# 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_spkb44944 # _entry.id spkb44944 # 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" "C5 H10 N2 O3" 146.144 GLN y GLUTAMINE C(CC(=O)N)[C@@H](C(=O)O)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" "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" "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 GLN 3 1 n LYS 4 1 n TYR 5 1 n LEU 6 1 n PHE 7 1 n ILE 8 1 n ALA 9 1 n SER 10 1 n MET 11 1 n ALA 12 1 n LEU 13 1 n ALA 14 1 n GLY 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 10:11:54)" _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 94.69 _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 90.40 1 1 A LYS 2 2 92.16 1 2 A GLN 3 2 92.07 1 3 A LYS 4 2 92.89 1 4 A TYR 5 2 95.86 1 5 A LEU 6 2 96.19 1 6 A PHE 7 2 96.28 1 7 A ILE 8 2 97.30 1 8 A ALA 9 2 98.36 1 9 A SER 10 2 97.03 1 10 A MET 11 2 93.78 1 11 A ALA 12 2 98.36 1 12 A LEU 13 2 94.58 1 13 A ALA 14 2 96.94 1 14 A GLY 15 2 90.47 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 LYS . 2 A 2 A 3 1 n GLN . 3 A 3 A 4 1 n LYS . 4 A 4 A 5 1 n TYR . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n PHE . 7 A 7 A 8 1 n ILE . 8 A 8 A 9 1 n ALA . 9 A 9 A 10 1 n SER . 10 A 10 A 11 1 n MET . 11 A 11 A 12 1 n ALA . 12 A 12 A 13 1 n LEU . 13 A 13 A 14 1 n ALA . 14 A 14 A 15 1 n GLY . 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 ? -3.663 -1.376 -7.928 1.00 94.82 1 A 1 ATOM 2 C CA . MET A 1 1 ? -4.361 -2.253 -6.969 1.00 96.47 1 A 1 ATOM 3 C C . MET A 1 1 ? -4.611 -1.527 -5.654 1.00 96.90 1 A 1 ATOM 4 O O . MET A 1 1 ? -3.774 -0.764 -5.190 1.00 95.65 1 A 1 ATOM 5 C CB . MET A 1 1 ? -3.522 -3.499 -6.682 1.00 93.30 1 A 1 ATOM 6 C CG . MET A 1 1 ? -3.638 -4.530 -7.786 1.00 86.12 1 A 1 ATOM 7 S SD . MET A 1 1 ? -2.722 -6.030 -7.397 1.00 83.95 1 A 1 ATOM 8 C CE . MET A 1 1 ? -3.305 -7.086 -8.710 1.00 75.96 1 A 1 ATOM 9 N N . LYS A 1 2 ? -5.762 -1.770 -5.062 1.00 96.50 2 A 1 ATOM 10 C CA . LYS A 1 2 ? -6.118 -1.145 -3.788 1.00 97.34 2 A 1 ATOM 11 C C . LYS A 1 2 ? -5.404 -1.843 -2.630 1.00 97.66 2 A 1 ATOM 12 O O . LYS A 1 2 ? -5.066 -1.213 -1.632 1.00 97.04 2 A 1 ATOM 13 C CB . LYS A 1 2 ? -7.631 -1.215 -3.600 1.00 96.50 2 A 1 ATOM 14 