# 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_spkb10037 # _entry.id spkb10037 # 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" "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" # _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 LEU 3 1 n ILE 4 1 n LEU 5 1 n LEU 6 1 n ILE 7 1 n SER 8 1 n LEU 9 1 n PRO 10 1 n MET 11 1 n ALA 12 1 n PHE 13 # _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 16:07:08)" _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 94.21 _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 90.70 1 1 A PHE 2 2 94.50 1 2 A LEU 3 2 95.59 1 3 A ILE 4 2 96.73 1 4 A LEU 5 2 95.03 1 5 A LEU 6 2 95.28 1 6 A ILE 7 2 96.65 1 7 A SER 8 2 96.92 1 8 A LEU 9 2 95.64 1 9 A PRO 10 2 96.42 1 10 A MET 11 2 90.11 1 11 A ALA 12 2 93.31 1 12 A PHE 13 2 90.31 1 13 # _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 LEU . 3 A 3 A 4 1 n ILE . 4 A 4 A 5 1 n LEU . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n ILE . 7 A 7 A 8 1 n SER . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n PRO . 10 A 10 A 11 1 n MET . 11 A 11 A 12 1 n ALA . 12 A 12 A 13 1 n PHE . 13 A 13 # _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 ? -2.214 6.339 12.058 1.00 93.70 1 A 1 ATOM 2 C CA . MET A 1 1 ? -1.257 6.419 10.949 1.00 94.65 1 A 1 ATOM 3 C C . MET A 1 1 ? -1.909 6.012 9.629 1.00 95.36 1 A 1 ATOM 4 O O . MET A 1 1 ? -1.911 4.840 9.255 1.00 94.84 1 A 1 ATOM 5 C CB . MET A 1 1 ? -0.047 5.532 11.222 1.00 91.95 1 A 1 ATOM 6 C CG . MET A 1 1 ? 0.760 5.981 12.421 1.00 88.28 1 A 1 ATOM 7 S SD . MET A 1 1 ? 2.516 5.750 12.192 1.00 87.49 1 A 1 ATOM 8 C CE . MET A 1 1 ? 3.167 6.680 13.565 1.00 79.36 1 A 1 ATOM 9 N N . PHE A 1 2 ? -2.462 7.007 8.926 1.00 96.05 2 A 1 ATOM 10 C CA . PHE A 1 2 ? -3.162 6.766 7.671 1.00 97.16 2 A 1 ATOM 11 C C . PHE A 1 2 ? -2.196 6.654 6.495 1.00 97.84 2 A 1 ATOM 12 O O . PHE A 1 2 ? -2.419 5.884 5.564 1.00 97.57 2 A 1 ATOM 13 C CB . PHE A 1 2 ? -4.167 7.891 7.425 1.00 96.75 2 A 1 ATOM 14 C CG . PHE A 1 2 ? -4.943 7.716 6.157 1.00 95.15 2 A 1 ATOM 15 C CD1 . PHE A 1 2 ? -5.941 6.765 6.074 1.00 92.23 2 A 1 ATOM 16 C CD2 . PHE A 1 2 ? -4.672 8.506 5.059 1.00 92.41 2 A 1 ATOM 17 C CE1 . PHE A 1 2 ? -6.661 6.597 4.907 1.00 91.60 2 A 1 ATOM 18 C CE2 . PHE A 1 2 ? -5.386 8.342 3.883 1.00 90.90 2 A 1 ATOM 19 C CZ . PHE A 1 2 ? -6.381 7.387 3.810 1.00 91.89 2 A 1 ATOM 20 N N . LEU A 1 3 ? -1.113 7.414 6.540 1.00 97.45 3 A 1 ATOM 21 C CA . LEU A 1 3 ? -0.116 7.411 5.474 1.00 97.53 3 A 1 ATOM 22 C C . LEU A 1 3 ? 0.622 6.080 5.398 1.00 97.86 3 A 1 ATOM 23 O O . LEU A 1 3 ? 1.112 5.691 4.341 1.00 97.55 3 A 1 ATOM 24 C CB . LEU A 1 3 ? 