1.00 96.77 5 A 1 ATOM 33 C CA . LYS A 1 5 ? -6.719 -2.904 -0.973 1.00 96.67 5 A 1 ATOM 34 C C . LYS A 1 5 ? -5.574 -2.067 -1.533 1.00 96.78 5 A 1 ATOM 35 O O . LYS A 1 5 ? -4.434 -2.188 -1.097 1.00 96.50 5 A 1 ATOM 36 C CB . LYS A 1 5 ? -6.926 -4.155 -1.817 1.00 96.37 5 A 1 ATOM 37 C CG . LYS A 1 5 ? -6.021 -5.293 -1.401 1.00 92.14 5 A 1 ATOM 38 C CD . LYS A 1 5 ? -6.540 -5.960 -0.137 1.00 88.02 5 A 1 ATOM 39 C CE . LYS A 1 5 ? -7.192 -7.292 -0.443 1.00 84.49 5 A 1 ATOM 40 N NZ . LYS A 1 5 ? -7.713 -7.919 0.788 1.00 77.57 5 A 1 ATOM 41 N N . MET A 1 6 ? -5.895 -1.243 -2.500 1.00 95.84 6 A 1 ATOM 42 C CA . MET A 1 6 ? -4.904 -0.363 -3.112 1.00 95.91 6 A 1 ATOM 43 C C . MET A 1 6 ? -4.430 0.696 -2.124 1.00 96.70 6 A 1 ATOM 44 O O . MET A 1 6 ? -3.255 1.053 -2.101 1.00 96.33 6 A 1 ATOM 45 C CB . MET A 1 6 ? -5.508 0.312 -4.339 1.00 95.05 6 A 1 ATOM 46 C CG . MET A 1 6 ? -5.569 -0.607 -5.539 1.00 89.98 6 A 1 ATOM 47 S SD . MET A 1 6 ? -4.497 -0.036 -6.843 1.00 83.62 6 A 1 ATOM 48 C CE . MET A 1 6 ? -4.866 -1.240 -8.112 1.00 74.58 6 A 1 ATOM 49 N N . ALA A 1 7 ? -5.362 1.183 -1.324 1.00 96.29 7 A 1 ATOM 50 C CA . ALA A 1 7 ? -5.044 2.198 -0.327 1.00 96.78 7 A 1 ATOM 51 C C . ALA A 1 7 ? -4.118 1.625 0.736 1.00 97.42 7 A 1 ATOM 52 O O . ALA A 1 7 ? -3.176 2.280 1.176 1.00 96.81 7 A 1 ATOM 53 C CB . ALA A 1 7 ? -6.324 2.719 0.314 1.00 96.23 7 A 1 ATOM 54 N N . VAL A 1 8 ? -4.385 0.396 1.131 1.00 97.09 8 A 1 ATOM 55 C CA . VAL A 1 8 ? -3.573 -0.284 2.138 1.00 97.07 8 A 1 ATOM 56 C C . VAL A 1 8 ? -2.178 -0.556 1.590 1.00 97.22 8 A 1 ATOM 57 O O . VAL A 1 8 ? -1.185 -0.501 2.315 1.00 96.68 8 A 1 ATOM 58 C CB . VAL A 1 8 ? -4.233 -1.603 2.564 1.00 96.60 8 A 1 ATOM 59 C CG1 . VAL A 1 8 ? -3.344 -2.363 3.533 1.00 94.52 8 A 1 ATOM 60 C CG2 . VAL A 1 8 ? -5.588 -1.333 3.202 1.00 94.49 8 A 1 ATOM 61 N N . PHE A 1 9 ? -2.114 -0.844 0.314 1.00 96.31 9 A 1 ATOM 62 C CA . PHE A 1 9 ? -0.846 -1.115 -0.348 1.00 96.04 9 A 1 ATOM 63 C C . PHE A 1 9 ? 0.040 0.120 -0.329 1.00 96.57 9 A 1 ATOM 64 O O . PHE A 1 9 ? 