# 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_spkb24873 # _entry.id spkb24873 # 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" "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 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" "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 ALA 2 1 n LEU 3 1 n LEU 4 1 n MET 5 1 n THR 6 1 n CYS 7 1 n PHE 8 1 n VAL 9 1 n ILE 10 1 n VAL 11 1 n PHE 12 1 n ALA 13 1 n ALA 14 1 n SER 15 # _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 03:47:33)" _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 95.03 _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 82.36 1 1 A ALA 2 2 93.81 1 2 A LEU 3 2 95.35 1 3 A LEU 4 2 95.61 1 4 A MET 5 2 94.25 1 5 A THR 6 2 97.00 1 6 A CYS 7 2 97.63 1 7 A PHE 8 2 95.93 1 8 A VAL 9 2 97.76 1 9 A ILE 10 2 97.54 1 10 A VAL 11 2 97.73 1 11 A PHE 12 2 95.50 1 12 A ALA 13 2 97.87 1 13 A ALA 14 2 97.73 1 14 A SER 15 2 91.67 1 15 # _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 ALA . 2 A 2 A 3 1 n LEU . 3 A 3 A 4 1 n LEU . 4 A 4 A 5 1 n MET . 5 A 5 A 6 1 n THR . 6 A 6 A 7 1 n CYS . 7 A 7 A 8 1 n PHE . 8 A 8 A 9 1 n VAL . 9 A 9 A 10 1 n ILE . 10 A 10 A 11 1 n VAL . 11 A 11 A 12 1 n PHE . 12 A 12 A 13 1 n ALA . 13 A 13 A 14 1 n ALA . 14 A 14 A 15 1 n SER . 15 A 15 # _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 ? 3.155 4.199 15.039 1.00 89.34 1 A 1 ATOM 2 C CA . MET A 1 1 ? 2.203 4.598 13.986 1.00 89.16 1 A 1 ATOM 3 C C . MET A 1 1 ? 2.571 3.971 12.646 1.00 89.31 1 A 1 ATOM 4 O O . MET A 1 1 ? 3.712 4.073 12.211 1.00 86.49 1 A 1 ATOM 5 C CB . MET A 1 1 ? 2.200 6.113 13.836 1.00 84.30 1 A 1 ATOM 6 C CG . MET A 1 1 ? 1.628 6.814 15.052 1.00 78.59 1 A 1 ATOM 7 S SD . MET A 1 1 ? 2.910 7.571 16.030 1.00 75.57 1 A 1 ATOM 8 C CE . MET A 1 1 ? 1.936 8.332 17.319 1.00 66.15 1 A 1 ATOM 9 N N . ALA A 1 2 ? 1.608 3.336 11.996 1.00 89.89 2 A 1 ATOM 10 C CA . ALA A 1 2 ? 1.840 2.664 10.716 1.00 94.83 2 A 1 ATOM 11 C C . ALA A 1 2 ? 1.053 3.328 9.582 1.00 96.84 2 A 1 ATOM 12 O O . ALA A 1 2 ? 0.562 2.654 8.678 1.00 95.48 2 A 1 ATOM 13 C CB . ALA A 1 2 ? 1.465 1.196 10.835 1.00 92.02 2 A 1 ATOM 14 N N . LEU A 1 3 ? 0.923 4.648 9.639 1.00 96.91 3 A 1 ATOM 15 C CA . LEU A 1 3 ? 0.183 5.391 8.620 1.00 97.52 3 A 1 ATOM 16 C C . LEU A 1 3 ? 0.923 5.367 7.288 1.00 97.98 3 A 1 ATOM 17 O O . LEU A 1 3 ? 0.331 5.135 6.235 1.00 97.42 3 A 1 ATOM 18 C CB . LEU A 1 3 ? -0.031 6.832 9.085 1.00 97.05 3 A 1 ATOM 19 C CG . LEU A 1 3 ? -1.487 7.289 9.064 1.00 94.02 3 A 1 ATOM 20 C CD1 . LEU A 1 3 ? -1.595 8.702 9.623 1.00 91.61 3 A 1 ATOM 21 C CD2 . LEU A 1 3 ? -2.061 7.227 7.663 1.00 90.29 3 A 1 ATOM 22 N N . LEU A 1 4 ? 2.216 5.603 7.333 1.00 97.97 4 A 1 ATOM 23 C CA . LEU A 1 4 ? 3.054 5.612 6.139 1.00 98.11 4 A 1 ATOM 24 C C . LEU A 1 4 ? 