# 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_spkb24839 # _entry.id spkb24839 # 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" "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" "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 ARG 2 1 n PHE 3 1 n PHE 4 1 n ALA 5 1 n THR 6 1 n LEU 7 1 n VAL 8 1 n LEU 9 1 n ALA 10 1 n LEU 11 1 n PRO 12 1 n ALA 13 1 n LEU 14 1 n ALA 15 1 n MET 16 1 n ALA 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 06:02:20)" _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 92.88 _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 86.65 1 1 A ARG 2 2 85.86 1 2 A PHE 3 2 89.19 1 3 A PHE 4 2 92.31 1 4 A ALA 5 2 96.40 1 5 A THR 6 2 95.75 1 6 A LEU 7 2 94.63 1 7 A VAL 8 2 96.46 1 8 A LEU 9 2 95.57 1 9 A ALA 10 2 96.99 1 10 A LEU 11 2 95.11 1 11 A PRO 12 2 96.72 1 12 A ALA 13 2 96.95 1 13 A LEU 14 2 94.39 1 14 A ALA 15 2 97.20 1 15 A MET 16 2 90.16 1 16 A ALA 17 2 89.13 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 ARG . 2 A 2 A 3 1 n PHE . 3 A 3 A 4 1 n PHE . 4 A 4 A 5 1 n ALA . 5 A 5 A 6 1 n THR . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n VAL . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n ALA . 10 A 10 A 11 1 n LEU . 11 A 11 A 12 1 n PRO . 12 A 12 A 13 1 n ALA . 13 A 13 A 14 1 n LEU . 14 A 14 A 15 1 n ALA . 15 A 15 A 16 1 n MET . 16 A 16 A 17 1 n ALA . 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 ? -7.200 7.100 9.400 1.00 91.60 1 A 1 ATOM 2 C CA . MET A 1 1 ? -6.036 7.492 8.586 1.00 92.33 1 A 1 ATOM 3 C C . MET A 1 1 ? -5.077 6.318 8.382 1.00 93.60 1 A 1 ATOM 4 O O . MET A 1 1 ? -4.359 6.255 7.393 1.00 91.25 1 A 1 ATOM 5 C CB . MET A 1 1 ? -5.302 8.660 9.254 1.00 88.41 1 A 1 ATOM 6 C CG . MET A 1 1 ? -4.867 8.358 10.681 1.00 83.69 1 A 1 ATOM 7 S SD . MET A 1 1 ? -4.303 9.847 11.529 1.00 81.00 1 A 1 ATOM 8 C CE . MET A 1 1 ? -5.696 10.154 12.579 1.00 71.29 1 A 1 ATOM 9 N N . ARG A 1 2 ? -5.074 5.397 9.337 1.00 90.93 2 A 1 ATOM 10 C CA . ARG A 1 2 ? -4.204 4.225 9.249 1.00 93.97 2 A 1 ATOM 11 C C . ARG A 1 2 ? -4.629 3.315 8.098 1.00 95.59 2 A 1 ATOM 12 O O . ARG A 1 2 ? -3.796 2.652 7.477 1.00 94.34 2 A 1 ATOM 13 C CB . ARG A 1 2 ? -4.238 3.457 10.572 1.00 91.98 2 A 1 ATOM 14 C CG . ARG A 1 2 ? -3.203 2.360 10.642 1.00 87.71 2 A 1 ATOM 15 C CD . ARG A 1 2 ? -3.722 1.065 10.017 1.00 86.24 2 A 1 ATOM 16 N NE . ARG A 1 2 ? -3.523 -0.085 10.900 1.00 80.56 2 A 1 ATOM 17 C CZ . ARG