C CG . LYS A 1 2 ? -8.372 -0.435 -4.676 1.00 91.98 2 A 1 ATOM 15 C CD . LYS A 1 2 ? -9.863 -0.677 -4.601 1.00 89.75 2 A 1 ATOM 16 C CE . LYS A 1 2 ? -10.566 0.031 -5.747 1.00 84.34 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? -12.003 -0.330 -5.796 1.00 78.37 2 A 1 ATOM 18 N N . GLN A 1 3 ? -5.188 -3.123 -2.770 1.00 97.32 3 A 1 ATOM 19 C CA . GLN A 1 3 ? -4.509 -3.902 -1.732 1.00 97.87 3 A 1 ATOM 20 C C . GLN A 1 3 ? -3.096 -3.377 -1.499 1.00 98.03 3 A 1 ATOM 21 O O . GLN A 1 3 ? -2.633 -3.298 -0.362 1.00 96.72 3 A 1 ATOM 22 C CB . GLN A 1 3 ? -4.453 -5.373 -2.156 1.00 96.96 3 A 1 ATOM 23 C CG . GLN A 1 3 ? -5.842 -5.997 -2.208 1.00 90.82 3 A 1 ATOM 24 C CD . GLN A 1 3 ? -6.286 -6.473 -0.836 1.00 89.33 3 A 1 ATOM 25 O OE1 . GLN A 1 3 ? -5.462 -6.767 0.014 1.00 82.24 3 A 1 ATOM 26 N NE2 . GLN A 1 3 ? -7.582 -6.566 -0.612 1.00 79.35 3 A 1 ATOM 27 N N . LYS A 1 4 ? -2.422 -3.000 -2.571 1.00 97.66 4 A 1 ATOM 28 C CA . LYS A 1 4 ? -1.061 -2.485 -2.469 1.00 97.89 4 A 1 ATOM 29 C C . LYS A 1 4 ? -1.034 -1.172 -1.701 1.00 98.19 4 A 1 ATOM 30 O O . LYS A 1 4 ? -0.135 -0.937 -0.898 1.00 97.86 4 A 1 ATOM 31 C CB . LYS A 1 4 ? -0.469 -2.301 -3.864 1.00 97.56 4 A 1 ATOM 32 C CG . LYS A 1 4 ? -0.127 -3.628 -4.519 1.00 93.66 4 A 1 ATOM 33 C CD . LYS A 1 4 ? 1.044 -4.289 -3.821 1.00 90.11 4 A 1 ATOM 34 C CE . LYS A 1 4 ? 1.341 -5.670 -4.367 1.00 85.05 4 A 1 ATOM 35 N NZ . LYS A 1 4 ? 2.471 -6.298 -3.626 1.00 78.00 4 A 1 ATOM 36 N N . TYR A 1 5 ? -2.016 -0.332 -1.939 1.00 97.57 5 A 1 ATOM 37 C CA . TYR A 1 5 ? -2.087 0.943 -1.240 1.00 97.85 5 A 1 ATOM 38 C C . TYR A 1 5 ? -2.257 0.728 0.259 1.00 97.98 5 A 1 ATOM 39 O O . TYR A 1 5 ? -1.709 1.477 1.066 1.00 97.68 5 A 1 ATOM 40 C CB . TYR A 1 5 ? -3.253 1.769 -1.776 1.00 97.83 5 A 1 ATOM 41 C CG . TYR A 1 5 ? -2.857 2.556 -3.005 1.00 96.51 5 A 1 ATOM 42 C CD1 . TYR A 1 5 ? -2.011 3.653 -2.890 1.00 93.79 5 A 1 ATOM 43 C CD2 . TYR A 1 5 ? -3.328 2.202 -4.258 1.00 94.76 5 A 1 ATOM 44 C CE1 . TYR A 1 5 ? -1.637 4.375 -4.012 1.00 94.01 5 A 1 ATOM 45 C CE2 . TYR A 1 5 ? -2.957 2.923 -5.387 1.00 94.27 5 A 1 ATOM 46 C CZ . TYR A 1 5 ? -2.113 4.007 -5.253 1.00 94.95 5 A 1 ATOM 47 O OH . TYR A 1 5 ? -1.746 4.723 -6.361 1.00 93.10 5 A 1 