# 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_spkb24686 # _entry.id spkb24686 # 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" "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" "C3 H7 N O3" 105.093 SER y SERINE C([C@@H](C(=O)O)N)O ? "L-PEPTIDE LINKING" "C9 H11 N O3" 181.189 TYR y TYROSINE c1cc(ccc1C[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 LYS 2 1 n ARG 3 1 n LEU 4 1 n GLY 5 1 n LEU 6 1 n ALA 7 1 n ALA 8 1 n LEU 9 1 n TYR 10 1 n ILE 11 1 n GLY 12 1 n SER 13 1 n ALA 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 @ 2025-07-08 05:52:02)" _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 88.64 _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 78.62 1 1 A LYS 2 2 80.91 1 2 A ARG 3 2 84.11 1 3 A LEU 4 2 87.40 1 4 A GLY 5 2 92.84 1 5 A LEU 6 2 92.04 1 6 A ALA 7 2 95.84 1 7 A ALA 8 2 95.95 1 8 A LEU 9 2 92.13 1 9 A TYR 10 2 90.25 1 10 A ILE 11 2 90.72 1 11 A GLY 12 2 93.68 1 12 A SER 13 2 92.39 1 13 A ALA 14 2 94.03 1 14 A LEU 15 2 87.75 1 15 A ALA 16 2 83.08 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 LYS . 2 A 2 A 3 1 n ARG . 3 A 3 A 4 1 n LEU . 4 A 4 A 5 1 n GLY . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n ALA . 7 A 7 A 8 1 n ALA . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n TYR . 10 A 10 A 11 1 n ILE . 11 A 11 A 12 1 n GLY . 12 A 12 A 13 1 n SER . 13 A 13 A 14 1 n ALA . 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 ? 11.242 -3.763 5.649 1.00 81.43 1 A 1 ATOM 2 C CA . MET A 1 1 ? 10.235 -3.266 6.603 1.00 85.20 1 A 1 ATOM 3 C C . MET A 1 1 ? 9.385 -2.159 5.968 1.00 87.19 1 A 1 ATOM 4 O O . MET A 1 1 ? 9.386 -1.020 6.418 1.00 83.28 1 A 1 ATOM 5 C CB . MET A 1 1 ? 10.945 -2.731 7.839 1.00 78.54 1 A 1 ATOM 6 C CG . MET A 1 1 ? 10.136 -2.892 9.089 1.00 76.22 1 A 1 ATOM 7 S SD . MET A 1 1 ? 10.856 -1.988 10.450 1.00 73.90 1 A 1 ATOM 8 C CE . MET A 1 1 ? 11.220 -3.331 11.552 1.00 63.21 1 A 1 ATOM 9 N N . LYS A 1 2 ? 8.670 -2.510 4.912 1.00 84.32 2 A 1 ATOM 10 C CA . LYS A 1 2 ? 7.826 -1.526 4.230 1.00 87.62 2 A 1 ATOM 11 C C . LYS A 1 2 ? 6.529 -2.175 3.760 1.00 89.94 2 A 1 ATOM 12 O O . LYS A 1 2 ? 6.527 -2.964 2.824 1.00 87.67 2 A 1 ATOM 13 C CB . LYS A 1 2 ? 