# 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_spkb16841 # _entry.id spkb16841 # 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 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" "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 LYS 2 1 n PHE 3 1 n GLY 4 1 n SER 5 1 n LEU 6 1 n LEU 7 1 n GLY 8 1 n LEU 9 1 n SER 10 1 n LEU 11 1 n VAL 12 1 n GLY 13 1 n LEU 14 1 n SER 15 1 n VAL 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 @ 2025-07-06 07:23:38)" _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 79.82 _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 68.26 1 1 A LYS 2 2 68.31 1 2 A PHE 3 2 66.61 1 3 A GLY 4 2 78.59 1 4 A SER 5 2 81.11 1 5 A LEU 6 2 79.32 1 6 A LEU 7 2 81.66 1 7 A GLY 8 2 84.25 1 8 A LEU 9 2 82.81 1 9 A SER 10 2 86.77 1 10 A LEU 11 2 85.63 1 11 A VAL 12 2 86.87 1 12 A GLY 13 2 88.61 1 13 A LEU 14 2 84.84 1 14 A SER 15 2 86.34 1 15 A VAL 16 2 85.40 1 16 A ALA 17 2 79.09 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 LYS . 2 A 2 A 3 1 n PHE . 3 A 3 A 4 1 n GLY . 4 A 4 A 5 1 n SER . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n GLY . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n SER . 10 A 10 A 11 1 n LEU . 11 A 11 A 12 1 n VAL . 12 A 12 A 13 1 n GLY . 13 A 13 A 14 1 n LEU . 14 A 14 A 15 1 n SER . 15 A 15 A 16 1 n VAL . 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 ? -10.109 -1.082 9.294 1.00 71.13 1 A 1 ATOM 2 C CA . MET A 1 1 ? -9.260 -2.137 9.879 1.00 74.05 1 A 1 ATOM 3 C C . MET A 1 1 ? -8.330 -2.731 8.831 1.00 75.06 1 A 1 ATOM 4 O O . MET A 1 1 ? -7.116 -2.557 8.888 1.00 70.59 1 A 1 ATOM 5 C CB . MET A 1 1 ? -10.133 -3.237 10.478 1.00 68.73 1 A 1 ATOM 6 C CG . MET A 1 1 ? -10.908 -2.749 11.689 1.00 68.34 1 A 1 ATOM 7 S SD . MET A 1 1 ? -9.798 -2.290 13.006 1.00 62.36 1 A 1 ATOM 8 C CE . MET A 1 1 ? -10.969 -1.697 14.209 1.00 55.79 1 A 1 ATOM 9 N N . LYS A 1 2 ? -8.925 -3.403 7.875 1.00 72.32 2 A 1 ATOM 10 C CA . LYS A 1 2 ? -8.121 -3.998 6.814 1.00 74.50 2 A 1 ATOM 11 C C . LYS A 1 2 ? -8.034 -3.064 5.621 1.00 75.23 2 A 1 ATOM 12 O O . LYS A 1 2 ? -8.850 -3.134 4.707 1.00 72.82 2 A 1 ATOM 13 C CB . LYS A 1 2 ? -8.718 -5.332 6.387 1.00 70.70 2 A 1 ATOM 14 C CG . LYS A 1 2 ? -8.241 -6.486 7.238 1.00 68.61 2 