# 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_spkb34034 # _entry.id spkb34034 # 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" "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" "C4 H9 N O3" 119.119 THR y THREONINE C[C@H]([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 PHE 3 1 n PHE 4 1 n ILE 5 1 n ALA 6 1 n THR 7 1 n ILE 8 1 n PHE 9 1 n ALA 10 1 n THR 11 1 n GLY 12 1 n ALA 13 1 n LEU 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 @ 2025-07-13 11:13:40)" _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 94.08 _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 89.38 1 1 A LYS 2 2 91.83 1 2 A PHE 3 2 91.92 1 3 A PHE 4 2 93.90 1 4 A ILE 5 2 96.13 1 5 A ALA 6 2 97.92 1 6 A THR 7 2 96.08 1 7 A ILE 8 2 96.42 1 8 A PHE 9 2 95.12 1 9 A ALA 10 2 97.53 1 10 A THR 11 2 95.83 1 11 A GLY 12 2 96.75 1 12 A ALA 13 2 96.63 1 13 A LEU 14 2 92.43 1 14 A ALA 15 2 88.15 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 PHE . 3 A 3 A 4 1 n PHE . 4 A 4 A 5 1 n ILE . 5 A 5 A 6 1 n ALA . 6 A 6 A 7 1 n THR . 7 A 7 A 8 1 n ILE . 8 A 8 A 9 1 n PHE . 9 A 9 A 10 1 n ALA . 10 A 10 A 11 1 n THR . 11 A 11 A 12 1 n GLY . 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 # _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 ? 8.767 -4.252 -2.948 1.00 93.29 1 A 1 ATOM 2 C CA . MET A 1 1 ? 8.793 -4.005 -1.499 1.00 94.83 1 A 1 ATOM 3 C C . MET A 1 1 ? 7.427 -4.302 -0.882 1.00 95.57 1 A 1 ATOM 4 O O . MET A 1 1 ? 6.397 -4.132 -1.533 1.00 93.46 1 A 1 ATOM 5 C CB . MET A 1 1 ? 9.172 -2.555 -1.218 1.00 91.46 1 A 1 ATOM 6 C CG . MET A 1 1 ? 10.561 -2.222 -1.713 1.00 87.22 1 A 1 ATOM 7 S SD . MET A 1 1 ? 11.004 -0.507 -1.427 1.00 84.42 1 A 1 ATOM 8 C CE . MET A 1 1 ? 11.134 -0.504 0.363 1.00 74.80 1 A 1 ATOM 9 N N . LYS A 1 2 ? 7.434 -4.751 0.371 1.00 95.34 2 A 1 ATOM 10 C CA . LYS A 1 2 ? 6.186 -5.088 1.061 1.00 96.58 2 A 1 ATOM 11 C C . LYS A 1 2 ? 5.355 -3.835 1.353 1.00 97.37 2 A 1 ATOM 12 O O . LYS A 1 2 ? 4.131 -3.858 1.267 1.00 96.94 2 A 1 ATOM 13 C CB . LYS A 1 2 ? 6.489 -5.817 2.364 1.00 95.43 2 A 1 ATOM 14 C CG . LYS A 1 2 ? 5.232 -6.363 3.000 1.00 91.63 2 A 1 ATOM 15 C CD . LYS A 1 2 ? 