A 1 2 ? -3.878 -1.323 10.605 1.00 78.93 2 A 1 ATOM 18 N NH1 . ARG A 1 2 ? -4.439 -1.599 9.447 1.00 71.69 2 A 1 ATOM 19 N NH2 . ARG A 1 2 ? -3.680 -2.299 11.480 1.00 72.49 2 A 1 ATOM 20 N N . PHE A 1 3 ? -5.903 3.302 7.801 1.00 91.10 3 A 1 ATOM 21 C CA . PHE A 1 3 ? -6.442 2.482 6.724 1.00 93.24 3 A 1 ATOM 22 C C . PHE A 1 3 ? -5.840 2.879 5.379 1.00 95.50 3 A 1 ATOM 23 O O . PHE A 1 3 ? -5.746 2.065 4.464 1.00 94.59 3 A 1 ATOM 24 C CB . PHE A 1 3 ? -7.960 2.634 6.677 1.00 92.16 3 A 1 ATOM 25 C CG . PHE A 1 3 ? -8.659 1.339 6.373 1.00 89.76 3 A 1 ATOM 26 C CD1 . PHE A 1 3 ? -8.663 0.306 7.295 1.00 86.43 3 A 1 ATOM 27 C CD2 . PHE A 1 3 ? -9.315 1.162 5.167 1.00 86.27 3 A 1 ATOM 28 C CE1 . PHE A 1 3 ? -9.312 -0.893 7.019 1.00 85.02 3 A 1 ATOM 29 C CE2 . PHE A 1 3 ? -9.965 -0.033 4.879 1.00 83.80 3 A 1 ATOM 30 C CZ . PHE A 1 3 ? -9.965 -1.063 5.807 1.00 83.27 3 A 1 ATOM 31 N N . PHE A 1 4 ? -5.433 4.121 5.273 1.00 95.02 4 A 1 ATOM 32 C CA . PHE A 1 4 ? -4.839 4.633 4.046 1.00 95.44 4 A 1 ATOM 33 C C . PHE A 1 4 ? -3.536 3.904 3.735 1.00 96.22 4 A 1 ATOM 34 O O . PHE A 1 4 ? -3.250 3.581 2.585 1.00 95.62 4 A 1 ATOM 35 C CB . PHE A 1 4 ? -4.572 6.133 4.182 1.00 94.92 4 A 1 ATOM 36 C CG . PHE A 1 4 ? -5.232 6.935 3.094 1.00 92.88 4 A 1 ATOM 37 C CD1 . PHE A 1 4 ? -4.820 6.805 1.778 1.00 89.78 4 A 1 ATOM 38 C CD2 . PHE A 1 4 ? -6.266 7.814 3.387 1.00 89.99 4 A 1 ATOM 39 C CE1 . PHE A 1 4 ? -5.428 7.536 0.767 1.00 88.68 4 A 1 ATOM 40 C CE2 . PHE A 1 4 ? -6.876 8.552 2.384 1.00 88.39 4 A 1 ATOM 41 C CZ . PHE A 1 4 ? -6.458 8.412 1.070 1.00 88.44 4 A 1 ATOM 42 N N . ALA A 1 5 ? -2.745 3.646 4.761 1.00 96.41 5 A 1 ATOM 43 C CA . ALA A 1 5 ? -1.469 2.955 4.598 1.00 96.56 5 A 1 ATOM 44 C C . ALA A 1 5 ? -1.674 1.544 4.060 1.00 96.97 5 A 1 ATOM 45 O O . ALA A 1 5 ? -0.927 1.084 3.201 1.00 96.22 5 A 1 ATOM 46 C CB . ALA A 1 5 ? -0.740 2.906 5.934 1.00 95.86 5 A 1 ATOM 47 N N . THR A 1 6 ? -2.679 0.868 4.561 1.00 97.03 6 A 1 ATOM 48 C CA . THR A 1 6 ? -2.981 -0.495 4.133 1.00 96.97 6 A 1 ATOM 49 C C . THR A 1 6 ? -3.476 -0.519 2.690 1.00 97.32 6 A 1 ATOM 50 O O . THR A 1 6 ? -3.071 -1.371 1.901 1.00 96.85 6 A 1 ATOM 51 C CB . THR A 1 6 ? -4.043 -1.122 5.045 1.00 96.40 6 A 1 ATOM 52 O OG1 . THR A 1 6 ? -3.645 -0.980 6.406 1.00 93.60 6 A 1 ATOM 53 C CG2 . THR A 1 6 ? -4.208 -2.602 4.732 1.00 92.07 6 A 1 ATOM 54 N N . LEU A 1 7 ? -4.335 0.420 2.350 1.00 96.84 7 A 1 ATOM 55 C CA . LEU A 1 