A 1 ATOM 15 C CD . LYS A 1 2 ? -6.793 -6.804 6.951 1.00 65.47 2 A 1 ATOM 16 C CE . LYS A 1 2 ? -6.343 -8.058 7.664 1.00 60.49 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? -4.957 -8.439 7.265 1.00 54.68 2 A 1 ATOM 18 N N . PHE A 1 3 ? -7.057 -2.184 5.637 1.00 71.63 3 A 1 ATOM 19 C CA . PHE A 1 3 ? -6.842 -1.261 4.532 1.00 72.46 3 A 1 ATOM 20 C C . PHE A 1 3 ? -5.973 -1.940 3.485 1.00 76.04 3 A 1 ATOM 21 O O . PHE A 1 3 ? -5.457 -3.036 3.696 1.00 70.34 3 A 1 ATOM 22 C CB . PHE A 1 3 ? -6.151 0.009 5.013 1.00 68.75 3 A 1 ATOM 23 C CG . PHE A 1 3 ? -6.565 0.426 6.393 1.00 66.69 3 A 1 ATOM 24 C CD1 . PHE A 1 3 ? -5.827 0.036 7.491 1.00 65.25 3 A 1 ATOM 25 C CD2 . PHE A 1 3 ? -7.693 1.199 6.577 1.00 62.49 3 A 1 ATOM 26 C CE1 . PHE A 1 3 ? -6.199 0.414 8.765 1.00 60.14 3 A 1 ATOM 27 C CE2 . PHE A 1 3 ? -8.077 1.581 7.851 1.00 59.92 3 A 1 ATOM 28 C CZ . PHE A 1 3 ? -7.329 1.184 8.948 1.00 58.96 3 A 1 ATOM 29 N N . GLY A 1 4 ? -5.785 -1.281 2.359 1.00 77.92 4 A 1 ATOM 30 C CA . GLY A 1 4 ? -4.905 -1.830 1.343 1.00 78.31 4 A 1 ATOM 31 C C . GLY A 1 4 ? -3.468 -1.724 1.804 1.00 80.52 4 A 1 ATOM 32 O O . GLY A 1 4 ? -2.855 -0.673 1.663 1.00 77.59 4 A 1 ATOM 33 N N . SER A 1 5 ? -2.942 -2.801 2.361 1.00 81.61 5 A 1 ATOM 34 C CA . SER A 1 5 ? -1.578 -2.807 2.891 1.00 83.29 5 A 1 ATOM 35 C C . SER A 1 5 ? -0.580 -2.302 1.856 1.00 84.53 5 A 1 ATOM 36 O O . SER A 1 5 ? 0.317 -1.523 2.166 1.00 81.81 5 A 1 ATOM 37 C CB . SER A 1 5 ? -1.184 -4.217 3.328 1.00 80.89 5 A 1 ATOM 38 O OG . SER A 1 5 ? -2.074 -4.692 4.323 1.00 74.56 5 A 1 ATOM 39 N N . LEU A 1 6 ? -0.756 -2.739 0.632 1.00 80.98 6 A 1 ATOM 40 C CA . LEU A 1 6 ? 0.125 -2.312 -0.450 1.00 82.32 6 A 1 ATOM 41 C C . LEU A 1 6 ? -0.058 -0.837 -0.764 1.00 85.08 6 A 1 ATOM 42 O O . LEU A 1 6 ? 0.883 -0.168 -1.193 1.00 82.52 6 A 1 ATOM 43 C CB . LEU A 1 6 ? -0.142 -3.142 -1.702 1.00 79.89 6 A 1 ATOM 44 C CG . LEU A 1 6 ? 0.172 -4.626 -1.542 1.00 77.54 6 A 1 ATOM 45 C CD1 . LEU A 1 6 ? -0.172 -5.371 -2.820 1.00 73.90 6 A 1 ATOM 46 C CD2 . LEU A 1 6 ? 