5.497 -6.826 4.427 1.00 89.44 2 A 1 ATOM 16 C CE . LYS A 1 2 ? 5.562 -5.634 5.359 1.00 84.97 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? 5.658 -6.075 6.777 1.00 78.78 2 A 1 ATOM 18 N N . PHE A 1 3 ? 6.027 -2.758 1.694 1.00 95.34 3 A 1 ATOM 19 C CA . PHE A 1 3 ? 5.340 -1.510 2.022 1.00 96.41 3 A 1 ATOM 20 C C . PHE A 1 3 ? 4.555 -0.970 0.831 1.00 97.55 3 A 1 ATOM 21 O O . PHE A 1 3 ? 3.581 -0.234 1.002 1.00 96.69 3 A 1 ATOM 22 C CB . PHE A 1 3 ? 6.352 -0.468 2.491 1.00 95.43 3 A 1 ATOM 23 C CG . PHE A 1 3 ? 6.988 -0.834 3.814 1.00 92.36 3 A 1 ATOM 24 C CD1 . PHE A 1 3 ? 6.358 -1.707 4.682 1.00 89.08 3 A 1 ATOM 25 C CD2 . PHE A 1 3 ? 8.209 -0.290 4.180 1.00 89.18 3 A 1 ATOM 26 C CE1 . PHE A 1 3 ? 6.932 -2.043 5.898 1.00 87.05 3 A 1 ATOM 27 C CE2 . PHE A 1 3 ? 8.786 -0.616 5.394 1.00 86.64 3 A 1 ATOM 28 C CZ . PHE A 1 3 ? 8.147 -1.495 6.252 1.00 85.41 3 A 1 ATOM 29 N N . PHE A 1 4 ? 4.964 -1.340 -0.377 1.00 95.69 4 A 1 ATOM 30 C CA . PHE A 1 4 ? 4.259 -0.908 -1.585 1.00 96.43 4 A 1 ATOM 31 C C . PHE A 1 4 ? 2.818 -1.393 -1.558 1.00 97.38 4 A 1 ATOM 32 O O . PHE A 1 4 ? 1.914 -0.708 -2.032 1.00 97.11 4 A 1 ATOM 33 C CB . PHE A 1 4 ? 4.966 -1.445 -2.826 1.00 96.07 4 A 1 ATOM 34 C CG . PHE A 1 4 ? 6.000 -0.486 -3.353 1.00 94.40 4 A 1 ATOM 35 C CD1 . PHE A 1 4 ? 7.029 -0.044 -2.547 1.00 91.33 4 A 1 ATOM 36 C CD2 . PHE A 1 4 ? 5.915 -0.021 -4.659 1.00 92.01 4 A 1 ATOM 37 C CE1 . PHE A 1 4 ? 7.969 0.855 -3.030 1.00 90.78 4 A 1 ATOM 38 C CE2 . PHE A 1 4 ? 6.853 0.871 -5.148 1.00 91.01 4 A 1 ATOM 39 C CZ . PHE A 1 4 ? 7.882 1.311 -4.333 1.00 90.71 4 A 1 ATOM 40 N N . ILE A 1 5 ? 2.597 -2.569 -0.989 1.00 97.59 5 A 1 ATOM 41 C CA . ILE A 1 5 ? 1.255 -3.127 -0.887 1.00 97.52 5 A 1 ATOM 42 C C . ILE A 1 5 ? 0.368 -2.209 -0.057 1.00 97.70 5 A 1 ATOM 43 O O . ILE A 1 5 ? -0.797 -1.974 -0.386 1.00 97.56 5 A 1 ATOM 44 C CB . ILE A 1 5 ? 1.290 -4.524 -0.259 1.00 97.24 5 A 1 ATOM 45 C CG1 . ILE A 1 5 ? 2.255 -5.427 -1.034 1.00 95.30 5 A 1 ATOM 46 C CG2 . ILE A 1 5 ? -0.113 -5.123 -0.253 1.00 95.10 5 A 1 ATOM 47 C CD1 . ILE A 1 5 ? 1.916 -5.525 -2.510 1.00 91.00 5 A 1 ATOM 48 N N . ALA A 1 6 ? 