# 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_spkb39247 # _entry.id spkb39247 # 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 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" "C4 H9 N O3" 119.119 THR y THREONINE C[C@H]([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 ALA 2 1 n ARG 3 1 n TYR 4 1 n PHE 5 1 n ILE 6 1 n LEU 7 1 n ALA 8 1 n ALA 9 1 n ALA 10 1 n LEU 11 1 n LEU 12 1 n LEU 13 1 n THR 14 1 n ALA 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 @ 2025-07-06 12:06:28)" _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 95.00 _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 87.55 1 1 A ALA 2 2 95.58 1 2 A ARG 3 2 90.85 1 3 A TYR 4 2 95.62 1 4 A PHE 5 2 95.25 1 5 A ILE 6 2 97.12 1 6 A LEU 7 2 96.20 1 7 A ALA 8 2 97.85 1 8 A ALA 9 2 98.06 1 9 A ALA 10 2 98.10 1 10 A LEU 11 2 97.16 1 11 A LEU 12 2 97.28 1 12 A LEU 13 2 96.20 1 13 A THR 14 2 94.58 1 14 A ALA 15 2 91.46 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 ARG . 3 A 3 A 4 1 n TYR . 4 A 4 A 5 1 n PHE . 5 A 5 A 6 1 n ILE . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n ALA . 8 A 8 A 9 1 n ALA . 9 A 9 A 10 1 n ALA . 10 A 10 A 11 1 n LEU . 11 A 11 A 12 1 n LEU . 12 A 12 A 13 1 n LEU . 13 A 13 A 14 1 n THR . 14 A 14 A 15 1 n ALA . 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 ? -2.595 4.641 13.223 1.00 92.32 1 A 1 ATOM 2 C CA . MET A 1 1 ? -1.565 4.349 12.221 1.00 93.38 1 A 1 ATOM 3 C C . MET A 1 1 ? -2.077 3.362 11.169 1.00 94.19 1 A 1 ATOM 4 O O . MET A 1 1 ? -1.509 2.290 10.983 1.00 92.81 1 A 1 ATOM 5 C CB . MET A 1 1 ? -0.338 3.753 12.907 1.00 89.78 1 A 1 ATOM 6 C CG . MET A 1 1 ? 0.381 4.750 13.786 1.00 84.02 1 A 1 ATOM 7 S SD . MET A 1 1 ? 1.785 3.993 14.616 1.00 81.51 1 A 1 ATOM 8 C CE . MET A 1 1 ? 2.474 5.424 15.423 1.00 72.40 1 A 1 ATOM 9 N N . ALA A 1 2 ? -3.141 3.729 10.503 1.00 93.59 2 A 1 ATOM 10 C CA . ALA A 1 2 ? -3.723 2.871 9.477 1.00 96.14 2 A 1 ATOM 11 C C . ALA A 1 2 ? -3.484 3.436 8.080 1.00 97.29 2 A 1 ATOM 12 O O . ALA A 1 2 ? -3.377 2.696 7.104 1.00 96.30 2 A 1 ATOM 13 C CB . ALA A 1 2 ? -5.217 2.698 9.738 1.00 94.57 2 A 1 ATOM 14 N N . ARG A 1 3 ? -3.402 4.750 7.985 1.00 96.64 