1.629 -4.837 -1.174 1.00 72.31 6 A 1 ATOM 47 N N . LEU A 1 7 ? -1.259 -0.331 -0.538 1.00 84.84 7 A 1 ATOM 48 C CA . LEU A 1 7 ? -1.539 1.079 -0.785 1.00 84.59 7 A 1 ATOM 49 C C . LEU A 1 7 ? -0.701 1.956 0.129 1.00 86.66 7 A 1 ATOM 50 O O . LEU A 1 7 ? -0.117 2.948 -0.309 1.00 84.68 7 A 1 ATOM 51 C CB . LEU A 1 7 ? -3.023 1.368 -0.570 1.00 82.65 7 A 1 ATOM 52 C CG . LEU A 1 7 ? -3.950 0.675 -1.561 1.00 80.03 7 A 1 ATOM 53 C CD1 . LEU A 1 7 ? -5.400 0.985 -1.222 1.00 76.29 7 A 1 ATOM 54 C CD2 . LEU A 1 7 ? -3.630 1.098 -2.982 1.00 73.55 7 A 1 ATOM 55 N N . GLY A 1 8 ? -0.644 1.590 1.396 1.00 83.12 8 A 1 ATOM 56 C CA . GLY A 1 8 ? 0.151 2.346 2.353 1.00 83.85 8 A 1 ATOM 57 C C . GLY A 1 8 ? 1.629 2.274 2.034 1.00 85.88 8 A 1 ATOM 58 O O . GLY A 1 8 ? 2.335 3.283 2.046 1.00 84.17 8 A 1 ATOM 59 N N . LEU A 1 9 ? 2.100 1.078 1.735 1.00 85.49 9 A 1 ATOM 60 C CA . LEU A 1 9 ? 3.510 0.879 1.417 1.00 86.22 9 A 1 ATOM 61 C C . LEU A 1 9 ? 3.891 1.588 0.129 1.00 88.48 9 A 1 ATOM 62 O O . LEU A 1 9 ? 4.952 2.210 0.043 1.00 86.13 9 A 1 ATOM 63 C CB . LEU A 1 9 ? 3.810 -0.615 1.290 1.00 84.06 9 A 1 ATOM 64 C CG . LEU A 1 9 ? 3.712 -1.385 2.601 1.00 80.48 9 A 1 ATOM 65 C CD1 . LEU A 1 9 ? 3.877 -2.876 2.349 1.00 76.76 9 A 1 ATOM 66 C CD2 . LEU A 1 9 ? 4.746 -0.898 3.593 1.00 74.85 9 A 1 ATOM 67 N N . SER A 1 10 ? 3.031 1.505 -0.856 1.00 87.80 10 A 1 ATOM 68 C CA . SER A 1 10 ? 3.300 2.138 -2.141 1.00 88.30 10 A 1 ATOM 69 C C . SER A 1 10 ? 3.335 3.651 -1.997 1.00 89.30 10 A 1 ATOM 70 O O . SER A 1 10 ? 4.186 4.322 -2.585 1.00 87.54 10 A 1 ATOM 71 C CB . SER A 1 10 ? 2.238 1.739 -3.166 1.00 86.88 10 A 1 ATOM 72 O OG . SER A 1 10 ? 0.985 2.274 -2.817 1.00 80.77 10 A 1 ATOM 73 N N . LEU A 1 11 ? 2.413 4.175 -1.200 1.00 88.56 11 A 1 ATOM 74 C CA . LEU A 1 11 ? 2.345 5.612 -0.978 1.00 89.34 11 A 1 ATOM 75 C C . LEU A 1 11 ? 3.567 6.102 -0.217 1.00 90.91 11 A 1 ATOM 76 O O . LEU A 1 11 ? 4.156 7.129 -0.559 1.00 89.25 11 A 1 ATOM 77 C CB . LEU A 1 11 ? 1.078 5.969 -0.205 1.00 87.63 11 A 1 ATOM 78 C CG . LEU A 1 11 ? 0.846 7.469 -0.073 1.00 82.40 11 A 1 ATOM 79 C CD1 . LEU A 1 11 ? 0.581 8.088 -1.433 1.00 78.65 11 A 1 ATOM 80 C CD2 . LEU A 1 11 ? -0.314 7.743 0.874 1.00 78.32 11 A 1 ATOM 81 N N . VAL A 1 12 ? 3.943 5.367 0.818 1.00 88.84 12 A 1 ATOM 82 C CA . VAL A 1 12 ? 5.113 5.721 1.618 1.00 88.52 12 A 1 ATOM 83 C C . VAL A 1 12 ? 6.378 5.650 0.781 1.00 89.74 12 A 1 ATOM 84 O O . VAL A 1 12 ? 