# 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_spkb42747 # _entry.id spkb42747 # 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" "C2 H5 N O2" 75.067 GLY y GLYCINE C(C(=O)O)N ? "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" "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" # _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 GLY 2 1 n SER 3 1 n PHE 4 1 n LEU 5 1 n SER 6 1 n PHE 7 1 n PHE 8 1 n LEU 9 1 n ILE 10 1 n SER 11 1 n SER 12 1 n ARG 13 1 n THR 14 1 n LEU 15 1 n ALA 16 # _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 @ 2025-07-09 18:03:23)" _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 85.59 _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 66.76 1 1 A GLY 2 2 84.54 1 2 A SER 3 2 81.95 1 3 A PHE 4 2 82.66 1 4 A LEU 5 2 87.11 1 5 A SER 6 2 90.91 1 6 A PHE 7 2 86.65 1 7 A PHE 8 2 87.86 1 8 A LEU 9 2 90.05 1 9 A ILE 10 2 90.03 1 10 A SER 11 2 91.68 1 11 A SER 12 2 91.62 1 12 A ARG 13 2 82.40 1 13 A THR 14 2 88.67 1 14 A LEU 15 2 86.58 1 15 A ALA 16 2 83.93 1 16 # _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 GLY . 2 A 2 A 3 1 n SER . 3 A 3 A 4 1 n PHE . 4 A 4 A 5 1 n LEU . 5 A 5 A 6 1 n SER . 6 A 6 A 7 1 n PHE . 7 A 7 A 8 1 n PHE . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n ILE . 10 A 10 A 11 1 n SER . 11 A 11 A 12 1 n SER . 12 A 12 A 13 1 n ARG . 13 A 13 A 14 1 n THR . 14 A 14 A 15 1 n LEU . 15 A 15 A 16 1 n ALA . 16 A 16 # _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 ? -11.023 -8.661 -1.859 1.00 71.84 1 A 1 ATOM 2 C CA . MET A 1 1 ? -10.187 -7.444 -1.812 1.00 74.03 1 A 1 ATOM 3 C C . MET A 1 1 ? -10.718 -6.471 -0.770 1.00 74.86 1 A 1 ATOM 4 O O . MET A 1 1 ? -11.887 -6.090 -0.821 1.00 67.98 1 A 1 ATOM 5 C CB . MET A 1 1 ? -10.163 -6.752 -3.176 1.00 67.60 1 A 1 ATOM 6 C CG . MET A 1 1 ? -9.356 -7.511 -4.209 1.00 63.29 1 A 1 ATOM 7 S SD . MET A 1 1 ? -9.433 -6.733 -5.829 1.00 60.78 1 A 1 ATOM 8 C CE . MET A 1 1 ? -8.246 -7.728 -6.714 1.00 53.70 1 A 1 ATOM 9 N N . GLY A 1 2 ? -9.860 -6.077 0.163 1.00 80.84 2 A 1 ATOM 10 C CA . GLY A 1 2 ? -10.242 -5.145 1.211 1.00 84.74 2 A 1 ATOM 11 C C . GLY A 1 2 ? -9.372 -3.903 1.221 1.00 88.03 2 A 1 ATOM 12 O O . GLY A 1 2 ? -8.585 -3.681 0.302 1.00 84.56 2 A 1 ATOM 13 N N . SER A 1 3 ? -9.502 -3.085 2.276 1.00 81.58 3 A 1 ATOM 14 C CA . SER A 1 3 ? -8.727 -1.856 2.425 1.00 86.21 3 A 1 ATOM 15 C C . SER A 1 3 ? -7.248 -2.154 2.645 1.00 89.04 3 A 1 ATOM 16 O O . SER A 1 3 ? -6.386 -1.365 2.266 1.00 84.60 3 A 1 ATOM 17 C CB . SER A 1 3 ? -9.271 -1.030 3.585 1.00 79.54 3 A 1 ATOM 18 O OG . SER A 1 3 ? -10.592 -0.603 3.322 1.00 70.71 3 A 1 ATOM 19 N N . PHE A 1 4 ? -6.960 -3.303 3.239 1.00 86.02 4 A 1 ATOM 20 C CA . PHE A 1 4 ? -5.588 -3.739 3.493 1.00 87.72 4 A 1 ATOM 21 C C . PHE A 1 4 ? -4.806 -3.888 2.189 1.00 90.30 4 A 1 ATOM 22 O O . PHE A 1 4 ? -3.626 -3.537 2.121 1.00 88.32 4 A 1 ATOM 23 C CB . PHE A 1 4 ? -5.600 -5.066 4.262 1.00 85.23 4 A 1 ATOM 24 C CG . PHE A 1 4 ? -4.336 -5.870 4.092 1.00 82.07 4 A 1 ATOM 25 C CD1 . PHE A 1 4 ? -3.153 -5.435 4.655 1.00 79.96 4 A 1 ATOM 26 C CD2 . PHE A 1 4 ? -4.338 -7.044 3.362 1.00 78.85 4 A 1 ATOM 27 C CE1 . PHE A 1 4 ? -1.979 -6.163 4.499 1.00 77.04 4 A 1 ATOM 28 C CE2 . PHE A 1 4 ? -3.167 -7.775 3.197 1.00 76.29 4 A 1 ATOM 29 C CZ . PHE A 1 4 ? -1.991 -7.333 3.766 1.00 77.47 4 A 1 ATOM 30 N N . LEU A 1 5 ? -5.461 -4.394 1.157 1.00 90.61 5 A 1 ATOM 31 C CA . LEU A 1 5 ? -4.832 -4.581 -0.144 1.00 90.52 5 A 1 ATOM 32 C C . LEU A 1 5 ? -4.451 -3.244 -0.766 1.00 92.16 5 A 1 ATOM 33 O O . LEU A 1 5 ? -3.409 -3.117 -1.407 1.00 91.03 5 A 1 ATOM 34 C CB . LEU A 1 5 ? -5.772 -5.361 -1.077 1.00 89.56 5 A 1 ATOM 35 C CG . LEU A 1 5 ? -5.404 -6.828 -1.284 1.00 84.40 5 A 1 ATOM 36 C CD1 . LEU A 1 5 ? -4.072 -6.949 -1.995 1.00 80.13 5 A 1 ATOM 37 C CD2 . LEU A 1 5 ? -5.379 -7.565 0.040 1.00 78.48 5 A 1 ATOM 38 N N . SER A 1 6 ? -5.304 -2.234 -0.577 1.00 92.36 6 A 1 ATOM 39 C CA . SER A 1 6 ? -5.063 -0.894 -1.102 1.00 93.00 6 A 1 ATOM 40 C C . SER A 1 6 ? -3.909 -0.221 -0.365 1.00 93.74 6 A 1 ATOM 41 O O . SER A 1 6 ? -3.068 0.433 -0.978 1.00 91.85 6 A 1 ATOM 42 C CB . SER A 1 6 ? -6.324 -0.042 -0.988 1.00 91.29 6 A 1 ATOM 43 O OG . SER A 1 6 ? -6.170 1.168 -1.683 1.00 83.23 6 A 1 ATOM 44 N N . PHE A 1 7 ? -3.864 -0.385 0.960 1.00 90.51 7 A 1 ATOM 45 C CA . PHE A 1 7 ? -2.805 0.201 1.776 1.00 90.74 7 A 1 ATOM 46 C C . PHE A 1 7 ? -1.481 -0.523 1.544 1.00 92.04 7 A 1 ATOM 47 O O . PHE A 1 7 ? -0.409 0.074 1.626 1.00 90.45 7 A 1 ATOM 48 C CB . PHE A 1 7 ? -3.190 0.131 3.253 1.00 89.94 7 A 1 ATOM 49 C CG . PHE A 1 7 ? -2.491 1.166 4.099 1.00 86.93 7 A 1 ATOM 50 C CD1 . PHE A 1 7 ? -1.174 0.995 4.484 1.00 84.39 7 A 1 ATOM 51 C CD2 . PHE A 1 7 ? -3.164 2.310 4.501 1.00 84.10 7 A 1 ATOM 52 C CE1 . PHE A 1 7 ? -0.524 1.951 5.247 1.00 81.74 7 A 1 ATOM 53 C CE2 . PHE A 1 7 ? -2.521 3.269 5.270 1.00 81.02 7 A 1 ATOM 54 C CZ . PHE A 1 7 ? -1.201 3.089 5.642 1.00 81.25 7 A 1 ATOM 55 N N . PHE A 1 8 ? -1.561 -1.808 1.249 1.00 91.81 8 A 1 ATOM 56 C CA . PHE A 1 8 ? -0.376 -2.622 1.002 1.00 91.65 8 A 1 ATOM 57 C C . PHE A 1 8 ? 