8.581 -0.932 3.052 1.00 84.48 2 A 1 ATOM 14 C CG . LYS A 1 2 ? 9.600 0.093 3.517 1.00 79.44 2 A 1 ATOM 15 C CD . LYS A 1 2 ? 10.132 0.928 2.391 1.00 78.36 2 A 1 ATOM 16 C CE . LYS A 1 2 ? 11.053 2.004 2.944 1.00 70.69 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? 12.431 1.782 2.496 1.00 65.69 2 A 1 ATOM 18 N N . ARG A 1 3 ? 5.448 -1.831 4.384 1.00 91.09 3 A 1 ATOM 19 C CA . ARG A 1 3 ? 4.136 -2.394 4.056 1.00 93.64 3 A 1 ATOM 20 C C . ARG A 1 3 ? 3.461 -1.615 2.928 1.00 95.32 3 A 1 ATOM 21 O O . ARG A 1 3 ? 2.237 -1.573 2.838 1.00 92.79 3 A 1 ATOM 22 C CB . ARG A 1 3 ? 3.271 -2.356 5.315 1.00 91.29 3 A 1 ATOM 23 C CG . ARG A 1 3 ? 3.955 -3.021 6.488 1.00 86.77 3 A 1 ATOM 24 C CD . ARG A 1 3 ? 3.395 -4.396 6.705 1.00 83.82 3 A 1 ATOM 25 N NE . ARG A 1 3 ? 2.344 -4.334 7.713 1.00 77.63 3 A 1 ATOM 26 C CZ . ARG A 1 3 ? 2.570 -4.409 9.010 1.00 75.53 3 A 1 ATOM 27 N NH1 . ARG A 1 3 ? 3.787 -4.524 9.489 1.00 69.44 3 A 1 ATOM 28 N NH2 . ARG A 1 3 ? 1.551 -4.359 9.844 1.00 67.92 3 A 1 ATOM 29 N N . LEU A 1 4 ? 4.239 -1.004 2.061 1.00 88.63 4 A 1 ATOM 30 C CA . LEU A 1 4 ? 3.694 -0.230 0.945 1.00 89.98 4 A 1 ATOM 31 C C . LEU A 1 4 ? 2.956 -1.135 -0.032 1.00 92.44 4 A 1 ATOM 32 O O . LEU A 1 4 ? 2.014 -0.704 -0.692 1.00 89.59 4 A 1 ATOM 33 C CB . LEU A 1 4 ? 4.831 0.496 0.231 1.00 88.53 4 A 1 ATOM 34 C CG . LEU A 1 4 ? 5.479 1.578 1.085 1.00 86.14 4 A 1 ATOM 35 C CD1 . LEU A 1 4 ? 6.717 2.111 0.382 1.00 82.91 4 A 1 ATOM 36 C CD2 . LEU A 1 4 ? 4.500 2.707 1.349 1.00 80.95 4 A 1 ATOM 37 N N . GLY A 1 5 ? 3.392 -2.375 -0.120 1.00 91.64 5 A 1 ATOM 38 C CA . GLY A 1 5 ? 2.745 -3.333 -1.013 1.00 92.02 5 A 1 ATOM 39 C C . GLY A 1 5 ? 1.288 -3.556 -0.644 1.00 94.05 5 A 1 ATOM 40 O O . GLY A 1 5 ? 0.436 -3.743 -1.510 1.00 93.65 5 A 1 ATOM 41 N N . LEU A 1 6 ? 1.007 -3.528 0.641 1.00 94.08 6 A 1 ATOM 42 C CA . LEU A 1 6 ? -0.361 -3.734 1.120 1.00 94.97 6 A 1 ATOM 43 C C . LEU A 1 6 ? -1.061 -2.404 1.374 1.00 95.92 6 A 1 ATOM 44 O O . LEU A 1 6 ? -2.229 -2.235 1.030 1.00 95.02 6 A 1 ATOM 45 C CB . LEU A 1 6 ? -0.321 -4.554 2.408 1.00 93.91 6 A 1 ATOM 46 C CG . LEU A 1 6 ? 0.279 -5.942 2.208 1.00 90.20 6 A 1 ATOM 47 C CD1 . LEU A 1 6 ? 