0.923 -1.699 1.022 1.00 97.96 6 A 1 ATOM 49 C CA . ALA A 1 6 ? 0.190 -0.784 1.890 1.00 98.00 6 A 1 ATOM 50 C C . ALA A 1 6 ? -0.139 0.504 1.143 1.00 98.15 6 A 1 ATOM 51 O O . ALA A 1 6 ? -1.204 1.092 1.334 1.00 97.81 6 A 1 ATOM 52 C CB . ALA A 1 6 ? 1.014 -0.477 3.130 1.00 97.70 6 A 1 ATOM 53 N N . THR A 1 7 ? 0.775 0.930 0.285 1.00 97.54 7 A 1 ATOM 54 C CA . THR A 1 7 ? 0.574 2.136 -0.515 1.00 97.53 7 A 1 ATOM 55 C C . THR A 1 7 ? -0.603 1.949 -1.464 1.00 97.87 7 A 1 ATOM 56 O O . THR A 1 7 ? -1.422 2.853 -1.643 1.00 97.67 7 A 1 ATOM 57 C CB . THR A 1 7 ? 1.827 2.463 -1.327 1.00 97.20 7 A 1 ATOM 58 O OG1 . THR A 1 7 ? 2.944 2.572 -0.447 1.00 93.03 7 A 1 ATOM 59 C CG2 . THR A 1 7 ? 1.650 3.775 -2.081 1.00 91.70 7 A 1 ATOM 60 N N . ILE A 1 8 ? -0.688 0.780 -2.069 1.00 97.67 8 A 1 ATOM 61 C CA . ILE A 1 8 ? -1.786 0.468 -2.982 1.00 97.42 8 A 1 ATOM 62 C C . ILE A 1 8 ? -3.111 0.504 -2.235 1.00 97.53 8 A 1 ATOM 63 O O . ILE A 1 8 ? -4.114 1.016 -2.736 1.00 97.32 8 A 1 ATOM 64 C CB . ILE A 1 8 ? -1.588 -0.908 -3.624 1.00 97.25 8 A 1 ATOM 65 C CG1 . ILE A 1 8 ? -0.275 -0.948 -4.413 1.00 95.91 8 A 1 ATOM 66 C CG2 . ILE A 1 8 ? -2.768 -1.239 -4.535 1.00 95.50 8 A 1 ATOM 67 C CD1 . ILE A 1 8 ? -0.224 0.094 -5.513 1.00 92.77 8 A 1 ATOM 68 N N . PHE A 1 9 ? -3.109 -0.047 -1.035 1.00 97.58 9 A 1 ATOM 69 C CA . PHE A 1 9 ? -4.312 -0.070 -0.215 1.00 97.23 9 A 1 ATOM 70 C C . PHE A 1 9 ? -4.766 1.349 0.109 1.00 97.55 9 A 1 ATOM 71 O O . PHE A 1 9 ? -5.953 1.663 0.044 1.00 97.39 9 A 1 ATOM 72 C CB . PHE A 1 9 ? -4.048 -0.839 1.071 1.00 96.77 9 A 1 ATOM 73 C CG . PHE A 1 9 ? -5.281 -0.974 1.924 1.00 94.97 9 A 1 ATOM 74 C CD1 . PHE A 1 9 ? -6.525 -1.139 1.350 1.00 92.99 9 A 1 ATOM 75 C CD2 . PHE A 1 9 ? -5.184 -0.945 3.307 1.00 93.66 9 A 1 ATOM 76 C CE1 . PHE A 1 9 ? -7.663 -1.265 2.136 1.00 92.69 9 A 1 ATOM 77 C CE2 . PHE A 1 9 ? -6.315 -1.074 4.100 1.00 92.74 9 A 1 ATOM 78 C CZ . PHE A 1 9 ? -7.557 -1.231 3.512 1.00 92.76 9 A 1 ATOM 79 N N . ALA A 1 10 ? -3.818 2.202 0.452 1.00 97.68 10 A 1 ATOM 80 C CA . ALA A 1 10 ? -4.129 3.591 0.770 1.00 97.65 10 A 1 ATOM 81 C C . ALA A 1 10 ? -4.685 4.311 -0.451 1.00 