# 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_spkb14013 # _entry.id spkb14013 # 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 H15 N4 O2" 175.209 ARG y ARGININE C(C[C@@H](C(=O)O)N)CNC(=[NH2+])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" "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" "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 PHE 2 1 n SER 3 1 n ARG 4 1 n ARG 5 1 n ASN 6 1 n LEU 7 1 n LEU 8 1 n ALA 9 1 n LEU 10 1 n GLY 11 1 n LEU 12 1 n ALA 13 1 n ALA 14 1 n THR 15 1 n VAL 16 1 n SER 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 20:28:58)" _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 86.52 _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 77.87 1 1 A PHE 2 2 78.50 1 2 A SER 3 2 87.87 1 3 A ARG 4 2 84.64 1 4 A ARG 5 2 84.35 1 5 A ASN 6 2 88.85 1 6 A LEU 7 2 90.70 1 7 A LEU 8 2 90.94 1 8 A ALA 9 2 92.53 1 9 A LEU 10 2 89.83 1 10 A GLY 11 2 94.47 1 11 A LEU 12 2 88.27 1 12 A ALA 13 2 93.10 1 13 A ALA 14 2 93.74 1 14 A THR 15 2 86.61 1 15 A VAL 16 2 87.31 1 16 A SER 17 2 76.30 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 PHE . 2 A 2 A 3 1 n SER . 3 A 3 A 4 1 n ARG . 4 A 4 A 5 1 n ARG . 5 A 5 A 6 1 n ASN . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n ALA . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n GLY . 11 A 11 A 12 1 n LEU . 12 A 12 A 13 1 n ALA . 13 A 13 A 14 1 n ALA . 14 A 14 A 15 1 n THR . 15 A 15 A 16 1 n VAL . 16 A 16 A 17 1 n SER . 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 ? -10.492 1.649 -3.369 1.00 79.94 1 A 1 ATOM 2 C CA . MET A 1 1 ? -10.447 0.999 -2.050 1.00 84.65 1 A 1 ATOM 3 C C . MET A 1 1 ? -9.048 0.448 -1.776 1.00 86.74 1 A 1 ATOM 4 O O . MET A 1 1 ? -8.532 -0.363 -2.532 1.00 82.44 1 A 1 ATOM 5 C CB . MET A 1 1 ? -11.464 -0.140 -1.992 1.00 77.65 1 A 1 ATOM 6 C CG . MET A 1 1 ? -11.279 -1.162 -3.098 1.00 74.08 1 A 1 ATOM 7 S SD . MET A 1 1 ? -12.313 -2.622 -2.887 1.00 72.79 1 A 1 ATOM 8 C CE . MET A 1 1 ? -13.941 -1.904 -3.069 1.00 64.63 1 A 1 ATOM 9 N N . PHE A 1 2 ? -8.431 0.898 -0.698 1.00 82.76 2 A 1 ATOM 10 C CA . PHE A 1 2 ? -7.098 0.447 -0.323 1.00 84.93 2 A 1 ATOM 11 C C . PHE A 1 2 ? -7.120 -0.227 1.039 1.00 89.06 2 A 1 ATOM 12 O O . PHE A 1 2 ? -7.731 0.285 1.980 1.00 85.56 2 A 1 ATOM 13 C CB . PHE A 1 2 ? -6.137 1.627 -0.293 1.00 80.42 2 A 1 ATOM 14 C CG . PHE A 1 2 ? -5.984 2.294 -1.628 1.00 76.60 2 A 1 ATOM 15 C CD1 . PHE A 1 2 ? -5.188 1.729 -2.605 1.00 75.44 2 A 1 ATOM 16 C CD2 . PHE A 1 2 ? -6.633 3.487 -1.901 1.00 74.45 2 A 1 ATOM 17 C CE1 . PHE A 1 2 ? -5.043 2.343 -3.839 1.00 72.00 2 A 1 ATOM 18 C CE2 . PHE A 1 2 ? -6.493 4.105 -3.132 1.00 71.81 2 A 1 ATOM 19 C CZ . PHE A 1 2 ? -5.696 3.530 -4.104 1.00 70.45 2 A 1 ATOM 20 N N . SER A 1 3 ? -6.445 -1.363 1.136 1.00 88.94 3 A 1 ATOM 21 C CA . SER A 1 3 ? -6.375 -2.103 2.388 1.00 90.53 3 A 1 ATOM 22 C C . SER A 1 3 ? -5.489 -1.370 3.389 1.00 92.85 3 A 1 ATOM 23 O O . SER A 1 3 ? -4.772 -0.436 3.026 1.00 90.94 3 A 1 ATOM 24 C CB . SER A 1 3 ? -5.834 -3.506 2.132 1.00 86.58 3 A 1 ATOM 25 O OG . SER A 1 3 ? -6.690 -4.225 1.269 1.00 77.37 3 A 1 ATOM 26 N N . ARG A 1 4 ? -5.561 -1.814 4.642 1.00 92.06 4 A 1 ATOM 27 C CA . ARG A 1 4 ? -4.741 -1.199 5.685 1.00 94.18 4 A 1 ATOM 28 C C . ARG A 1 4 ? -3.259 -1.322 5.349 1.00 95.74 4 A 1 ATOM 29 O O . ARG A 1 4 ? -2.478 -0.408 5.609 1.00 94.58 4 A 1 ATOM 30 C CB . ARG A 1 4 ? -5.032 -1.861 7.034 1.00 92.95 4 A 1 ATOM 31 C CG . ARG A 1 4 ? -4.736 -3.351 7.030 1.00 87.30 4 A 1 ATOM 32 C CD . ARG A 1 4 ? -4.869 -3.937 8.422 1.00 84.12 4 A 1 ATOM 33 N NE . ARG A 1 4 ? -6.275 -4.052 8.826 1.00 77.73 4 A 1 ATOM 34 C CZ . ARG A 1 4 ? -6.660 -4.693 9.917 1.00 75.57 4 A 1 ATOM 35 N NH1 . ARG A 1 4 ? -5.772 -5.273 10.713 1.00 68.43 4 A 1 ATOM 36 N NH2 . ARG A 1 4 ? -7.947 -4.763 10.222 1.00 68.43 4 A 1 ATOM 37 N N . ARG A 1 5 ? -2.892 -2.455 4.766 1.00 94.46 5 A 1 ATOM 38 C CA . ARG A 1 5 ? -1.506 -2.700 4.371 1.00 94.49 5 A 1 ATOM 39 C C . ARG A 1 5 ? -1.097 -1.765 3.238 1.00 95.43 5 A 1 ATOM 40 O O . ARG A 1 5 ? 0.018 -1.252 3.219 1.00 93.91 5 A 1 ATOM 41 C CB . ARG A 1 5 ? -1.337 -4.152 3.925 1.00 93.00 5 A 1 ATOM 42 C CG . ARG A 1 5 ? -0.917 -5.061 5.065 1.00 86.48 5 A 1 ATOM 43 C CD . ARG A 1 5 ? 0.551 -4.868 5.388 1.00 84.10 5 A 1 ATOM 44 N NE . ARG A 1 5 ? 1.055 -5.942 6.238 1.00 77.54 5 A 1 ATOM 45 C CZ . ARG A 1 5 ? 1.415 -7.127 5.771 1.00 74.18 5 A 1 ATOM 46 N NH1 . ARG A 1 5 ? 1.319 -7.396 4.485 1.00 67.45 5 A 1 ATOM 47 N NH2 . ARG A 1 5 ? 1.865 -8.055 6.606 1.00 66.80 5 A 1 ATOM 48 N N . ASN A 1 6 ? -2.011 -1.563 2.298 1.00 92.12 6 A 1 ATOM 49 C CA . ASN A 1 6 ? -1.762 -0.661 1.179 1.00 92.15 6 A 1 ATOM 50 C C . ASN A 1 6 ? -1.583 0.768 1.670 1.00 93.38 6 A 1 ATOM 51 O O . ASN A 1 6 ? -0.743 1.511 1.164 1.00 92.22 6 A 1 ATOM 52 C CB . ASN A 1 6 ? -2.919 -0.721 0.186 1.00 91.06 6 A 1 ATOM 53 C