0.493 -6.616 3.552 1.00 86.77 6 A 1 ATOM 48 C CD2 . LEU A 1 6 ? -0.635 -6.793 1.335 1.00 85.45 6 A 1 ATOM 49 N N . ALA A 1 7 ? -0.345 -1.468 1.971 1.00 95.73 7 A 1 ATOM 50 C CA . ALA A 1 7 ? -0.917 -0.159 2.272 1.00 95.86 7 A 1 ATOM 51 C C . ALA A 1 7 ? -1.251 0.603 0.996 1.00 96.52 7 A 1 ATOM 52 O O . ALA A 1 7 ? -2.285 1.260 0.903 1.00 95.91 7 A 1 ATOM 53 C CB . ALA A 1 7 ? 0.057 0.642 3.126 1.00 95.17 7 A 1 ATOM 54 N N . ALA A 1 8 ? -0.383 0.514 0.004 1.00 96.06 8 A 1 ATOM 55 C CA . ALA A 1 8 ? -0.599 1.208 -1.262 1.00 96.12 8 A 1 ATOM 56 C C . ALA A 1 8 ? -1.861 0.697 -1.948 1.00 96.53 8 A 1 ATOM 57 O O . ALA A 1 8 ? -2.635 1.470 -2.505 1.00 95.59 8 A 1 ATOM 58 C CB . ALA A 1 8 ? 0.609 1.011 -2.168 1.00 95.47 8 A 1 ATOM 59 N N . LEU A 1 9 ? -2.062 -0.603 -1.911 1.00 94.97 9 A 1 ATOM 60 C CA . LEU A 1 9 ? -3.244 -1.202 -2.528 1.00 94.91 9 A 1 ATOM 61 C C . LEU A 1 9 ? -4.488 -0.915 -1.697 1.00 95.55 9 A 1 ATOM 62 O O . LEU A 1 9 ? -5.573 -0.718 -2.242 1.00 94.74 9 A 1 ATOM 63 C CB . LEU A 1 9 ? -3.036 -2.708 -2.660 1.00 94.51 9 A 1 ATOM 64 C CG . LEU A 1 9 ? -1.927 -3.072 -3.643 1.00 91.01 9 A 1 ATOM 65 C CD1 . LEU A 1 9 ? -1.648 -4.568 -3.577 1.00 85.77 9 A 1 ATOM 66 C CD2 . LEU A 1 9 ? -2.325 -2.688 -5.065 1.00 85.55 9 A 1 ATOM 67 N N . TYR A 1 10 ? -4.323 -0.896 -0.397 1.00 94.61 10 A 1 ATOM 68 C CA . TYR A 1 10 ? -5.437 -0.623 0.509 1.00 93.72 10 A 1 ATOM 69 C C . TYR A 1 10 ? -5.990 0.779 0.266 1.00 94.57 10 A 1 ATOM 70 O O . TYR A 1 10 ? -7.200 0.972 0.152 1.00 94.03 10 A 1 ATOM 71 C CB . TYR A 1 10 ? -4.958 -0.762 1.953 1.00 93.14 10 A 1 ATOM 72 C CG . TYR A 1 10 ? -6.019 -0.348 2.942 1.00 90.60 10 A 1 ATOM 73 C CD1 . TYR A 1 10 ? -7.128 -1.158 3.172 1.00 88.23 10 A 1 ATOM 74 C CD2 . TYR A 1 10 ? -5.911 0.851 3.636 1.00 87.80 10 A 1 ATOM 75 C CE1 . TYR A 1 10 ? -8.106 -0.773 4.080 1.00 86.62 10 A 1 ATOM 76 C CE2 . TYR A 1 10 ? -6.891 1.240 4.543 1.00 86.83 10 A 1 ATOM 77 C CZ . TYR A 1 10 ? -7.984 0.423 4.760 1.00 87.52 10 A 1 ATOM 78 O OH . TYR A 1 10 ? -8.954 0.811 5.655 1.00 85.37 10 A 1 ATOM 79 N N . ILE A 1 11 ? -5.100 1.740 0.180 1.00 93.46 11 A 1 ATOM 80 C CA . ILE A 1 11 ? -5.505 3.127 -0.049 1.00 92.95 11 A 1 ATOM 81 C C . ILE A 1 11 ? -5.711 3.386 -1.538 1.00 93.48 11 A 1 ATOM 82 O O . ILE A 1 11 ? -6.644 4.081 -1.940 1.00 