0.397 -2.133 -0.218 1.00 92.91 8 A 1 ATOM 58 O O . PHE A 1 8 ? 1.620 -2.014 -0.176 1.00 91.96 8 A 1 ATOM 59 C CB . PHE A 1 8 ? -0.788 -4.081 0.815 1.00 91.12 8 A 1 ATOM 60 C CG . PHE A 1 8 ? 0.371 -4.993 0.523 1.00 88.40 8 A 1 ATOM 61 C CD1 . PHE A 1 8 ? 1.357 -5.198 1.468 1.00 85.11 8 A 1 ATOM 62 C CD2 . PHE A 1 8 ? 0.466 -5.637 -0.700 1.00 85.02 8 A 1 ATOM 63 C CE1 . PHE A 1 8 ? 2.430 -6.034 1.204 1.00 82.67 8 A 1 ATOM 64 C CE2 . PHE A 1 8 ? 1.538 -6.473 -0.971 1.00 82.67 8 A 1 ATOM 65 C CZ . PHE A 1 8 ? 2.519 -6.672 -0.018 1.00 83.13 8 A 1 ATOM 66 N N . LEU A 1 9 ? -0.310 -1.854 -1.310 1.00 92.98 9 A 1 ATOM 67 C CA . LEU A 1 9 ? 0.339 -1.381 -2.532 1.00 93.28 9 A 1 ATOM 68 C C . LEU A 1 9 ? 0.844 0.049 -2.378 1.00 94.06 9 A 1 ATOM 69 O O . LEU A 1 9 ? 1.892 0.403 -2.921 1.00 93.51 9 A 1 ATOM 70 C CB . LEU A 1 9 ? -0.627 -1.495 -3.723 1.00 92.99 9 A 1 ATOM 71 C CG . LEU A 1 9 ? -1.780 -0.499 -3.731 1.00 86.41 9 A 1 ATOM 72 C CD1 . LEU A 1 9 ? -1.479 0.651 -4.686 1.00 83.78 9 A 1 ATOM 73 C CD2 . LEU A 1 9 ? -3.067 -1.191 -4.151 1.00 83.41 9 A 1 ATOM 74 N N . ILE A 1 10 ? 0.119 0.874 -1.633 1.00 92.86 10 A 1 ATOM 75 C CA . ILE A 1 10 ? 0.515 2.263 -1.400 1.00 92.17 10 A 1 ATOM 76 C C . ILE A 1 10 ? 1.727 2.328 -0.477 1.00 92.54 10 A 1 ATOM 77 O O . ILE A 1 10 ? 2.650 3.115 -0.699 1.00 90.80 10 A 1 ATOM 78 C CB . ILE A 1 10 ? -0.656 3.077 -0.809 1.00 91.72 10 A 1 ATOM 79 C CG1 . ILE A 1 10 ? -1.801 3.194 -1.821 1.00 88.52 10 A 1 ATOM 80 C CG2 . ILE A 1 10 ? -0.181 4.475 -0.403 1.00 88.38 10 A 1 ATOM 81 C CD1 . ILE A 1 10 ? -3.121 3.603 -1.207 1.00 83.29 10 A 1 ATOM 82 N N . SER A 1 11 ? 1.726 1.499 0.560 1.00 94.31 11 A 1 ATOM 83 C CA . SER A 1 11 ? 2.827 1.450 1.514 1.00 94.00 11 A 1 ATOM 84 C C . SER A 1 11 ? 4.105 0.956 0.844 1.00 94.34 11 A 1 ATOM 85 O O . SER A 1 11 ? 5.202 1.395 1.178 1.00 92.73 11 A 1 ATOM 86 C CB . SER A 1 11 ? 2.469 0.540 2.688 1.00 92.38 11 A 1 ATOM 87 O OG . SER A 1 11 ? 3.421 0.657 3.711 1.00 82.33 11 A 1 ATOM 88 N N . SER A 1 12 ? 3.959 0.056 -0.107 1.00 93.78 12 A 1 ATOM 89 C CA . SER A 1 12 ? 