97.95 10 A 1 ATOM 82 O O . ALA A 1 10 ? -5.642 5.074 -0.349 1.00 97.38 10 A 1 ATOM 83 C CB . ALA A 1 10 ? -2.880 4.302 1.273 1.00 96.99 10 A 1 ATOM 84 N N . THR A 1 11 ? -4.090 4.062 -1.601 1.00 97.85 11 A 1 ATOM 85 C CA . THR A 1 11 ? -4.534 4.685 -2.846 1.00 97.64 11 A 1 ATOM 86 C C . THR A 1 11 ? -5.917 4.182 -3.233 1.00 97.81 11 A 1 ATOM 87 O O . THR A 1 11 ? -6.773 4.956 -3.661 1.00 96.67 11 A 1 ATOM 88 C CB . THR A 1 11 ? -3.553 4.385 -3.981 1.00 96.63 11 A 1 ATOM 89 O OG1 . THR A 1 11 ? -2.245 4.810 -3.605 1.00 92.34 11 A 1 ATOM 90 C CG2 . THR A 1 11 ? -3.964 5.115 -5.250 1.00 91.87 11 A 1 ATOM 91 N N . GLY A 1 12 ? -6.140 2.883 -3.085 1.00 96.97 12 A 1 ATOM 92 C CA . GLY A 1 12 ? -7.427 2.290 -3.419 1.00 96.58 12 A 1 ATOM 93 C C . GLY A 1 12 ? -8.533 2.799 -2.520 1.00 97.13 12 A 1 ATOM 94 O O . GLY A 1 12 ? -9.646 3.052 -2.975 1.00 96.31 12 A 1 ATOM 95 N N . ALA A 1 13 ? -8.233 2.958 -1.245 1.00 96.96 13 A 1 ATOM 96 C CA . ALA A 1 13 ? -9.213 3.450 -0.280 1.00 96.94 13 A 1 ATOM 97 C C . ALA A 1 13 ? -9.569 4.906 -0.562 1.00 97.46 13 A 1 ATOM 98 O O . ALA A 1 13 ? -10.705 5.324 -0.349 1.00 96.06 13 A 1 ATOM 99 C CB . ALA A 1 13 ? -8.669 3.313 1.134 1.00 95.75 13 A 1 ATOM 100 N N . LEU A 1 14 ? -8.596 5.669 -1.023 1.00 96.22 14 A 1 ATOM 101 C CA . LEU A 1 14 ? -8.808 7.082 -1.332 1.00 95.91 14 A 1 ATOM 102 C C . LEU A 1 14 ? -9.655 7.235 -2.583 1.00 96.36 14 A 1 ATOM 103 O O . LEU A 1 14 ? -10.501 8.127 -2.669 1.00 94.92 14 A 1 ATOM 104 C CB . LEU A 1 14 ? -7.461 7.787 -1.500 1.00 94.44 14 A 1 ATOM 105 C CG . LEU A 1 14 ? -7.553 9.311 -1.489 1.00 90.22 14 A 1 ATOM 106 C CD1 . LEU A 1 14 ? -6.235 9.903 -1.018 1.00 86.43 14 A 1 ATOM 107 C CD2 . LEU A 1 14 ? -7.901 9.857 -2.860 1.00 84.91 14 A 1 ATOM 108 N N . ALA A 1 15 ? -9.427 6.374 -3.561 1.00 93.19 15 A 1 ATOM 109 C CA . ALA A 1 15 ? -10.158 6.417 -4.826 1.00 92.00 15 A 1 ATOM 110 C C . ALA A 1 15 ? -11.637 6.113 -4.590 1.00 90.90 15 A 1 ATOM 111 O O . ALA A 1 15 ? -12.487 6.824 -5.150 1.00 85.44 15 A 1 ATOM 112 C CB . ALA A 1 15 ? -9.552 5.426 -5.813 1.00 87.65 15 A 1 ATOM 113 O OXT . ALA A 1 15 ? -11.948 5.166 -3.879 1.00 79.74 15 A 1 #