7.193 6.574 0.780 1.00 88.17 12 A 1 ATOM 85 C CB . VAL A 1 12 ? 5.247 4.799 2.835 1.00 86.44 12 A 1 ATOM 86 C CG1 . VAL A 1 12 ? 6.569 5.049 3.557 1.00 82.02 12 A 1 ATOM 87 C CG2 . VAL A 1 12 ? 4.085 5.018 3.783 1.00 84.36 12 A 1 ATOM 88 N N . GLY A 1 13 ? 6.546 4.552 0.080 1.00 88.36 13 A 1 ATOM 89 C CA . GLY A 1 13 ? 7.732 4.376 -0.750 1.00 88.20 13 A 1 ATOM 90 C C . GLY A 1 13 ? 7.810 5.400 -1.862 1.00 89.44 13 A 1 ATOM 91 O O . GLY A 1 13 ? 8.892 5.874 -2.213 1.00 88.42 13 A 1 ATOM 92 N N . LEU A 1 14 ? 6.656 5.751 -2.417 1.00 88.72 14 A 1 ATOM 93 C CA . LEU A 1 14 ? 6.601 6.721 -3.505 1.00 88.40 14 A 1 ATOM 94 C C . LEU A 1 14 ? 6.704 8.151 -2.993 1.00 90.26 14 A 1 ATOM 95 O O . LEU A 1 14 ? 7.442 8.969 -3.550 1.00 87.88 14 A 1 ATOM 96 C CB . LEU A 1 14 ? 5.299 6.548 -4.286 1.00 86.64 14 A 1 ATOM 97 C CG . LEU A 1 14 ? 5.216 7.404 -5.544 1.00 82.17 14 A 1 ATOM 98 C CD1 . LEU A 1 14 ? 6.248 6.959 -6.559 1.00 78.43 14 A 1 ATOM 99 C CD2 . LEU A 1 14 ? 3.816 7.332 -6.132 1.00 76.20 14 A 1 ATOM 100 N N . SER A 1 15 ? 5.958 8.449 -1.939 1.00 88.49 15 A 1 ATOM 101 C CA . SER A 1 15 ? 5.931 9.798 -1.380 1.00 88.31 15 A 1 ATOM 102 C C . SER A 1 15 ? 7.198 10.121 -0.596 1.00 89.22 15 A 1 ATOM 103 O O . SER A 1 15 ? 7.796 11.183 -0.771 1.00 87.19 15 A 1 ATOM 104 C CB . SER A 1 15 ? 4.715 9.975 -0.470 1.00 86.33 15 A 1 ATOM 105 O OG . SER A 1 15 ? 4.685 11.277 0.068 1.00 78.51 15 A 1 ATOM 106 N N . VAL A 1 16 ? 7.592 9.217 0.277 1.00 88.31 16 A 1 ATOM 107 C CA . VAL A 1 16 ? 8.777 9.424 1.116 1.00 88.79 16 A 1 ATOM 108 C C . VAL A 1 16 ? 10.061 9.333 0.303 1.00 89.64 16 A 1 ATOM 109 O O . VAL A 1 16 ? 11.015 10.084 0.534 1.00 87.38 16 A 1 ATOM 110 C CB . VAL A 1 16 ? 8.826 8.411 2.269 1.00 85.13 16 A 1 ATOM 111 C CG1 . VAL A 1 16 ? 10.077 8.620 3.113 1.00 78.61 16 A 1 ATOM 112 C CG2 . VAL A 1 16 ? 7.590 8.536 3.138 1.00 79.92 16 A 1 ATOM 113 N N . ALA A 1 17 ? 10.089 8.409 -0.632 1.00 85.68 17 A 1 ATOM 114 C CA . ALA A 1 17 ? 11.271 8.207 -1.457 1.00 83.73 17 A 1 ATOM 115 C C . ALA A 1 17 ? 11.476 9.387 -2.401 1.00 81.21 17 A 1 ATOM 116 O O . ALA A 1 17 ? 10.640 9.609 -3.286 1.00 76.27 17 A 1 ATOM 117 C CB . ALA A 1 17 ? 11.168 6.907 -2.238 1.00 76.73 17 A 1 ATOM 118 O OXT . ALA A 1 17 ? 12.472 10.091 -2.250 1.00 70.95 17 A 1 #