3.063 4.240 5.477 1.00 98.22 4 A 1 ATOM 25 O O . LEU A 1 4 ? 2.958 4.125 4.258 1.00 97.84 4 A 1 ATOM 26 C CB . LEU A 1 4 ? 4.480 6.039 6.511 1.00 97.78 4 A 1 ATOM 27 C CG . LEU A 1 4 ? 5.142 6.974 5.503 1.00 93.69 4 A 1 ATOM 28 C CD1 . LEU A 1 4 ? 5.387 6.268 4.181 1.00 91.01 4 A 1 ATOM 29 C CD2 . LEU A 1 4 ? 4.287 8.215 5.296 1.00 90.26 4 A 1 ATOM 30 N N . MET A 1 5 ? 3.193 3.202 6.285 1.00 98.18 5 A 1 ATOM 31 C CA . MET A 1 5 ? 3.220 1.829 5.779 1.00 98.20 5 A 1 ATOM 32 C C . MET A 1 5 ? 1.884 1.455 5.138 1.00 98.31 5 A 1 ATOM 33 O O . MET A 1 5 ? 1.841 0.896 4.049 1.00 97.86 5 A 1 ATOM 34 C CB . MET A 1 5 ? 3.537 0.859 6.916 1.00 97.88 5 A 1 ATOM 35 C CG . MET A 1 5 ? 4.798 0.062 6.650 1.00 94.61 5 A 1 ATOM 36 S SD . MET A 1 5 ? 5.057 -1.229 7.857 1.00 88.49 5 A 1 ATOM 37 C CE . MET A 1 5 ? 6.518 -2.007 7.173 1.00 80.49 5 A 1 ATOM 38 N N . THR A 1 6 ? 0.798 1.775 5.814 1.00 98.34 6 A 1 ATOM 39 C CA . THR A 1 6 ? -0.538 1.465 5.311 1.00 98.36 6 A 1 ATOM 40 C C . THR A 1 6 ? -0.824 2.217 4.016 1.00 98.50 6 A 1 ATOM 41 O O . THR A 1 6 ? -1.314 1.643 3.043 1.00 98.11 6 A 1 ATOM 42 C CB . THR A 1 6 ? -1.592 1.805 6.376 1.00 97.92 6 A 1 ATOM 43 O OG1 . THR A 1 6 ? -1.780 0.675 7.227 1.00 94.26 6 A 1 ATOM 44 C CG2 . THR A 1 6 ? -2.940 2.155 5.762 1.00 93.53 6 A 1 ATOM 45 N N . CYS A 1 7 ? -0.521 3.498 3.991 1.00 98.26 7 A 1 ATOM 46 C CA . CYS A 1 7 ? -0.741 4.328 2.807 1.00 98.37 7 A 1 ATOM 47 C C . CYS A 1 7 ? 0.113 3.841 1.636 1.00 98.39 7 A 1 ATOM 48 O O . CYS A 1 7 ? -0.330 3.838 0.492 1.00 97.88 7 A 1 ATOM 49 C CB . CYS A 1 7 ? -0.412 5.780 3.132 1.00 98.19 7 A 1 ATOM 50 S SG . CYS A 1 7 ? -1.359 6.935 2.124 1.00 94.69 7 A 1 ATOM 51 N N . PHE A 1 8 ? 1.320 3.425 1.937 1.00 97.80 8 A 1 ATOM 52 C CA . PHE A 1 8 ? 2.240 2.929 0.919 1.00 97.76 8 A 1 ATOM 53 C C . PHE A 1 8 ? 1.698 1.665 0.261 1.00 97.91 8 A 1 ATOM 54 O O . PHE A 1 8 ? 1.734 1.527 -0.962 1.00 97.58 8 A 1 ATOM 55 C CB . PHE A 1 8 ? 3.601 2.650 1.551 1.00 97.41 8 A 1 ATOM 56 C CG . PHE A 1 8 ? 4.663 2.319 0.539 1.00 96.37 8 A 1 ATOM 57 C CD1 . PHE A 1 8 ? 5.056 3.256 -0.402 1.00 94.50 8 A 1 ATOM 58 C CD2 . PHE A 1 8 ? 5.264 1.072 0.539 1.00 94.84 8 A 1 ATOM 59 C CE1 . PHE A 1 8 ? 6.033 2.956 -1.336 1.00 93.70 8 A 1 ATOM 60 C CE2 . PHE A 1 8 ? 6.245 0.767 -0.397 1.00 93.43 8 A 1 ATOM 61 C CZ . PHE A 1 8 ? 6.630 1.708 -1.335 1.00 93.94 8 A 1 ATOM 62 N N . VAL A 1 9 ? 1.187 0.743 1.073 1.00 98.21 9 A 1 ATOM 63 C CA . VAL A 1 9 ? 0.631 -0.514 0.566 1.00 98.24 9 A 1 ATOM 64 C C . VAL A 1 9 ? -0.598 -0.249 -0.299 1.00 98.34 9 A 1 ATOM 65 O O . VAL A 1 9 ? -0.790 -0.884 -1.336 1.00 98.00 9 A 1 ATOM 66 C CB . VAL A 1 9 ? 0.259 -1.458 1.720 1.00 97.92 9 A 1 ATOM 67 C CG1 . VAL A 1 9 ? -0.375 -2.736 1.189 1.00 96.82 9 A 1 ATOM 68 C CG2 . VAL A 1 9 ? 