# 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_spkb41712 # _entry.id spkb41712 # 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" "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 ALA 3 1 n SER 4 1 n ILE 5 1 n VAL 6 1 n LEU 7 1 n VAL 8 1 n SER 9 1 n PHE 10 1 n LEU 11 1 n GLY 12 1 n LEU 13 1 n VAL 14 1 n SER 15 1 n GLY 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 @ 2025-07-09 00:37:03)" _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 95.30 _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 87.51 1 1 A LYS 2 2 89.67 1 2 A ALA 3 2 97.95 1 3 A SER 4 2 96.53 1 4 A ILE 5 2 96.96 1 5 A VAL 6 2 98.17 1 6 A LEU 7 2 95.90 1 7 A VAL 8 2 97.70 1 8 A SER 9 2 97.55 1 9 A PHE 10 2 96.40 1 10 A LEU 11 2 96.15 1 11 A GLY 12 2 97.96 1 12 A LEU 13 2 95.98 1 13 A VAL 14 2 96.97 1 14 A SER 15 2 95.24 1 15 A GLY 16 2 90.91 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 LYS . 2 A 2 A 3 1 n ALA . 3 A 3 A 4 1 n SER . 4 A 4 A 5 1 n ILE . 5 A 5 A 6 1 n VAL . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n VAL . 8 A 8 A 9 1 n SER . 9 A 9 A 10 1 n PHE . 10 A 10 A 11 1 n LEU . 11 A 11 A 12 1 n GLY . 12 A 12 A 13 1 n LEU . 13 A 13 A 14 1 n VAL . 14 A 14 A 15 1 n SER . 15 A 15 A 16 1 n GLY . 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 ? -6.396 6.134 8.463 1.00 93.27 1 A 1 ATOM 2 C CA . MET A 1 1 ? -5.291 6.446 7.533 1.00 94.31 1 A 1 ATOM 3 C C . MET A 1 1 ? -4.418 5.220 7.269 1.00 94.86 1 A 1 ATOM 4 O O . MET A 1 1 ? -3.807 5.108 6.212 1.00 91.88 1 A 1 ATOM 5 C CB . MET A 1 1 ? -4.421 7.581 8.095 1.00 89.51 1 A 1 ATOM 6 C CG . MET A 1 1 ? -5.174 8.899 8.149 1.00 85.26 1 A 1 ATOM 7 S SD . MET A 1 1 ? -4.191 10.235 8.831 1.00 80.42 1 A 1 ATOM 8 C CE . MET A 1 1 ? -5.385 11.552 8.800 1.00 70.58 1 A 1 ATOM 9 N N . LYS A 1 2 ? -4.380 4.305 8.242 1.00 95.84 2 A 1 ATOM 10 C CA . LYS A 1 2 ? -3.585 3.080 8.092 1.00 96.74 2 A 1 ATOM 11 C C . LYS A 1 2 ? -4.039 2.267 6.886 1.00 97.12 2 A 1 ATOM 12 O O . LYS A 1 2 ? -3.222 1.875 6.051 1.00 96.34 2 A 1 ATOM 13 C CB . LYS A 1 2 ? -3.679 2.230 9.364 1.00 94.94 2 A 1 ATOM 14 C CG . LYS A 1 2 ? -2.623 2.588 10.398 1.00 87.67 2 A 1 ATOM 15 C CD . LYS A 1 2 ? -1.256 2.053 9.997 1.00 85.63 2 A 1 ATOM 16 C CE . LYS A 1 2 ? -0.212 2.308 11.070 1.00 79.96 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? 