3 A 1 ATOM 15 C CA . ARG A 1 3 ? -3.179 5.414 6.695 1.00 97.38 3 A 1 ATOM 16 C C . ARG A 1 3 ? -1.803 5.073 6.121 1.00 97.92 3 A 1 ATOM 17 O O . ARG A 1 3 ? -1.636 4.971 4.911 1.00 97.44 3 A 1 ATOM 18 C CB . ARG A 1 3 ? -3.315 6.929 6.862 1.00 96.67 3 A 1 ATOM 19 C CG . ARG A 1 3 ? -4.430 7.476 5.977 1.00 92.73 3 A 1 ATOM 20 C CD . ARG A 1 3 ? -3.981 7.562 4.537 1.00 91.19 3 A 1 ATOM 21 N NE . ARG A 1 3 ? -5.094 7.805 3.625 1.00 86.72 3 A 1 ATOM 22 C CZ . ARG A 1 3 ? -5.673 8.990 3.469 1.00 85.50 3 A 1 ATOM 23 N NH1 . ARG A 1 3 ? -5.276 10.044 4.153 1.00 78.22 3 A 1 ATOM 24 N NH2 . ARG A 1 3 ? -6.676 9.119 2.616 1.00 78.93 3 A 1 ATOM 25 N N . TYR A 1 4 ? -0.834 4.894 6.986 1.00 97.72 4 A 1 ATOM 26 C CA . TYR A 1 4 ? 0.524 4.560 6.554 1.00 97.88 4 A 1 ATOM 27 C C . TYR A 1 4 ? 0.560 3.211 5.839 1.00 98.06 4 A 1 ATOM 28 O O . TYR A 1 4 ? 1.335 3.004 4.906 1.00 97.84 4 A 1 ATOM 29 C CB . TYR A 1 4 ? 1.456 4.520 7.764 1.00 97.53 4 A 1 ATOM 30 C CG . TYR A 1 4 ? 1.619 5.875 8.413 1.00 96.38 4 A 1 ATOM 31 C CD1 . TYR A 1 4 ? 2.359 6.874 7.789 1.00 94.68 4 A 1 ATOM 32 C CD2 . TYR A 1 4 ? 1.037 6.147 9.643 1.00 94.36 4 A 1 ATOM 33 C CE1 . TYR A 1 4 ? 2.511 8.119 8.382 1.00 93.68 4 A 1 ATOM 34 C CE2 . TYR A 1 4 ? 1.185 7.390 10.243 1.00 93.12 4 A 1 ATOM 35 C CZ . TYR A 1 4 ? 1.925 8.371 9.607 1.00 93.58 4 A 1 ATOM 36 O OH . TYR A 1 4 ? 2.073 9.601 10.198 1.00 92.59 4 A 1 ATOM 37 N N . PHE A 1 5 ? -0.299 2.293 6.272 1.00 97.95 5 A 1 ATOM 38 C CA . PHE A 1 5 ? -0.367 0.963 5.674 1.00 98.01 5 A 1 ATOM 39 C C . PHE A 1 5 ? -0.898 1.048 4.246 1.00 98.24 5 A 1 ATOM 40 O O . PHE A 1 5 ? -0.405 0.373 3.345 1.00 98.02 5 A 1 ATOM 41 C CB . PHE A 1 5 ? -1.266 0.068 6.523 1.00 97.68 5 A 1 ATOM 42 C CG . PHE A 1 5 ? -0.801 -1.360 6.540 1.00 95.21 5 A 1 ATOM 43 C CD1 . PHE A 1 5 ? 0.360 -1.715 7.209 1.00 92.72 5 A 1 ATOM 44 C CD2 . PHE A 1 5 ? -1.532 -2.346 5.895 1.00 93.10 5 A 1 ATOM 45 C CE1 . PHE A 1 5 ? 0.792 -3.033 7.226 1.00 92.36 5 A 1 ATOM 46 C CE2 . PHE A 1 5 ? -1.107 -3.668 5.909 1.00 92.15 5 A 1 ATOM 47 C CZ . PHE A 1 5 ? 