# 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_spkb25363 # _entry.id spkb25363 # 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" "C4 H7 N O4" 133.103 ASP y "ASPARTIC ACID" C([C@@H](C(=O)O)N)C(=O)O ? "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" "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 ASP 2 1 n LYS 3 1 n VAL 4 1 n ILE 5 1 n LEU 6 1 n VAL 7 1 n LEU 8 1 n LEU 9 1 n MET 10 1 n SER 11 1 n LEU 12 1 n GLY 13 1 n ALA 14 1 n SER 15 1 n SER 16 # _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 @ 2025-07-05 03:52:20)" _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 93.75 _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 86.85 1 1 A ASP 2 2 93.00 1 2 A LYS 3 2 93.58 1 3 A VAL 4 2 97.48 1 4 A ILE 5 2 96.29 1 5 A LEU 6 2 95.56 1 6 A VAL 7 2 97.75 1 7 A LEU 8 2 95.34 1 8 A LEU 9 2 95.44 1 9 A MET 10 2 93.71 1 10 A SER 11 2 96.58 1 11 A LEU 12 2 95.46 1 12 A GLY 13 2 96.04 1 13 A ALA 14 2 95.19 1 14 A SER 15 2 90.46 1 15 A SER 16 2 82.43 1 16 # _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 ASP . 2 A 2 A 3 1 n LYS . 3 A 3 A 4 1 n VAL . 4 A 4 A 5 1 n ILE . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n VAL . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n MET . 10 A 10 A 11 1 n SER . 11 A 11 A 12 1 n LEU . 12 A 12 A 13 1 n GLY . 13 A 13 A 14 1 n ALA . 14 A 14 A 15 1 n SER . 15 A 15 A 16 1 n SER . 16 A 16 # _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 ? 7.180 -2.321 2.706 1.00 92.57 1 A 1 ATOM 2 C CA . MET A 1 1 ? 7.931 -3.576 2.763 1.00 94.88 1 A 1 ATOM 3 C C . MET A 1 1 ? 7.049 -4.735 2.322 1.00 94.90 1 A 1 ATOM 4 O O . MET A 1 1 ? 7.359 -5.435 1.364 1.00 92.70 1 A 1 ATOM 5 C CB . MET A 1 1 ? 8.437 -3.837 4.174 1.00 90.45 1 A 1 ATOM 6 C CG . MET A 1 1 ? 9.565 -2.903 4.597 1.00 81.85 1 A 1 ATOM 7 S SD . MET A 1 1 ? 8.922 -1.377 5.297 1.00 78.57 1 A 1 ATOM 8 C CE . MET A 1 1 ? 9.917 -1.279 6.787 1.00 68.91 1 A 1 ATOM 9 N N . ASP A 1 2 ? 5.946 -4.916 3.061 1.00 95.69 2 A 1 ATOM 10 C CA . ASP A 1 2 ? 5.015 -5.991 2.737 1.00 97.27 2 A 1 ATOM 11 C C . ASP A 1 2 ? 4.129 -5.611 1.559 1.00 97.82 2 A 1 ATOM 12 O O . ASP A 1 2 ? 3.979 -4.434 1.230 1.00 97.13 2 A 1 ATOM 13 C CB . ASP A 1 2 ? 