CG . ASN A 1 6 ? -2.559 -1.519 -1.048 1.00 87.13 6 A 1 ATOM 54 O OD1 . ASN A 1 6 ? -3.137 -2.554 -1.323 1.00 81.85 6 A 1 ATOM 55 N ND2 . ASN A 1 6 ? -1.595 -1.034 -1.812 1.00 80.88 6 A 1 ATOM 56 N N . LEU A 1 7 ? -2.381 1.145 2.660 1.00 92.65 7 A 1 ATOM 57 C CA . LEU A 1 7 ? -2.307 2.480 3.243 1.00 92.50 7 A 1 ATOM 58 C C . LEU A 1 7 ? -0.929 2.714 3.852 1.00 93.79 7 A 1 ATOM 59 O O . LEU A 1 7 ? -0.325 3.774 3.678 1.00 93.07 7 A 1 ATOM 60 C CB . LEU A 1 7 ? -3.393 2.638 4.315 1.00 92.44 7 A 1 ATOM 61 C CG . LEU A 1 7 ? -4.243 3.897 4.187 1.00 89.41 7 A 1 ATOM 62 C CD1 . LEU A 1 7 ? -3.377 5.145 4.198 1.00 86.24 7 A 1 ATOM 63 C CD2 . LEU A 1 7 ? -5.069 3.838 2.915 1.00 85.52 7 A 1 ATOM 64 N N . LEU A 1 8 ? -0.459 1.703 4.569 1.00 93.30 8 A 1 ATOM 65 C CA . LEU A 1 8 ? 0.851 1.783 5.210 1.00 93.07 8 A 1 ATOM 66 C C . LEU A 1 8 ? 1.964 1.795 4.169 1.00 94.26 8 A 1 ATOM 67 O O . LEU A 1 8 ? 2.899 2.592 4.249 1.00 93.28 8 A 1 ATOM 68 C CB . LEU A 1 8 ? 1.045 0.596 6.155 1.00 92.65 8 A 1 ATOM 69 C CG . LEU A 1 8 ? 1.810 0.941 7.427 1.00 88.98 8 A 1 ATOM 70 C CD1 . LEU A 1 8 ? 0.893 1.624 8.431 1.00 86.53 8 A 1 ATOM 71 C CD2 . LEU A 1 8 ? 2.430 -0.303 8.031 1.00 85.43 8 A 1 ATOM 72 N N . ALA A 1 9 ? 1.844 0.897 3.197 1.00 92.98 9 A 1 ATOM 73 C CA . ALA A 1 9 ? 2.841 0.787 2.136 1.00 92.41 9 A 1 ATOM 74 C C . ALA A 1 9 ? 2.847 2.034 1.261 1.00 93.77 9 A 1 ATOM 75 O O . ALA A 1 9 ? 3.897 2.457 0.777 1.00 92.41 9 A 1 ATOM 76 C CB . ALA A 1 9 ? 2.563 -0.449 1.291 1.00 91.07 9 A 1 ATOM 77 N N . LEU A 1 10 ? 1.677 2.608 1.070 1.00 92.44 10 A 1 ATOM 78 C CA . LEU A 1 10 ? 1.542 3.810 0.256 1.00 92.24 10 A 1 ATOM 79 C C . LEU A 1 10 ? 2.279 4.979 0.894 1.00 93.71 10 A 1 ATOM 80 O O . LEU A 1 10 ? 2.956 5.746 0.207 1.00 91.89 10 A 1 ATOM 81 C CB . LEU A 1 10 ? 0.065 4.155 0.088 1.00 90.85 10 A 1 ATOM 82 C CG . LEU A 1 10 ? -0.200 5.360 -0.798 1.00 88.47 10 A 1 ATOM 83 C CD1 . LEU A 1 10 ? 0.103 5.030 -2.252 1.00 85.40 10 A 1 ATOM 84 C CD2 . LEU A 1 10 ? -1.636 5.819 -0.647 1.00 83.65 10 A 1 ATOM 85 N N . GLY A 1 11 ? 2.128 5.103 2.200 1.00 94.06 11 A 1 ATOM 86 C CA . GLY A 1 11 ? 2.792 6.180 2.919 1.00 93.94 11 A 1 ATOM 87 C C . GLY A 1 11 ? 4.300 6.062 2.863 1.00 95.15 11 A 1 ATOM 88 O O . GLY A 1 11 ? 5.005 7.052 2.651 1.00 94.72 11 A 1 ATOM 89 N N . LEU A 1 12 ? 4.781 4.842 3.048 1.00 92.04 12 A 1 ATOM 90 C CA . LEU A 1 12 ? 6.217 4.586 3.020 1.00 91.33 12 A 1 ATOM 91 C C . LEU A 1 12 ? 