0.060 -4.012 6.577 1.00 92.33 5 A 1 ATOM 48 N N . ILE A 1 6 ? -1.904 1.881 4.049 1.00 98.18 6 A 1 ATOM 49 C CA . ILE A 1 6 ? -2.508 2.065 2.730 1.00 98.19 6 A 1 ATOM 50 C C . ILE A 1 6 ? -1.533 2.773 1.791 1.00 98.33 6 A 1 ATOM 51 O O . ILE A 1 6 ? -1.397 2.403 0.622 1.00 98.21 6 A 1 ATOM 52 C CB . ILE A 1 6 ? -3.818 2.868 2.841 1.00 98.08 6 A 1 ATOM 53 C CG1 . ILE A 1 6 ? -4.802 2.166 3.777 1.00 96.92 6 A 1 ATOM 54 C CG2 . ILE A 1 6 ? -4.448 3.037 1.457 1.00 96.53 6 A 1 ATOM 55 C CD1 . ILE A 1 6 ? -5.946 3.058 4.212 1.00 92.55 6 A 1 ATOM 56 N N . LEU A 1 7 ? -0.858 3.774 2.301 1.00 98.02 7 A 1 ATOM 57 C CA . LEU A 1 7 ? 0.109 4.530 1.507 1.00 97.88 7 A 1 ATOM 58 C C . LEU A 1 7 ? 1.273 3.643 1.079 1.00 98.13 7 A 1 ATOM 59 O O . LEU A 1 7 ? 1.721 3.705 -0.066 1.00 98.07 7 A 1 ATOM 60 C CB . LEU A 1 7 ? 0.629 5.712 2.325 1.00 97.65 7 A 1 ATOM 61 C CG . LEU A 1 7 ? -0.372 6.849 2.464 1.00 93.94 7 A 1 ATOM 62 C CD1 . LEU A 1 7 ? 0.020 7.759 3.617 1.00 92.82 7 A 1 ATOM 63 C CD2 . LEU A 1 7 ? -0.441 7.651 1.171 1.00 93.10 7 A 1 ATOM 64 N N . ALA A 1 8 ? 1.744 2.828 1.985 1.00 97.77 8 A 1 ATOM 65 C CA . ALA A 1 8 ? 2.854 1.924 1.706 1.00 97.82 8 A 1 ATOM 66 C C . ALA A 1 8 ? 2.444 0.849 0.709 1.00 98.17 8 A 1 ATOM 67 O O . ALA A 1 8 ? 3.210 0.497 -0.186 1.00 98.04 8 A 1 ATOM 68 C CB . ALA A 1 8 ? 3.328 1.275 3.000 1.00 97.43 8 A 1 ATOM 69 N N . ALA A 1 9 ? 1.232 0.331 0.862 1.00 98.09 9 A 1 ATOM 70 C CA . ALA A 1 9 ? 0.723 -0.711 -0.025 1.00 98.08 9 A 1 ATOM 71 C C . ALA A 1 9 ? 0.567 -0.191 -1.446 1.00 98.35 9 A 1 ATOM 72 O O . ALA A 1 9 ? 0.874 -0.893 -2.410 1.00 98.09 9 A 1 ATOM 73 C CB . ALA A 1 9 ? -0.616 -1.223 0.493 1.00 97.69 9 A 1 ATOM 74 N N . ALA A 1 10 ? 0.090 1.031 -1.584 1.00 98.16 10 A 1 ATOM 75 C CA . ALA A 1 10 ? -0.108 1.641 -2.895 1.00 98.15 10 A 1 ATOM 76 C C . ALA A 1 10 ? 1.224 1.856 -3.604 1.00 98.39 10 A 1 ATOM 77 O O . ALA A 1 10 ? 1.343 1.605 -4.804 1.00 97.99 10 A 1 ATOM 78 C CB . ALA A 1 10 ? -0.837 2.968 -2.741 1.00 97.83 10 A 1 ATOM 79 N N . LEU A 1 11 ? 2.216 2.300 -2.876 1.00 98.35 11 A 1 ATOM 80 C CA . LEU A 1 11 ? 3.546 2.538 -3.432 1.00 98.29 11 A 1 ATOM 81 C C . LEU A 1 11 ? 4.222 1.231 -3.809 1.00 98.47 11 A 1 ATOM 82 O O . LEU A 1 11 ? 4.883 1.139 -4.843 1.00 98.14 11 A 1 ATOM 83 C CB . LEU A 1 11 ? 