5.091 -0.492 -0.843 1.00 93.85 12 A 1 ATOM 90 C C . SER A 1 12 ? 5.693 0.548 -1.782 1.00 94.24 12 A 1 ATOM 91 O O . SER A 1 12 ? 6.910 0.623 -1.937 1.00 91.51 12 A 1 ATOM 92 C CB . SER A 1 12 ? 4.657 -1.724 -1.631 1.00 92.12 12 A 1 ATOM 93 O OG . SER A 1 12 ? 5.778 -2.412 -2.124 1.00 84.25 12 A 1 ATOM 94 N N . ARG A 1 13 ? 4.842 1.348 -2.418 1.00 93.01 13 A 1 ATOM 95 C CA . ARG A 1 13 ? 5.295 2.390 -3.344 1.00 92.20 13 A 1 ATOM 96 C C . ARG A 1 13 ? 5.938 3.554 -2.604 1.00 92.57 13 A 1 ATOM 97 O O . ARG A 1 13 ? 6.866 4.175 -3.114 1.00 88.16 13 A 1 ATOM 98 C CB . ARG A 1 13 ? 4.129 2.893 -4.191 1.00 89.64 13 A 1 ATOM 99 C CG . ARG A 1 13 ? 3.614 1.878 -5.180 1.00 83.20 13 A 1 ATOM 100 C CD . ARG A 1 13 ? 2.554 2.494 -6.074 1.00 82.20 13 A 1 ATOM 101 N NE . ARG A 1 13 ? 3.152 3.073 -7.281 1.00 77.13 13 A 1 ATOM 102 C CZ . ARG A 1 13 ? 3.299 2.423 -8.430 1.00 73.51 13 A 1 ATOM 103 N NH1 . ARG A 1 13 ? 2.904 1.167 -8.557 1.00 66.93 13 A 1 ATOM 104 N NH2 . ARG A 1 13 ? 3.844 3.032 -9.468 1.00 67.88 13 A 1 ATOM 105 N N . THR A 1 14 ? 5.461 3.842 -1.407 1.00 92.45 14 A 1 ATOM 106 C CA . THR A 1 14 ? 5.997 4.935 -0.594 1.00 92.09 14 A 1 ATOM 107 C C . THR A 1 14 ? 7.440 4.646 -0.177 1.00 92.58 14 A 1 ATOM 108 O O . THR A 1 14 ? 8.252 5.561 -0.049 1.00 89.11 14 A 1 ATOM 109 C CB . THR A 1 14 ? 5.138 5.157 0.656 1.00 89.59 14 A 1 ATOM 110 O OG1 . THR A 1 14 ? 3.773 5.322 0.277 1.00 83.51 14 A 1 ATOM 111 C CG2 . THR A 1 14 ? 5.575 6.394 1.414 1.00 81.36 14 A 1 ATOM 112 N N . LEU A 1 15 ? 7.748 3.380 0.033 1.00 92.87 15 A 1 ATOM 113 C CA . LEU A 1 15 ? 9.084 2.953 0.435 1.00 92.10 15 A 1 ATOM 114 C C . LEU A 1 15 ? 9.894 2.421 -0.748 1.00 92.55 15 A 1 ATOM 115 O O . LEU A 1 15 ? 10.932 1.782 -0.558 1.00 89.49 15 A 1 ATOM 116 C CB . LEU A 1 15 ? 8.969 1.884 1.525 1.00 89.14 15 A 1 ATOM 117 C CG . LEU A 1 15 ? 8.513 2.407 2.884 1.00 83.32 15 A 1 ATOM 118 C CD1 . LEU A 1 15 ? 7.940 1.280 3.730 1.00 78.69 15 A 1 ATOM 119 C CD2 . LEU A 1 15 ? 9.684 3.057 3.610 1.00 74.52 15 A 1 ATOM 120 N N . ALA A 1 16 ? 9.427 2.706 -1.946 1.00 89.92 16 A 1 ATOM 121 C CA . ALA A 1 16 ? 10.084 2.228 -3.163 1.00 87.96 16 A 1 ATOM 122 C C . ALA A 1 16 ? 10.361 3.389 -4.118 1.00 86.28 16 A 1 ATOM 123 O O . ALA A 1 16 ? 10.875 3.155 -5.219 1.00 83.17 16 A 1 ATOM 124 C CB . ALA A 1 16 ? 9.227 1.156 -3.825 1.00 81.53 16 A 1 ATOM 125 O OXT . ALA A 1 16 ? 10.092 4.556 -3.779 1.00 74.72 16 A 1 #