1.115 1.755 10.688 1.00 72.77 2 A 1 ATOM 18 N N . ALA A 1 3 ? -5.344 2.015 6.780 1.00 97.68 3 A 1 ATOM 19 C CA . ALA A 1 3 ? -5.893 1.235 5.674 1.00 98.12 3 A 1 ATOM 20 C C . ALA A 1 3 ? -5.611 1.906 4.332 1.00 98.36 3 A 1 ATOM 21 O O . ALA A 1 3 ? -5.311 1.237 3.343 1.00 97.90 3 A 1 ATOM 22 C CB . ALA A 1 3 ? -7.395 1.043 5.874 1.00 97.67 3 A 1 ATOM 23 N N . SER A 1 4 ? -5.693 3.222 4.305 1.00 98.20 4 A 1 ATOM 24 C CA . SER A 1 4 ? -5.432 3.991 3.087 1.00 98.26 4 A 1 ATOM 25 C C . SER A 1 4 ? -3.979 3.825 2.638 1.00 98.39 4 A 1 ATOM 26 O O . SER A 1 4 ? -3.706 3.602 1.460 1.00 97.84 4 A 1 ATOM 27 C CB . SER A 1 4 ? -5.744 5.469 3.319 1.00 97.66 4 A 1 ATOM 28 O OG . SER A 1 4 ? -5.545 6.204 2.138 1.00 88.83 4 A 1 ATOM 29 N N . ILE A 1 5 ? -3.043 3.910 3.585 1.00 98.22 5 A 1 ATOM 30 C CA . ILE A 1 5 ? -1.617 3.766 3.293 1.00 98.18 5 A 1 ATOM 31 C C . ILE A 1 5 ? -1.303 2.364 2.786 1.00 98.25 5 A 1 ATOM 32 O O . ILE A 1 5 ? -0.495 2.186 1.871 1.00 97.90 5 A 1 ATOM 33 C CB . ILE A 1 5 ? -0.775 4.079 4.540 1.00 98.04 5 A 1 ATOM 34 C CG1 . ILE A 1 5 ? -0.994 5.533 4.994 1.00 96.57 5 A 1 ATOM 35 C CG2 . ILE A 1 5 ? 0.711 3.834 4.268 1.00 95.97 5 A 1 ATOM 36 C CD1 . ILE A 1 5 ? -0.583 6.564 3.950 1.00 92.52 5 A 1 ATOM 37 N N . VAL A 1 6 ? -1.939 1.355 3.382 1.00 98.65 6 A 1 ATOM 38 C CA . VAL A 1 6 ? -1.728 -0.037 2.978 1.00 98.65 6 A 1 ATOM 39 C C . VAL A 1 6 ? -2.098 -0.232 1.509 1.00 98.61 6 A 1 ATOM 40 O O . VAL A 1 6 ? -1.341 -0.830 0.742 1.00 98.35 6 A 1 ATOM 41 C CB . VAL A 1 6 ? -2.545 -0.997 3.859 1.00 98.50 6 A 1 ATOM 42 C CG1 . VAL A 1 6 ? -2.455 -2.426 3.338 1.00 97.45 6 A 1 ATOM 43 C CG2 . VAL A 1 6 ? -2.041 -0.942 5.296 1.00 96.98 6 A 1 ATOM 44 N N . LEU A 1 7 ? -3.253 0.273 1.119 1.00 98.17 7 A 1 ATOM 45 C CA . LEU A 1 7 ? -3.719 0.141 -0.262 1.00 98.08 7 A 1 ATOM 46 C C . LEU A 1 7 ? -2.802 0.887 -1.231 1.00 98.16 7 A 1 ATOM 47 O O . LEU A 1 7 ? -2.461 0.372 -2.298 1.00 97.95 7 A 1 ATOM 48 C CB . LEU A 1 7 ? -5.149 0.670 -0.377 1.00 97.87 7 A 1 ATOM 49 C CG . LEU A 1 7 ? -6.189 -0.180 0.349 1.00 94.14 7 A 1 ATOM 50 C CD1 . LEU A 1 7 ? -7.529 0.544 0.379 1.00 90.74 7 A 1 ATOM 51 C CD2 . LEU A 1 7 ? -6.345 -1.536 -0.330 1.00 92.10 7 A 1 ATOM 52 N N . VAL A 1 8 ? -2.400 2.089 -0.862 1.00 98.42 8 A 1 ATOM 53 C CA . VAL A 1 8 ? -1.511 2.895 -1.702 1.00 98.33 8 A 1 ATOM 54 C C . VAL A 1 8 ? -0.157 2.209 -1.863 1.00 98.35 8 A 1 ATOM 55 O O . VAL A 1 8 ? 