7 ? -4.877 0.504 0.996 1.00 96.71 7 A 1 ATOM 56 C C . LEU A 1 7 ? -3.834 1.024 0.013 1.00 97.05 7 A 1 ATOM 57 O O . LEU A 1 7 ? -3.743 0.545 -1.117 1.00 96.86 7 A 1 ATOM 58 C CB . LEU A 1 7 ? -6.101 1.422 0.990 1.00 96.49 7 A 1 ATOM 59 C CG . LEU A 1 7 ? -7.319 0.843 1.706 1.00 92.58 7 A 1 ATOM 60 C CD1 . LEU A 1 7 ? -8.330 1.943 1.986 1.00 90.24 7 A 1 ATOM 61 C CD2 . LEU A 1 7 ? -7.960 -0.249 0.860 1.00 90.26 7 A 1 ATOM 62 N N . VAL A 1 8 ? -3.067 1.991 0.441 1.00 97.25 8 A 1 ATOM 63 C CA . VAL A 1 8 ? -2.028 2.578 -0.401 1.00 97.17 8 A 1 ATOM 64 C C . VAL A 1 8 ? -0.884 1.594 -0.623 1.00 97.35 8 A 1 ATOM 65 O O . VAL A 1 8 ? -0.274 1.572 -1.690 1.00 97.09 8 A 1 ATOM 66 C CB . VAL A 1 8 ? -1.491 3.880 0.226 1.00 96.74 8 A 1 ATOM 67 C CG1 . VAL A 1 8 ? -0.291 4.403 -0.552 1.00 94.91 8 A 1 ATOM 68 C CG2 . VAL A 1 8 ? -2.582 4.940 0.254 1.00 94.72 8 A 1 ATOM 69 N N . LEU A 1 9 ? -0.589 0.780 0.376 1.00 97.08 9 A 1 ATOM 70 C CA . LEU A 1 9 ? 0.495 -0.193 0.283 1.00 96.98 9 A 1 ATOM 71 C C . LEU A 1 9 ? 0.041 -1.455 -0.444 1.00 97.46 9 A 1 ATOM 72 O O . LEU A 1 9 ? 0.859 -2.179 -1.009 1.00 97.02 9 A 1 ATOM 73 C CB . LEU A 1 9 ? 1.004 -0.547 1.689 1.00 96.59 9 A 1 ATOM 74 C CG . LEU A 1 9 ? 2.252 0.218 2.130 1.00 94.20 9 A 1 ATOM 75 C CD1 . LEU A 1 9 ? 3.444 -0.175 1.265 1.00 92.67 9 A 1 ATOM 76 C CD2 . LEU A 1 9 ? 2.028 1.710 2.066 1.00 92.53 9 A 1 ATOM 77 N N . ALA A 1 10 ? -1.243 -1.711 -0.428 1.00 97.06 10 A 1 ATOM 78 C CA . ALA A 1 10 ? -1.796 -2.902 -1.068 1.00 96.99 10 A 1 ATOM 79 C C . ALA A 1 10 ? -1.704 -2.825 -2.590 1.00 97.56 10 A 1 ATOM 80 O O . ALA A 1 10 ? -1.475 -3.835 -3.254 1.00 96.95 10 A 1 ATOM 81 C CB . ALA A 1 10 ? -3.247 -3.089 -0.638 1.00 96.39 10 A 1 ATOM 82 N N . LEU A 1 11 ? -1.873 -1.641 -3.136 1.00 97.24 11 A 1 ATOM 83 C CA . LEU A 1 11 ? -1.822 -1.452 -4.586 1.00 97.32 11 A 1 ATOM 84 C C . LEU A 1 11 ? -0.390 -1.437 -5.120 1.00 97.76 11 A 1 ATOM 85 O O . LEU A 1 11 ? -0.051 -2.211 -6.018 1.00 97.27 11 A 1 ATOM 86 C CB . LEU A 1 11 ? -2.553 -0.158 -4.960 1.00 96.78 11 A 1 ATOM 87 C CG . LEU A 1 11 ? -3.108 -0.163 -6.380 1.00 93.27 11 A 1 ATOM 88 C CD1 . LEU A 1 11 ? -4.246 -1.168 -6.505 1.00 91.12 11 A 1 ATOM 89 C CD2 . LEU A 1 11 ? -3.584 1.231 -6.758 1.00 90.08 11 A 1 ATOM 90 N N . PRO A 1 12 ? 0.454 -0.552 -4.590 1.00 97.57 12 A 1 ATOM 91 C CA . PRO A 1 12 ? 1.850 -0.458 -5.039 1.00 97.24 12 A 1 ATOM 92 C C . PRO A 1 12 ? 