1.246 0.032 -0.101 1.00 96.66 9 A 1 ATOM 65 C CB . PHE A 1 9 ? -1.100 -1.551 -1.786 1.00 95.95 9 A 1 ATOM 66 C CG . PHE A 1 9 ? 0.115 -2.155 -2.436 1.00 95.01 9 A 1 ATOM 67 C CD1 . PHE A 1 9 ? 0.487 -3.458 -2.151 1.00 92.80 9 A 1 ATOM 68 C CD2 . PHE A 1 9 ? 0.876 -1.415 -3.324 1.00 93.36 9 A 1 ATOM 69 C CE1 . PHE A 1 9 ? 1.607 -4.017 -2.744 1.00 92.55 9 A 1 ATOM 70 C CE2 . PHE A 1 9 ? 2.003 -1.973 -3.917 1.00 92.07 9 A 1 ATOM 71 C CZ . PHE A 1 9 ? 2.366 -3.273 -3.626 1.00 92.18 9 A 1 ATOM 72 N N . ALA A 1 10 ? -0.569 1.258 -0.584 1.00 97.14 10 A 1 ATOM 73 C CA . ALA A 1 10 ? 0.157 2.525 -0.589 1.00 97.17 10 A 1 ATOM 74 C C . ALA A 1 10 ? 0.659 2.868 0.807 1.00 97.53 10 A 1 ATOM 75 O O . ALA A 1 10 ? 1.776 3.349 0.974 1.00 97.11 10 A 1 ATOM 76 C CB . ALA A 1 10 ? -0.745 3.637 -1.103 1.00 96.59 10 A 1 ATOM 77 N N . ALA A 1 11 ? -0.183 2.619 1.790 1.00 97.46 11 A 1 ATOM 78 C CA . ALA A 1 11 ? 0.164 2.905 3.178 1.00 97.39 11 A 1 ATOM 79 C C . ALA A 1 11 ? 1.277 1.986 3.657 1.00 97.68 11 A 1 ATOM 80 O O . ALA A 1 11 ? 2.183 2.409 4.373 1.00 96.56 11 A 1 ATOM 81 C CB . ALA A 1 11 ? -1.065 2.749 4.058 1.00 96.56 11 A 1 ATOM 82 N N . SER A 1 12 ? 1.205 0.732 3.247 1.00 97.47 12 A 1 ATOM 83 C CA . SER A 1 12 ? 2.201 -0.262 3.626 1.00 97.44 12 A 1 ATOM 84 C C . SER A 1 12 ? 3.550 0.051 2.997 1.00 97.80 12 A 1 ATOM 85 O O . SER A 1 12 ? 4.596 -0.208 3.587 1.00 97.03 12 A 1 ATOM 86 C CB . SER A 1 12 ? 1.747 -1.649 3.196 1.00 96.73 12 A 1 ATOM 87 O OG . SER A 1 12 ? 2.671 -2.613 3.613 1.00 90.99 12 A 1 ATOM 88 N N . LEU A 1 13 ? 3.516 0.606 1.811 1.00 96.84 13 A 1 ATOM 89 C CA . LEU A 1 13 ? 4.731 0.972 1.088 1.00 96.83 13 A 1 ATOM 90 C C . LEU A 1 13 ? 5.556 1.972 1.881 1.00 97.16 13 A 1 ATOM 91 O O . LEU A 1 13 ? 6.773 1.842 1.999 1.00 96.78 13 A 1 ATOM 92 C CB . LEU A 1 13 ? 4.366 1.564 -0.271 1.00 96.27 13 A 1 ATOM 93 C CG . LEU A 1 13 ? 5.561 1.810 -1.186 1.00 92.90 13 A 1 ATOM 94 C CD1 . LEU A 1 13 ? 5.997 0.513 -1.848 1.00 91.02 13 A 1 ATOM 95 C CD2 . LEU A 1 13 ? 