4.405 3.290 -2.415 1.00 98.00 11 A 1 ATOM 84 C CG . LEU A 1 11 ? 5.738 3.770 -2.967 1.00 96.43 11 A 1 ATOM 85 C CD1 . LEU A 1 11 ? 5.530 4.924 -3.940 1.00 94.95 11 A 1 ATOM 86 C CD2 . LEU A 1 11 ? 6.658 4.200 -1.839 1.00 94.64 11 A 1 ATOM 87 N N . LEU A 1 12 ? 4.049 0.225 -2.988 1.00 98.40 12 A 1 ATOM 88 C CA . LEU A 1 12 ? 4.652 -1.084 -3.219 1.00 98.31 12 A 1 ATOM 89 C C . LEU A 1 12 ? 4.000 -1.776 -4.406 1.00 98.38 12 A 1 ATOM 90 O O . LEU A 1 12 ? 4.671 -2.436 -5.196 1.00 97.97 12 A 1 ATOM 91 C CB . LEU A 1 12 ? 4.516 -1.942 -1.958 1.00 98.02 12 A 1 ATOM 92 C CG . LEU A 1 12 ? 5.727 -2.825 -1.686 1.00 96.85 12 A 1 ATOM 93 C CD1 . LEU A 1 12 ? 5.877 -3.084 -0.197 1.00 95.36 12 A 1 ATOM 94 C CD2 . LEU A 1 12 ? 5.612 -4.142 -2.432 1.00 94.95 12 A 1 ATOM 95 N N . LEU A 1 13 ? 2.692 -1.624 -4.547 1.00 98.02 13 A 1 ATOM 96 C CA . LEU A 1 13 ? 1.948 -2.236 -5.644 1.00 97.75 13 A 1 ATOM 97 C C . LEU A 1 13 ? 2.404 -1.670 -6.981 1.00 97.76 13 A 1 ATOM 98 O O . LEU A 1 13 ? 2.486 -2.391 -7.976 1.00 96.62 13 A 1 ATOM 99 C CB . LEU A 1 13 ? 0.452 -1.989 -5.455 1.00 97.24 13 A 1 ATOM 100 C CG . LEU A 1 13 ? -0.435 -2.790 -6.398 1.00 95.95 13 A 1 ATOM 101 C CD1 . LEU A 1 13 ? -0.444 -4.258 -5.997 1.00 93.60 13 A 1 ATOM 102 C CD2 . LEU A 1 13 ? -1.851 -2.243 -6.386 1.00 92.65 13 A 1 ATOM 103 N N . THR A 1 14 ? 2.702 -0.388 -7.000 1.00 97.10 14 A 1 ATOM 104 C CA . THR A 1 14 ? 3.170 0.278 -8.218 1.00 96.64 14 A 1 ATOM 105 C C . THR A 1 14 ? 4.610 -0.122 -8.535 1.00 96.80 14 A 1 ATOM 106 O O . THR A 1 14 ? 5.105 0.136 -9.631 1.00 94.66 14 A 1 ATOM 107 C CB . THR A 1 14 ? 3.077 1.803 -8.062 1.00 95.21 14 A 1 ATOM 108 O OG1 . THR A 1 14 ? 1.784 2.156 -7.567 1.00 91.39 14 A 1 ATOM 109 C CG2 . THR A 1 14 ? 3.279 2.502 -9.395 1.00 90.26 14 A 1 ATOM 110 N N . ALA A 1 15 ? 5.246 -0.772 -7.573 1.00 95.90 15 A 1 ATOM 111 C CA . ALA A 1 15 ? 6.635 -1.213 -7.712 1.00 94.42 15 A 1 ATOM 112 C C . ALA A 1 15 ? 7.581 -0.034 -7.881 1.00 93.29 15 A 1 ATOM 113 O O . ALA A 1 15 ? 7.697 0.503 -8.994 1.00 90.25 15 A 1 ATOM 114 C CB . ALA A 1 15 ? 6.778 -2.180 -8.876 1.00 91.73 15 A 1 ATOM 115 O OXT . ALA A 1 15 ? 8.170 0.364 -6.852 1.00 83.18 15 A 1 #