0.886 8.548 5.684 1.00 97.21 3 A 1 ATOM 25 C CG . LEU A 1 3 ? 0.321 9.952 5.519 1.00 93.46 3 A 1 ATOM 26 C CD1 . LEU A 1 3 ? 1.359 10.987 5.923 1.00 91.74 3 A 1 ATOM 27 C CD2 . LEU A 1 3 ? -0.125 10.185 4.083 1.00 91.93 3 A 1 ATOM 28 N N . ILE A 1 4 ? 0.704 5.394 6.513 1.00 97.74 4 A 1 ATOM 29 C CA . ILE A 1 4 ? 1.375 4.100 6.580 1.00 97.73 4 A 1 ATOM 30 C C . ILE A 1 4 ? 0.597 3.056 5.788 1.00 97.88 4 A 1 ATOM 31 O O . ILE A 1 4 ? 1.170 2.155 5.176 1.00 97.39 4 A 1 ATOM 32 C CB . ILE A 1 4 ? 1.541 3.626 8.039 1.00 97.48 4 A 1 ATOM 33 C CG1 . ILE A 1 4 ? 2.178 4.723 8.894 1.00 95.92 4 A 1 ATOM 34 C CG2 . ILE A 1 4 ? 2.383 2.347 8.100 1.00 95.89 4 A 1 ATOM 35 C CD1 . ILE A 1 4 ? 3.536 5.167 8.392 1.00 93.80 4 A 1 ATOM 36 N N . LEU A 1 5 ? -0.714 3.183 5.797 1.00 97.40 5 A 1 ATOM 37 C CA . LEU A 1 5 ? -1.582 2.261 5.080 1.00 97.13 5 A 1 ATOM 38 C C . LEU A 1 5 ? -1.577 2.558 3.585 1.00 97.48 5 A 1 ATOM 39 O O . LEU A 1 5 ? -1.831 1.671 2.769 1.00 97.24 5 A 1 ATOM 40 C CB . LEU A 1 5 ? -3.011 2.353 5.625 1.00 96.85 5 A 1 ATOM 41 C CG . LEU A 1 5 ? -3.167 2.024 7.109 1.00 92.26 5 A 1 ATOM 42 C CD1 . LEU A 1 5 ? -4.572 2.364 7.582 1.00 90.84 5 A 1 ATOM 43 C CD2 . LEU A 1 5 ? -2.866 0.556 7.371 1.00 91.04 5 A 1 ATOM 44 N N . LEU A 1 6 ? -1.276 3.811 3.229 1.00 97.23 6 A 1 ATOM 45 C CA . LEU A 1 6 ? -1.249 4.251 1.840 1.00 97.24 6 A 1 ATOM 46 C C . LEU A 1 6 ? -0.004 3.750 1.117 1.00 97.59 6 A 1 ATOM 47 O O . LEU A 1 6 ? -0.034 3.453 -0.072 1.00 97.47 6 A 1 ATOM 48 C CB . LEU A 1 6 ? -1.321 5.781 1.769 1.00 96.92 6 A 1 ATOM 49 C CG . LEU A 1 6 ? -2.534 6.334 1.037 1.00 92.61 6 A 1 ATOM 50 C CD1 . LEU A 1 6 ? -2.558 5.855 -0.403 1.00 91.76 6 A 1 ATOM 51 C CD2 . LEU A 1 6 ? -3.810 5.930 1.755 1.00 91.40 6 A 1 ATOM 52 N N . ILE A 1 7 ? 1.095 3.652 1.842 1.00 97.78 7 A 1 ATOM 53 C CA . ILE A 1 7 ? 2.359 3.212 1.260 1.00 97.64 7 A 1 ATOM 54 C C . ILE A 1 7 ? 2.425 1.691 1.136 1.00 97.92 7 A 1 ATOM 55 O O . ILE A 1 7 ? 3.303 1.152 0.464 1.00 97.56 7 A 1 ATOM 56 C CB . ILE A 1 7 ? 3.559 3.707 2.095 1.00 97.28 7 A 1 ATOM 57 C CG1 . ILE A 1 7 ? 3.485 3.172 3.524 1.00 95.44 7 A 1 ATOM 58 C CG2 . ILE A 1 7 ? 3.612 5.231 2.096 1.00 95.20 7 A 1 ATOM 59 C CD1 . ILE A 1 7 ? 4.743 3.410 4.326 1.00 94.41 7 A 1 ATOM 60 N N . SER A 1 8 ? 1.516 1.019 1.776 1.00 97.81 8 A 1 ATOM 61 C CA . SER A 1 8 ? 1.485 -0.438 1.763 1.00 97.68 8 A 1 ATOM 62 C C . SER A 1 8 ? 0.805 -0.973 0.508 1.00 97.76 8 A 1 ATOM 63 O O . SER A 1 8 ? 1.027 -2.114 0.109 1.00 97.25 8 A 1 ATOM 64 C CB . SER A 1 8 ? 0.768 -0.965 3.006 1.00 97.13 8 A 1 ATOM 65 O OG . SER A 1 8 ? 