2.646 -1.714 -4.720 1.00 97.55 12 A 1 ATOM 93 O O . PRO A 1 12 ? 3.618 -2.024 -5.406 1.00 96.74 12 A 1 ATOM 94 C CB . PRO A 1 12 ? 2.395 0.752 -4.266 1.00 96.21 12 A 1 ATOM 95 C CG . PRO A 1 12 ? 1.530 0.857 -3.065 1.00 94.76 12 A 1 ATOM 96 C CD . PRO A 1 12 ? 0.160 0.417 -3.534 1.00 96.94 12 A 1 ATOM 97 N N . ALA A 1 13 ? 2.247 -2.437 -3.691 1.00 97.28 13 A 1 ATOM 98 C CA . ALA A 1 13 ? 2.933 -3.663 -3.296 1.00 97.15 13 A 1 ATOM 99 C C . ALA A 1 13 ? 2.832 -4.709 -4.404 1.00 97.60 13 A 1 ATOM 100 O O . ALA A 1 13 ? 3.801 -5.401 -4.706 1.00 96.52 13 A 1 ATOM 101 C CB . ALA A 1 13 ? 2.328 -4.202 -2.004 1.00 96.22 13 A 1 ATOM 102 N N . LEU A 1 14 ? 1.673 -4.817 -5.018 1.00 97.18 14 A 1 ATOM 103 C CA . LEU A 1 14 ? 1.450 -5.772 -6.097 1.00 96.91 14 A 1 ATOM 104 C C . LEU A 1 14 ? 2.133 -5.315 -7.376 1.00 97.30 14 A 1 ATOM 105 O O . LEU A 1 14 ? 2.602 -6.132 -8.165 1.00 96.18 14 A 1 ATOM 106 C CB . LEU A 1 14 ? -0.052 -5.937 -6.341 1.00 96.19 14 A 1 ATOM 107 C CG . LEU A 1 14 ? -0.795 -6.666 -5.229 1.00 93.38 14 A 1 ATOM 108 C CD1 . LEU A 1 14 ? -2.292 -6.498 -5.398 1.00 89.69 14 A 1 ATOM 109 C CD2 . LEU A 1 14 ? -0.425 -8.143 -5.239 1.00 88.32 14 A 1 ATOM 110 N N . ALA A 1 15 ? 2.187 -4.022 -7.577 1.00 97.38 15 A 1 ATOM 111 C CA . ALA A 1 15 ? 2.826 -3.447 -8.757 1.00 97.36 15 A 1 ATOM 112 C C . ALA A 1 15 ? 4.333 -3.677 -8.731 1.00 97.66 15 A 1 ATOM 113 O O . ALA A 1 15 ? 4.975 -3.747 -9.775 1.00 97.00 15 A 1 ATOM 114 C CB . ALA A 1 15 ? 2.530 -1.955 -8.827 1.00 96.62 15 A 1 ATOM 115 N N . MET A 1 16 ? 4.891 -3.775 -7.533 1.00 96.78 16 A 1 ATOM 116 C CA . MET A 1 16 ? 6.323 -3.990 -7.360 1.00 96.09 16 A 1 ATOM 117 C C . MET A 1 16 ? 6.654 -5.475 -7.256 1.00 96.21 16 A 1 ATOM 118 O O . MET A 1 16 ? 7.811 -5.864 -7.386 1.00 94.10 16 A 1 ATOM 119 C CB . MET A 1 16 ? 6.807 -3.264 -6.101 1.00 94.13 16 A 1 ATOM 120 C CG . MET A 1 16 ? 7.224 -1.835 -6.385 1.00 89.35 16 A 1 ATOM 121 S SD . MET A 1 16 ? 8.943 -1.763 -6.868 1.00 82.13 16 A 1 ATOM 122 C CE . MET A 1 16 ? 9.140 0.004 -7.068 1.00 72.53 16 A 1 ATOM 123 N N . ALA A 1 17 ? 5.650 -6.282 -7.026 1.00 94.59 17 A 1 ATOM 124 C CA . ALA A 1 17 ? 5.835 -7.724 -6.884 1.00 92.82 17 A 1 ATOM 125 C C . ALA A 1 17 ? 6.262 -8.334 -8.220 1.00 90.66 17 A 1 ATOM 126 O O . ALA A 1 17 ? 7.456 -8.629 -8.385 1.00 85.46 17 A 1 ATOM 127 C CB . ALA A 1 17 ? 4.550 -8.362 -6.373 1.00 89.51 17 A 1 ATOM 128 O OXT . ALA A 1 17 ? 5.420 -8.521 -9.076 1.00 81.75 17 A 1 #