4.140 -6.314 3.943 1.00 95.57 2 A 1 ATOM 14 C CG . ASP A 1 2 ? 4.931 -6.971 5.055 1.00 88.73 2 A 1 ATOM 15 O OD1 . ASP A 1 2 ? 5.726 -7.876 4.755 1.00 87.48 2 A 1 ATOM 16 O OD2 . ASP A 1 2 ? 4.753 -6.571 6.215 1.00 84.28 2 A 1 ATOM 17 N N . LYS A 1 3 ? 3.522 -6.619 0.941 1.00 97.94 3 A 1 ATOM 18 C CA . LYS A 1 3 ? 2.637 -6.387 -0.202 1.00 98.29 3 A 1 ATOM 19 C C . LYS A 1 3 ? 1.372 -5.657 0.238 1.00 98.37 3 A 1 ATOM 20 O O . LYS A 1 3 ? 0.857 -4.804 -0.481 1.00 97.83 3 A 1 ATOM 21 C CB . LYS A 1 3 ? 2.277 -7.718 -0.849 1.00 97.85 3 A 1 ATOM 22 C CG . LYS A 1 3 ? 3.488 -8.444 -1.410 1.00 93.82 3 A 1 ATOM 23 C CD . LYS A 1 3 ? 3.587 -8.278 -2.909 1.00 91.06 3 A 1 ATOM 24 C CE . LYS A 1 3 ? 4.693 -9.150 -3.489 1.00 86.28 3 A 1 ATOM 25 N NZ . LYS A 1 3 ? 5.940 -8.400 -3.668 1.00 80.81 3 A 1 ATOM 26 N N . VAL A 1 4 ? 0.892 -5.999 1.413 1.00 98.50 4 A 1 ATOM 27 C CA . VAL A 1 4 ? -0.318 -5.384 1.960 1.00 98.54 4 A 1 ATOM 28 C C . VAL A 1 4 ? -0.125 -3.889 2.155 1.00 98.63 4 A 1 ATOM 29 O O . VAL A 1 4 ? -1.004 -3.085 1.828 1.00 98.29 4 A 1 ATOM 30 C CB . VAL A 1 4 ? -0.705 -6.027 3.298 1.00 98.09 4 A 1 ATOM 31 C CG1 . VAL A 1 4 ? -2.066 -5.525 3.749 1.00 94.81 4 A 1 ATOM 32 C CG2 . VAL A 1 4 ? -0.707 -7.540 3.187 1.00 95.48 4 A 1 ATOM 33 N N . ILE A 1 5 ? 1.021 -3.529 2.695 1.00 97.91 5 A 1 ATOM 34 C CA . ILE A 1 5 ? 1.341 -2.129 2.940 1.00 97.76 5 A 1 ATOM 35 C C . ILE A 1 5 ? 1.455 -1.370 1.631 1.00 97.99 5 A 1 ATOM 36 O O . ILE A 1 5 ? 0.960 -0.249 1.498 1.00 97.75 5 A 1 ATOM 37 C CB . ILE A 1 5 ? 2.654 -2.006 3.731 1.00 97.37 5 A 1 ATOM 38 C CG1 . ILE A 1 5 ? 2.556 -2.784 5.045 1.00 95.31 5 A 1 ATOM 39 C CG2 . ILE A 1 5 ? 2.989 -0.541 3.996 1.00 94.86 5 A 1 ATOM 40 C CD1 . ILE A 1 5 ? 1.487 -2.247 5.972 1.00 91.38 5 A 1 ATOM 41 N N . LEU A 1 6 ? 2.113 -1.974 0.676 1.00 97.97 6 A 1 ATOM 42 C CA . LEU A 1 6 ? 2.297 -1.362 -0.634 1.00 97.89 6 A 1 ATOM 43 C C . LEU A 1 6 ? 0.957 -1.132 -1.320 1.00 98.09 6 A 1 ATOM 44 O O . LEU A 1 6 ? 0.714 -0.068 -1.889 1.00 97.98 6 A 1 ATOM 45 C CB . LEU A 1 6 ? 3.178 -2.254 -1.514 1.00 97.39 6 A 1 ATOM 46 C CG . LEU A 1 6 ? 4.303 -1.500 -2.222 1.00 92.58 6 A 1 ATOM 47 C CD1 . LEU A 1 6 ? 5.482 -1.307 -1.280 1.00 91.42 6 A 1 ATOM 48 C CD2 . LEU A 1 6 ? 