0.822 -2.369 3.058 1.00 93.86 8 A 1 ATOM 66 N N . LEU A 1 9 ? -0.006 -0.139 -0.138 1.00 97.27 9 A 1 ATOM 67 C CA . LEU A 1 9 ? -0.742 -0.542 -1.334 1.00 97.15 9 A 1 ATOM 68 C C . LEU A 1 9 ? 0.060 -0.351 -2.624 1.00 97.34 9 A 1 ATOM 69 O O . LEU A 1 9 ? 0.201 -1.300 -3.403 1.00 96.42 9 A 1 ATOM 70 C CB . LEU A 1 9 ? -2.074 0.214 -1.411 1.00 96.64 9 A 1 ATOM 71 C CG . LEU A 1 9 ? -3.054 -0.292 -2.467 1.00 94.48 9 A 1 ATOM 72 C CD1 . LEU A 1 9 ? -3.616 -1.641 -2.077 1.00 93.06 9 A 1 ATOM 73 C CD2 . LEU A 1 9 ? -4.178 0.715 -2.668 1.00 92.77 9 A 1 ATOM 74 N N . PRO A 1 10 ? 0.581 0.869 -2.874 1.00 97.34 10 A 1 ATOM 75 C CA . PRO A 1 10 ? 1.332 1.136 -4.107 1.00 96.83 10 A 1 ATOM 76 C C . PRO A 1 10 ? 2.700 0.471 -4.136 1.00 97.00 10 A 1 ATOM 77 O O . PRO A 1 10 ? 3.290 0.303 -5.206 1.00 95.96 10 A 1 ATOM 78 C CB . PRO A 1 10 ? 1.476 2.661 -4.114 1.00 95.74 10 A 1 ATOM 79 C CG . PRO A 1 10 ? 1.430 3.037 -2.678 1.00 95.15 10 A 1 ATOM 80 C CD . PRO A 1 10 ? 0.480 2.069 -2.031 1.00 96.94 10 A 1 ATOM 81 N N . MET A 1 11 ? 3.221 0.089 -2.985 1.00 94.79 11 A 1 ATOM 82 C CA . MET A 1 11 ? 4.520 -0.557 -2.896 1.00 94.48 11 A 1 ATOM 83 C C . MET A 1 11 ? 4.403 -2.064 -3.115 1.00 95.15 11 A 1 ATOM 84 O O . MET A 1 11 ? 5.407 -2.767 -3.235 1.00 93.75 11 A 1 ATOM 85 C CB . MET A 1 11 ? 5.161 -0.279 -1.534 1.00 93.05 11 A 1 ATOM 86 C CG . MET A 1 11 ? 6.649 -0.520 -1.520 1.00 89.78 11 A 1 ATOM 87 S SD . MET A 1 11 ? 7.554 0.775 -2.358 1.00 83.47 11 A 1 ATOM 88 C CE . MET A 1 11 ? 7.567 2.026 -1.084 1.00 76.42 11 A 1 ATOM 89 N N . ALA A 1 12 ? 3.176 -2.545 -3.185 1.00 94.16 12 A 1 ATOM 90 C CA . ALA A 1 12 ? 2.923 -3.965 -3.376 1.00 93.22 12 A 1 ATOM 91 C C . ALA A 1 12 ? 2.722 -4.292 -4.854 1.00 93.92 12 A 1 ATOM 92 O O . ALA A 1 12 ? 1.652 -4.065 -5.408 1.00 92.91 12 A 1 ATOM 93 C CB . ALA A 1 12 ? 1.710 -4.393 -2.563 1.00 92.34 12 A 1 ATOM 94 N N . PHE A 1 13 ? 3.756 -4.860 -5.498 1.00 95.67 13 A 1 ATOM 95 C CA . PHE A 1 13 ? 3.689 -5.219 -6.915 1.00 94.05 13 A 1 ATOM 96 C C . PHE A 1 13 ? 3.115 -6.613 -7.103 1.00 92.46 13 A 1 ATOM 97 O O . PHE A 1 13 ? 3.744 -7.581 -6.653 1.00 89.05 13 A 1 ATOM 98 C CB . PHE A 1 13 ? 5.077 -5.160 -7.548 1.00 92.02 13 A 1 ATOM 99 C CG . PHE A 1 13 ? 5.647 -3.774 -7.658 1.00 90.41 13 A 1 ATOM 100 C CD1 . PHE A 1 13 ? 6.330 -3.209 -6.594 1.00 89.28 13 A 1 ATOM 101 C CD2 . PHE A 1 13 ? 5.496 -3.040 -8.818 1.00 89.74 13 A 1 ATOM 102 C CE1 . PHE A 1 13 ? 6.867 -1.939 -6.678 1.00 89.65 13 A 1 ATOM 103 C CE2 . PHE A 1 13 ? 6.027 -1.770 -8.921 1.00 90.32 13 A 1 ATOM 104 C CZ . PHE A 1 13 ? 6.716 -1.221 -7.845 1.00 88.20 13 A 1 ATOM 105 O OXT . PHE A 1 13 ? 2.041 -6.745 -7.711 1.00 82.85 13 A 1 #