ATOM 48 N N . LEU A 1 6 ? -3.008 -0.300 0.626 1.00 98.35 6 A 1 ATOM 49 C CA . LEU A 1 6 ? -3.220 -0.606 2.038 1.00 98.39 6 A 1 ATOM 50 C C . LEU A 1 6 ? -1.913 -1.027 2.696 1.00 98.47 6 A 1 ATOM 51 O O . LEU A 1 6 ? -1.628 -0.641 3.827 1.00 98.32 6 A 1 ATOM 52 C CB . LEU A 1 6 ? -4.255 -1.722 2.169 1.00 98.30 6 A 1 ATOM 53 C CG . LEU A 1 6 ? -5.672 -1.274 1.839 1.00 95.01 6 A 1 ATOM 54 C CD1 . LEU A 1 6 ? -6.594 -2.474 1.723 1.00 90.63 6 A 1 ATOM 55 C CD2 . LEU A 1 6 ? -6.193 -0.331 2.917 1.00 92.05 6 A 1 ATOM 56 N N . PHE A 1 7 ? -1.124 -1.811 1.988 1.00 97.98 7 A 1 ATOM 57 C CA . PHE A 1 7 ? 0.159 -2.269 2.508 1.00 97.97 7 A 1 ATOM 58 C C . PHE A 1 7 ? 1.105 -1.091 2.700 1.00 98.16 7 A 1 ATOM 59 O O . PHE A 1 7 ? 1.780 -0.990 3.724 1.00 97.84 7 A 1 ATOM 60 C CB . PHE A 1 7 ? 0.768 -3.284 1.550 1.00 97.79 7 A 1 ATOM 61 C CG . PHE A 1 7 ? 2.050 -3.865 2.081 1.00 96.99 7 A 1 ATOM 62 C CD1 . PHE A 1 7 ? 2.030 -4.753 3.141 1.00 94.23 7 A 1 ATOM 63 C CD2 . PHE A 1 7 ? 3.266 -3.510 1.521 1.00 94.94 7 A 1 ATOM 64 C CE1 . PHE A 1 7 ? 3.211 -5.284 3.640 1.00 94.12 7 A 1 ATOM 65 C CE2 . PHE A 1 7 ? 4.456 -4.036 2.017 1.00 94.37 7 A 1 ATOM 66 C CZ . PHE A 1 7 ? 4.424 -4.926 3.078 1.00 94.69 7 A 1 ATOM 67 N N . ILE A 1 8 ? 1.140 -0.211 1.722 1.00 98.24 8 A 1 ATOM 68 C CA . ILE A 1 8 ? 2.001 0.965 1.798 1.00 98.12 8 A 1 ATOM 69 C C . ILE A 1 8 ? 1.520 1.901 2.900 1.00 98.17 8 A 1 ATOM 70 O O . ILE A 1 8 ? 2.321 2.458 3.650 1.00 97.93 8 A 1 ATOM 71 C CB . ILE A 1 8 ? 2.023 1.701 0.450 1.00 97.98 8 A 1 ATOM 72 C CG1 . ILE A 1 8 ? 2.609 0.789 -0.632 1.00 96.93 8 A 1 ATOM 73 C CG2 . ILE A 1 8 ? 2.855 2.975 0.566 1.00 96.73 8 A 1 ATOM 74 C CD1 . ILE A 1 8 ? 2.398 1.334 -2.028 1.00 94.27 8 A 1 ATOM 75 N N . ALA A 1 9 ? 0.215 2.075 2.985 1.00 98.50 9 A 1 ATOM 76 C CA . ALA A 1 9 ? -0.364 2.945 4.005 1.00 98.44 9 A 1 ATOM 77 C C . ALA A 1 9 ? -0.061 2.411 5.398 1.00 98.50 9 A 1 ATOM 78 O O . ALA A 1 9 ? 0.208 3.179 6.319 1.00 98.12 9 A 1 ATOM 79 C CB . ALA A 1 9 ? -1.869 3.047 3.804 1.00 98.23 9 A 1 ATOM 80 N N . SER A 1 10 ? -0.111 1.107 5.552 1.00 98.28 10 A 1 ATOM 81 C CA . SER A 1 10 ? 0.170 0.477 6.839 1.00 98.24 10 A 1 ATOM 82 C C . SER A 1 10 ? 1.613 0.734 7.252 1.00 98.39 10 A 1 ATOM 83 O O . SER A 1 10 ? 