5.218 2.847 -2.241 1.00 90.25 13 A 1 ATOM 96 N N . PHE A 1 14 ? 4.899 2.976 2.413 1.00 97.14 14 A 1 ATOM 97 C CA . PHE A 1 14 ? 5.571 4.010 3.189 1.00 96.91 14 A 1 ATOM 98 C C . PHE A 1 14 ? 5.853 3.532 4.607 1.00 97.43 14 A 1 ATOM 99 O O . PHE A 1 14 ? 6.830 3.944 5.227 1.00 96.73 14 A 1 ATOM 100 C CB . PHE A 1 14 ? 4.712 5.271 3.221 1.00 96.12 14 A 1 ATOM 101 C CG . PHE A 1 14 ? 5.535 6.532 3.148 1.00 93.86 14 A 1 ATOM 102 C CD1 . PHE A 1 14 ? 6.090 7.080 4.290 1.00 92.01 14 A 1 ATOM 103 C CD2 . PHE A 1 14 ? 5.752 7.157 1.930 1.00 92.17 14 A 1 ATOM 104 C CE1 . PHE A 1 14 ? 6.853 8.235 4.223 1.00 91.36 14 A 1 ATOM 105 C CE2 . PHE A 1 14 ? 6.515 8.313 1.859 1.00 91.12 14 A 1 ATOM 106 C CZ . PHE A 1 14 ? 7.065 8.853 3.006 1.00 91.53 14 A 1 ATOM 107 N N . CYS A 1 15 ? 4.997 2.660 5.097 1.00 96.68 15 A 1 ATOM 108 C CA . CYS A 1 15 ? 5.147 2.120 6.447 1.00 96.76 15 A 1 ATOM 109 C C . CYS A 1 15 ? 6.351 1.184 6.523 1.00 97.16 15 A 1 ATOM 110 O O . CYS A 1 15 ? 7.030 1.109 7.544 1.00 95.47 15 A 1 ATOM 111 C CB . CYS A 1 15 ? 3.877 1.379 6.863 1.00 94.66 15 A 1 ATOM 112 S SG . CYS A 1 15 ? 3.723 1.211 8.645 1.00 88.28 15 A 1 ATOM 113 N N . LEU A 1 16 ? 6.589 0.474 5.449 1.00 94.17 16 A 1 ATOM 114 C CA . LEU A 1 16 ? 7.702 -0.464 5.381 1.00 93.99 16 A 1 ATOM 115 C C . LEU A 1 16 ? 9.005 0.245 5.033 1.00 94.88 16 A 1 ATOM 116 O O . LEU A 1 16 ? 10.085 -0.204 5.421 1.00 93.69 16 A 1 ATOM 117 C CB . LEU A 1 16 ? 7.405 -1.537 4.333 1.00 92.35 16 A 1 ATOM 118 C CG . LEU A 1 16 ? 8.413 -2.678 4.300 1.00 89.12 16 A 1 ATOM 119 C CD1 . LEU A 1 16 ? 8.179 -3.630 5.460 1.00 84.73 16 A 1 ATOM 120 C CD2 . LEU A 1 16 ? 8.325 -3.418 2.980 1.00 82.25 16 A 1 ATOM 121 N N . ALA A 1 17 ? 8.894 1.332 4.303 1.00 93.20 17 A 1 ATOM 122 C CA . ALA A 1 17 ? 10.047 2.114 3.872 1.00 92.04 17 A 1 ATOM 123 C C . ALA A 1 17 ? 10.855 2.601 5.074 1.00 90.50 17 A 1 ATOM 124 O O . ALA A 1 17 ? 12.095 2.441 5.064 1.00 87.73 17 A 1 ATOM 125 C CB . ALA A 1 17 ? 9.587 3.293 3.022 1.00 87.95 17 A 1 ATOM 126 O OXT . ALA A 1 17 ? 10.272 3.132 6.000 1.00 80.06 17 A 1 #