6.762 4.715 1.607 1.00 92.83 12 A 1 ATOM 92 O O . LEU A 1 12 ? 7.847 5.261 1.395 1.00 90.52 12 A 1 ATOM 93 C CB . LEU A 1 12 ? 6.509 3.193 3.580 1.00 89.60 12 A 1 ATOM 94 C CG . LEU A 1 12 ? 7.751 3.131 4.466 1.00 85.71 12 A 1 ATOM 95 C CD1 . LEU A 1 12 ? 7.666 1.953 5.420 1.00 82.29 12 A 1 ATOM 96 C CD2 . LEU A 1 12 ? 9.008 3.053 3.627 1.00 81.81 12 A 1 ATOM 97 N N . ALA A 1 13 ? 6.006 4.211 0.642 1.00 93.84 13 A 1 ATOM 98 C CA . ALA A 1 13 ? 6.413 4.279 -0.758 1.00 93.45 13 A 1 ATOM 99 C C . ALA A 1 13 ? 6.401 5.718 -1.265 1.00 94.57 13 A 1 ATOM 100 O O . ALA A 1 13 ? 7.206 6.090 -2.121 1.00 92.31 13 A 1 ATOM 101 C CB . ALA A 1 13 ? 5.494 3.414 -1.611 1.00 91.35 13 A 1 ATOM 102 N N . ALA A 1 14 ? 5.489 6.505 -0.744 1.00 94.46 14 A 1 ATOM 103 C CA . ALA A 1 14 ? 5.374 7.903 -1.147 1.00 94.09 14 A 1 ATOM 104 C C . ALA A 1 14 ? 6.506 8.741 -0.568 1.00 95.15 14 A 1 ATOM 105 O O . ALA A 1 14 ? 6.968 9.690 -1.200 1.00 92.85 14 A 1 ATOM 106 C CB . ALA A 1 14 ? 4.031 8.464 -0.698 1.00 92.14 14 A 1 ATOM 107 N N . THR A 1 15 ? 6.935 8.395 0.633 1.00 91.06 15 A 1 ATOM 108 C CA . THR A 1 15 ? 8.013 9.129 1.289 1.00 90.02 15 A 1 ATOM 109 C C . THR A 1 15 ? 9.373 8.775 0.703 1.00 90.20 15 A 1 ATOM 110 O O . THR A 1 15 ? 10.286 9.601 0.682 1.00 85.36 15 A 1 ATOM 111 C CB . THR A 1 15 ? 8.006 8.861 2.802 1.00 87.38 15 A 1 ATOM 112 O OG1 . THR A 1 15 ? 8.815 9.836 3.452 1.00 81.71 15 A 1 ATOM 113 C CG2 . THR A 1 15 ? 8.547 7.485 3.129 1.00 80.56 15 A 1 ATOM 114 N N . VAL A 1 16 ? 9.488 7.543 0.222 1.00 91.92 16 A 1 ATOM 115 C CA . VAL A 1 16 ? 10.739 7.080 -0.376 1.00 90.58 16 A 1 ATOM 116 C C . VAL A 1 16 ? 10.903 7.654 -1.778 1.00 91.20 16 A 1 ATOM 117 O O . VAL A 1 16 ? 9.922 7.893 -2.489 1.00 86.09 16 A 1 ATOM 118 C CB . VAL A 1 16 ? 10.797 5.540 -0.419 1.00 87.28 16 A 1 ATOM 119 C CG1 . VAL A 1 16 ? 9.872 4.997 -1.496 1.00 81.02 16 A 1 ATOM 120 C CG2 . VAL A 1 16 ? 12.213 5.062 -0.651 1.00 83.07 16 A 1 ATOM 121 N N . SER A 1 17 ? 12.143 7.874 -2.164 1.00 85.65 17 A 1 ATOM 122 C CA . SER A 1 17 ? 12.432 8.439 -3.487 1.00 81.82 17 A 1 ATOM 123 C C . SER A 1 17 ? 13.435 7.576 -4.247 1.00 78.46 17 A 1 ATOM 124 O O . SER A 1 17 ? 13.467 7.636 -5.483 1.00 72.61 17 A 1 ATOM 125 C CB . SER A 1 17 ? 12.975 9.859 -3.345 1.00 75.29 17 A 1 ATOM 126 O OG . SER A 1 17 ? 12.070 10.683 -2.663 1.00 69.81 17 A 1 ATOM 127 O OXT . SER A 1 17 ? 14.227 6.874 -3.615 1.00 70.47 17 A 1 #