4.741 -2.247 -3.468 1.00 91.13 6 A 1 ATOM 49 N N . VAL A 1 7 ? 0.104 -2.127 -1.261 1.00 98.29 7 A 1 ATOM 50 C CA . VAL A 1 7 ? -1.223 -2.045 -1.874 1.00 98.32 7 A 1 ATOM 51 C C . VAL A 1 7 ? -2.049 -0.950 -1.217 1.00 98.46 7 A 1 ATOM 52 O O . VAL A 1 7 ? -2.746 -0.191 -1.891 1.00 98.30 7 A 1 ATOM 53 C CB . VAL A 1 7 ? -1.955 -3.393 -1.770 1.00 98.01 7 A 1 ATOM 54 C CG1 . VAL A 1 7 ? -3.397 -3.267 -2.243 1.00 96.42 7 A 1 ATOM 55 C CG2 . VAL A 1 7 ? -1.235 -4.450 -2.589 1.00 96.48 7 A 1 ATOM 56 N N . LEU A 1 8 ? -1.965 -0.879 0.094 1.00 97.96 8 A 1 ATOM 57 C CA . LEU A 1 8 ? -2.701 0.129 0.849 1.00 97.76 8 A 1 ATOM 58 C C . LEU A 1 8 ? -2.252 1.530 0.466 1.00 98.00 8 A 1 ATOM 59 O O . LEU A 1 8 ? -3.076 2.417 0.228 1.00 97.77 8 A 1 ATOM 60 C CB . LEU A 1 8 ? -2.497 -0.086 2.346 1.00 97.26 8 A 1 ATOM 61 C CG . LEU A 1 8 ? -3.638 0.448 3.205 1.00 91.47 8 A 1 ATOM 62 C CD1 . LEU A 1 8 ? -4.705 -0.621 3.396 1.00 90.97 8 A 1 ATOM 63 C CD2 . LEU A 1 8 ? -3.123 0.922 4.548 1.00 91.57 8 A 1 ATOM 64 N N . LEU A 1 9 ? -0.950 1.723 0.418 1.00 97.90 9 A 1 ATOM 65 C CA . LEU A 1 9 ? -0.384 3.023 0.070 1.00 97.74 9 A 1 ATOM 66 C C . LEU A 1 9 ? -0.737 3.412 -1.356 1.00 97.87 9 A 1 ATOM 67 O O . LEU A 1 9 ? -1.089 4.561 -1.632 1.00 97.58 9 A 1 ATOM 68 C CB . LEU A 1 9 ? 1.135 2.986 0.249 1.00 97.11 9 A 1 ATOM 69 C CG . LEU A 1 9 ? 1.662 4.000 1.258 1.00 92.63 9 A 1 ATOM 70 C CD1 . LEU A 1 9 ? 2.824 3.430 2.050 1.00 91.57 9 A 1 ATOM 71 C CD2 . LEU A 1 9 ? 2.082 5.275 0.546 1.00 91.15 9 A 1 ATOM 72 N N . MET A 1 10 ? -0.645 2.459 -2.255 1.00 97.90 10 A 1 ATOM 73 C CA . MET A 1 10 ? -0.949 2.703 -3.664 1.00 97.63 10 A 1 ATOM 74 C C . MET A 1 10 ? -2.432 2.999 -3.854 1.00 97.71 10 A 1 ATOM 75 O O . MET A 1 10 ? -2.805 3.846 -4.663 1.00 97.17 10 A 1 ATOM 76 C CB . MET A 1 10 ? -0.540 1.497 -4.513 1.00 97.16 10 A 1 ATOM 77 C CG . MET A 1 10 ? -0.087 1.892 -5.906 1.00 94.28 10 A 1 ATOM 78 S SD . MET A 1 10 ? 1.315 0.909 -6.455 1.00 88.74 10 A 1 ATOM 79 C CE . MET A 1 10 ? 