91.75 11 A 1 ATOM 83 C CB . ILE A 1 11 ? -4.450 4.085 0.514 1.00 92.51 11 A 1 ATOM 84 C CG1 . ILE A 1 11 ? -4.273 3.851 2.019 1.00 89.56 11 A 1 ATOM 85 C CG2 . ILE A 1 11 ? -4.877 5.531 0.255 1.00 88.85 11 A 1 ATOM 86 C CD1 . ILE A 1 11 ? -3.067 4.570 2.590 1.00 83.19 11 A 1 ATOM 87 N N . GLY A 1 12 ? -4.830 2.836 -2.346 1.00 93.66 12 A 1 ATOM 88 C CA . GLY A 1 12 ? -4.935 3.016 -3.791 1.00 92.85 12 A 1 ATOM 89 C C . GLY A 1 12 ? -6.228 2.451 -4.347 1.00 94.29 12 A 1 ATOM 90 O O . GLY A 1 12 ? -6.838 3.036 -5.242 1.00 93.92 12 A 1 ATOM 91 N N . SER A 1 13 ? -6.653 1.323 -3.832 1.00 95.01 13 A 1 ATOM 92 C CA . SER A 1 13 ? -7.893 0.690 -4.283 1.00 94.77 13 A 1 ATOM 93 C C . SER A 1 13 ? -9.113 1.482 -3.835 1.00 95.42 13 A 1 ATOM 94 O O . SER A 1 13 ? -10.139 1.493 -4.513 1.00 93.75 13 A 1 ATOM 95 C CB . SER A 1 13 ? -7.982 -0.731 -3.737 1.00 93.10 13 A 1 ATOM 96 O OG . SER A 1 13 ? -9.104 -1.375 -4.272 1.00 82.30 13 A 1 ATOM 97 N N . ALA A 1 14 ? -9.003 2.146 -2.710 1.00 94.15 14 A 1 ATOM 98 C CA . ALA A 1 14 ? -10.111 2.932 -2.165 1.00 94.36 14 A 1 ATOM 99 C C . ALA A 1 14 ? -10.472 4.091 -3.087 1.00 95.37 14 A 1 ATOM 100 O O . ALA A 1 14 ? -11.630 4.496 -3.157 1.00 93.47 14 A 1 ATOM 101 C CB . ALA A 1 14 ? -9.734 3.457 -0.785 1.00 92.79 14 A 1 ATOM 102 N N . LEU A 1 15 ? -9.482 4.640 -3.782 1.00 91.57 15 A 1 ATOM 103 C CA . LEU A 1 15 ? -9.725 5.763 -4.689 1.00 91.47 15 A 1 ATOM 104 C C . LEU A 1 15 ? -10.440 5.308 -5.955 1.00 92.70 15 A 1 ATOM 105 O O . LEU A 1 15 ? -11.074 6.112 -6.645 1.00 89.87 15 A 1 ATOM 106 C CB . LEU A 1 15 ? -8.390 6.430 -5.039 1.00 89.42 15 A 1 ATOM 107 C CG . LEU A 1 15 ? -7.463 5.540 -5.885 1.00 85.15 15 A 1 ATOM 108 C CD1 . LEU A 1 15 ? -7.805 5.625 -7.368 1.00 81.69 15 A 1 ATOM 109 C CD2 . LEU A 1 15 ? -6.014 5.959 -5.672 1.00 80.10 15 A 1 ATOM 110 N N . ALA A 1 16 ? -10.335 4.043 -6.276 1.00 89.38 16 A 1 ATOM 111 C CA . ALA A 1 16 ? -10.949 3.499 -7.486 1.00 87.29 16 A 1 ATOM 112 C C . ALA A 1 16 ? -12.434 3.225 -7.246 1.00 85.64 16 A 1 ATOM 113 O O . ALA A 1 16 ? -13.196 3.151 -8.222 1.00 80.14 16 A 1 ATOM 114 C CB . ALA A 1 16 ? -10.213 2.230 -7.910 1.00 80.93 16 A 1 ATOM 115 O OXT . ALA A 1 16 ? -12.847 3.078 -6.096 1.00 75.12 16 A 1 #