1.896 1.021 8.413 1.00 97.88 10 A 1 ATOM 84 C CB . SER A 1 10 ? -0.083 -1.023 6.752 1.00 97.62 10 A 1 ATOM 85 O OG . SER A 1 10 ? 0.117 -1.617 8.007 1.00 91.78 10 A 1 ATOM 86 N N . MET A 1 11 ? 2.509 0.637 6.304 1.00 98.02 11 A 1 ATOM 87 C CA . MET A 1 11 ? 3.927 0.874 6.568 1.00 97.92 11 A 1 ATOM 88 C C . MET A 1 11 ? 4.169 2.346 6.894 1.00 98.18 11 A 1 ATOM 89 O O . MET A 1 11 ? 4.994 2.673 7.745 1.00 97.56 11 A 1 ATOM 90 C CB . MET A 1 11 ? 4.753 0.469 5.350 1.00 97.23 11 A 1 ATOM 91 C CG . MET A 1 11 ? 6.222 0.375 5.682 1.00 94.63 11 A 1 ATOM 92 S SD . MET A 1 11 ? 7.205 -0.173 4.292 1.00 86.69 11 A 1 ATOM 93 C CE . MET A 1 11 ? 8.816 -0.268 5.084 1.00 80.04 11 A 1 ATOM 94 N N . ALA A 1 12 ? 3.453 3.211 6.227 1.00 98.37 12 A 1 ATOM 95 C CA . ALA A 1 12 ? 3.576 4.646 6.462 1.00 98.47 12 A 1 ATOM 96 C C . ALA A 1 12 ? 3.106 5.002 7.866 1.00 98.61 12 A 1 ATOM 97 O O . ALA A 1 12 ? 3.668 5.885 8.511 1.00 98.20 12 A 1 ATOM 98 C CB . ALA A 1 12 ? 2.762 5.412 5.430 1.00 98.17 12 A 1 ATOM 99 N N . LEU A 1 13 ? 2.081 4.325 8.329 1.00 97.72 13 A 1 ATOM 100 C CA . LEU A 1 13 ? 1.549 4.563 9.669 1.00 97.58 13 A 1 ATOM 101 C C . LEU A 1 13 ? 2.536 4.082 10.720 1.00 97.66 13 A 1 ATOM 102 O O . LEU A 1 13 ? 2.678 4.696 11.780 1.00 96.38 13 A 1 ATOM 103 C CB . LEU A 1 13 ? 0.222 3.824 9.833 1.00 96.93 13 A 1 ATOM 104 C CG . LEU A 1 13 ? -0.458 4.103 11.170 1.00 93.71 13 A 1 ATOM 105 C CD1 . LEU A 1 13 ? -0.951 5.547 11.227 1.00 88.25 13 A 1 ATOM 106 C CD2 . LEU A 1 13 ? -1.627 3.151 11.376 1.00 88.43 13 A 1 ATOM 107 N N . ALA A 1 14 ? 3.205 2.989 10.434 1.00 97.61 14 A 1 ATOM 108 C CA . ALA A 1 14 ? 4.189 2.428 11.357 1.00 97.42 14 A 1 ATOM 109 C C . ALA A 1 14 ? 5.447 3.282 11.412 1.00 97.65 14 A 1 ATOM 110 O O . ALA A 1 14 ? 6.148 3.301 12.426 1.00 95.90 14 A 1 ATOM 111 C CB . ALA A 1 14 ? 4.536 1.001 10.943 1.00 96.10 14 A 1 ATOM 112 N N . GLY A 1 15 ? 5.736 3.980 10.324 1.00 95.52 15 A 1 ATOM 113 C CA . GLY A 1 15 ? 6.912 4.823 10.257 1.00 92.82 15 A 1 ATOM 114 C C . GLY A 1 15 ? 6.697 6.195 10.862 1.00 90.70 15 A 1 ATOM 115 O O . GLY A 1 15 ? 5.572 6.525 11.250 1.00 84.11 15 A 1 ATOM 116 O OXT . GLY A 1 15 ? 7.684 6.965 10.928 1.00 89.21 15 A 1 #