1.998 1.980 -7.713 1.00 79.06 10 A 1 ATOM 80 N N . SER A 1 11 ? -3.264 2.307 -3.106 1.00 98.14 11 A 1 ATOM 81 C CA . SER A 1 11 ? -4.708 2.512 -3.171 1.00 98.06 11 A 1 ATOM 82 C C . SER A 1 11 ? -5.070 3.917 -2.714 1.00 98.07 11 A 1 ATOM 83 O O . SER A 1 11 ? -5.904 4.584 -3.324 1.00 97.11 11 A 1 ATOM 84 C CB . SER A 1 11 ? -5.433 1.486 -2.309 1.00 97.37 11 A 1 ATOM 85 O OG . SER A 1 11 ? -5.558 0.256 -2.984 1.00 90.72 11 A 1 ATOM 86 N N . LEU A 1 12 ? -4.441 4.366 -1.635 1.00 97.92 12 A 1 ATOM 87 C CA . LEU A 1 12 ? -4.676 5.704 -1.111 1.00 97.70 12 A 1 ATOM 88 C C . LEU A 1 12 ? -4.200 6.758 -2.096 1.00 97.71 12 A 1 ATOM 89 O O . LEU A 1 12 ? -4.858 7.779 -2.296 1.00 96.63 12 A 1 ATOM 90 C CB . LEU A 1 12 ? -3.963 5.875 0.234 1.00 97.05 12 A 1 ATOM 91 C CG . LEU A 1 12 ? -4.878 5.855 1.454 1.00 94.04 12 A 1 ATOM 92 C CD1 . LEU A 1 12 ? -5.811 7.048 1.435 1.00 91.70 12 A 1 ATOM 93 C CD2 . LEU A 1 12 ? -5.661 4.559 1.510 1.00 90.93 12 A 1 ATOM 94 N N . GLY A 1 13 ? -3.052 6.507 -2.695 1.00 96.91 13 A 1 ATOM 95 C CA . GLY A 1 13 ? -2.496 7.432 -3.673 1.00 96.28 13 A 1 ATOM 96 C C . GLY A 1 13 ? -3.354 7.537 -4.919 1.00 96.13 13 A 1 ATOM 97 O O . GLY A 1 13 ? -3.490 8.610 -5.506 1.00 94.85 13 A 1 ATOM 98 N N . ALA A 1 14 ? -3.943 6.426 -5.319 1.00 96.65 14 A 1 ATOM 99 C CA . ALA A 1 14 ? -4.806 6.388 -6.498 1.00 96.04 14 A 1 ATOM 100 C C . ALA A 1 14 ? -6.161 7.021 -6.212 1.00 95.72 14 A 1 ATOM 101 O O . ALA A 1 14 ? -6.784 7.602 -7.096 1.00 92.96 14 A 1 ATOM 102 C CB . ALA A 1 14 ? -4.990 4.953 -6.971 1.00 94.60 14 A 1 ATOM 103 N N . SER A 1 15 ? -6.614 6.886 -4.981 1.00 94.26 15 A 1 ATOM 104 C CA . SER A 1 15 ? -7.895 7.444 -4.563 1.00 93.89 15 A 1 ATOM 105 C C . SER A 1 15 ? -7.780 8.924 -4.225 1.00 93.15 15 A 1 ATOM 106 O O . SER A 1 15 ? -8.742 9.682 -4.364 1.00 88.45 15 A 1 ATOM 107 C CB . SER A 1 15 ? -8.437 6.684 -3.360 1.00 91.13 15 A 1 ATOM 108 O OG . SER A 1 15 ? -9.844 6.645 -3.386 1.00 81.86 15 A 1 ATOM 109 N N . SER A 1 16 ? -6.609 9.310 -3.770 1.00 90.45 16 A 1 ATOM 110 C CA . SER A 1 16 ? -6.344 10.697 -3.389 1.00 87.81 16 A 1 ATOM 111 C C . SER A 1 16 ? -5.996 11.535 -4.614 1.00 83.43 16 A 1 ATOM 112 O O . SER A 1 16 ? -6.214 12.750 -4.588 1.00 77.31 16 A 1 ATOM 113 C CB . SER A 1 16 ? -5.216 10.767 -2.367 1.00 83.12 16 A 1 ATOM 114 O OG . SER A 1 16 ? -5.607 10.203 -1.141 1.00 76.85 16 A 1 ATOM 115 O OXT . SER A 1 16 ? -5.467 10.984 -5.586 1.00 78.06 16 A 1 #