1.492 -1.801 2.545 1.00 96.80 9 A 1 ATOM 69 N N . ILE A 1 10 ? -1.439 0.688 0.119 1.00 98.33 10 A 1 ATOM 70 C CA . ILE A 1 10 ? -2.652 1.029 -0.614 1.00 98.22 10 A 1 ATOM 71 C C . ILE A 1 10 ? -2.316 1.633 -1.975 1.00 98.23 10 A 1 ATOM 72 O O . ILE A 1 10 ? -2.910 1.276 -2.994 1.00 97.91 10 A 1 ATOM 73 C CB . ILE A 1 10 ? -3.517 2.008 0.197 1.00 98.05 10 A 1 ATOM 74 C CG1 . ILE A 1 10 ? -4.036 1.347 1.471 1.00 97.39 10 A 1 ATOM 75 C CG2 . ILE A 1 10 ? -4.701 2.489 -0.652 1.00 97.21 10 A 1 ATOM 76 C CD1 . ILE A 1 10 ? -4.554 2.339 2.493 1.00 95.01 10 A 1 ATOM 77 N N . VAL A 1 11 ? -1.374 2.550 -1.993 1.00 98.38 11 A 1 ATOM 78 C CA . VAL A 1 11 ? -0.960 3.205 -3.236 1.00 98.29 11 A 1 ATOM 79 C C . VAL A 1 11 ? -0.340 2.202 -4.200 1.00 98.27 11 A 1 ATOM 80 O O . VAL A 1 11 ? -0.609 2.232 -5.404 1.00 97.97 11 A 1 ATOM 81 C CB . VAL A 1 11 ? 0.036 4.333 -2.947 1.00 97.95 11 A 1 ATOM 82 C CG1 . VAL A 1 11 ? 0.586 4.909 -4.243 1.00 96.68 11 A 1 ATOM 83 C CG2 . VAL A 1 11 ? -0.636 5.428 -2.135 1.00 96.55 11 A 1 ATOM 84 N N . PHE A 1 12 ? 0.481 1.318 -3.673 1.00 98.03 12 A 1 ATOM 85 C CA . PHE A 1 12 ? 1.148 0.309 -4.488 1.00 97.76 12 A 1 ATOM 86 C C . PHE A 1 12 ? 0.155 -0.720 -5.015 1.00 97.93 12 A 1 ATOM 87 O O . PHE A 1 12 ? 0.265 -1.171 -6.154 1.00 97.62 12 A 1 ATOM 88 C CB . PHE A 1 12 ? 2.232 -0.380 -3.661 1.00 97.37 12 A 1 ATOM 89 C CG . PHE A 1 12 ? 3.349 -0.924 -4.513 1.00 95.35 12 A 1 ATOM 90 C CD1 . PHE A 1 12 ? 4.110 -0.075 -5.297 1.00 93.53 12 A 1 ATOM 91 C CD2 . PHE A 1 12 ? 3.628 -2.280 -4.517 1.00 93.94 12 A 1 ATOM 92 C CE1 . PHE A 1 12 ? 5.135 -0.567 -6.087 1.00 92.88 12 A 1 ATOM 93 C CE2 . PHE A 1 12 ? 4.657 -2.782 -5.306 1.00 93.41 12 A 1 ATOM 94 C CZ . PHE A 1 12 ? 5.409 -1.924 -6.091 1.00 92.65 12 A 1 ATOM 95 N N . ALA A 1 13 ? -0.821 -1.091 -4.194 1.00 98.03 13 A 1 ATOM 96 C CA . ALA A 1 13 ? -1.838 -2.070 -4.584 1.00 98.03 13 A 1 ATOM 97 C C . ALA A 1 13 ? -2.803 -1.487 -5.611 1.00 98.14 13 A 1 ATOM 98 O O . ALA A 1 13 ? -3.348 -2.210 -6.441 1.00 97.62 13 A 1 ATOM 99 C CB . ALA A 1 13 ? -2.611 -2.535 -3.356 1.00 97.54 13 A 1 ATOM 100 N N . ALA A 1 14 ? -3.036 -0.188 -5.555 1.00 98.10 14 A 1 ATOM 101 C CA . ALA A 1 14 ? -3.947 0.490 -6.474 1.00 98.00 14 A 1 ATOM 102 C C . ALA A 1 14 ? -3.250 0.862 -7.776 1.00 98.01 14 A 1 ATOM 103 O O . ALA A 1 14 ? -3.894 1.335 -8.715 1.00 97.12 14 A 1 ATOM 104 C CB . ALA A 1 14 ? -4.519 1.739 -5.809 1.00 97.41 14 A 1 ATOM 105 N N . SER A 1 15 ? -1.955 0.630 -7.835 1.00 96.69 15 A 1 ATOM 106 C CA . SER A 1 15 ? -1.157 0.962 -9.012 1.00 95.71 15 A 1 ATOM 107 C C . SER A 1 15 ? -1.647 0.199 -10.242 1.00 93.77 15 A 1 ATOM 108 O O . SER A 1 15 ? -1.956 0.832 -11.263 1.00 89.05 15 A 1 ATOM 109 C CB . SER A 1 15 ? 0.316 0.653 -8.753 1.00 92.94 15 A 1 ATOM 110 O OG . SER A 1 15 ? 1.109 1.756 -9.080 1.00 86.68 15 A 1 ATOM 111 O OXT . SER A 1 15 ? -1.700 -1.020 -10.178 1.00 86.83 15 A 1 #