0.395 2.151 -2.967 1.00 97.98 8 A 1 ATOM 56 C CB . VAL A 1 8 ? -1.329 4.302 -1.107 1.00 97.98 8 A 1 ATOM 57 C CG1 . VAL A 1 8 ? -0.295 5.097 -1.896 1.00 96.47 8 A 1 ATOM 58 C CG2 . VAL A 1 8 ? -2.655 5.049 -1.113 1.00 96.40 8 A 1 ATOM 59 N N . SER A 1 9 ? 0.373 1.668 -0.765 1.00 98.22 9 A 1 ATOM 60 C CA . SER A 1 9 ? 1.662 0.977 -0.787 1.00 98.17 9 A 1 ATOM 61 C C . SER A 1 9 ? 1.595 -0.269 -1.667 1.00 98.33 9 A 1 ATOM 62 O O . SER A 1 9 ? 2.530 -0.562 -2.413 1.00 97.95 9 A 1 ATOM 63 C CB . SER A 1 9 ? 2.075 0.584 0.628 1.00 97.77 9 A 1 ATOM 64 O OG . SER A 1 9 ? 2.247 1.734 1.431 1.00 94.83 9 A 1 ATOM 65 N N . PHE A 1 10 ? 0.479 -1.003 -1.577 1.00 98.13 10 A 1 ATOM 66 C CA . PHE A 1 10 ? 0.271 -2.204 -2.388 1.00 98.11 10 A 1 ATOM 67 C C . PHE A 1 10 ? 0.300 -1.867 -3.869 1.00 98.19 10 A 1 ATOM 68 O O . PHE A 1 10 ? 0.976 -2.535 -4.654 1.00 97.75 10 A 1 ATOM 69 C CB . PHE A 1 10 ? -1.069 -2.852 -2.031 1.00 97.92 10 A 1 ATOM 70 C CG . PHE A 1 10 ? -0.904 -4.186 -1.345 1.00 97.09 10 A 1 ATOM 71 C CD1 . PHE A 1 10 ? -0.471 -4.252 -0.032 1.00 94.19 10 A 1 ATOM 72 C CD2 . PHE A 1 10 ? -1.184 -5.362 -2.027 1.00 94.88 10 A 1 ATOM 73 C CE1 . PHE A 1 10 ? -0.310 -5.480 0.600 1.00 94.60 10 A 1 ATOM 74 C CE2 . PHE A 1 10 ? -1.030 -6.594 -1.401 1.00 94.49 10 A 1 ATOM 75 C CZ . PHE A 1 10 ? -0.596 -6.652 -0.084 1.00 95.07 10 A 1 ATOM 76 N N . LEU A 1 11 ? -0.426 -0.831 -4.249 1.00 98.33 11 A 1 ATOM 77 C CA . LEU A 1 11 ? -0.480 -0.409 -5.645 1.00 98.14 11 A 1 ATOM 78 C C . LEU A 1 11 ? 0.904 -0.009 -6.147 1.00 98.20 11 A 1 ATOM 79 O O . LEU A 1 11 ? 1.284 -0.340 -7.274 1.00 97.60 11 A 1 ATOM 80 C CB . LEU A 1 11 ? -1.456 0.763 -5.789 1.00 97.75 11 A 1 ATOM 81 C CG . LEU A 1 11 ? -1.747 1.149 -7.238 1.00 95.63 11 A 1 ATOM 82 C CD1 . LEU A 1 11 ? -2.508 0.040 -7.953 1.00 91.43 11 A 1 ATOM 83 C CD2 . LEU A 1 11 ? -2.556 2.439 -7.282 1.00 92.14 11 A 1 ATOM 84 N N . GLY A 1 12 ? 1.658 0.692 -5.312 1.00 98.01 12 A 1 ATOM 85 C CA . GLY A 1 12 ? 3.007 1.123 -5.670 1.00 97.95 12 A 1 ATOM 86 C C . GLY A 1 12 ? 3.955 -0.045 -5.862 1.00 98.22 12 A 1 ATOM 87 O O . GLY A 1 12 ? 4.725 -0.080 -6.822 1.00 97.66 12 A 1 ATOM 88 N N . LEU A 1 13 ? 3.893 -1.028 -4.954 1.00 98.05 13 A 1 ATOM 89 C CA . LEU A 1 13 ? 4.753 -2.208 -5.031 1.00 98.03 13 A 1 ATOM 90 C C . LEU A 1 13 ? 4.386 -3.087 -6.220 1.00 98.12 13 A 1 ATOM 91 O O . LEU A 1 13 ? 5.268 -3.588 -6.922 1.00 97.26 13 A 1 ATOM 92 C CB . LEU A 1 13 ? 4.644 -3.013 -3.732 1.00 97.65 13 A 1 ATOM 93 C CG . LEU A 1 13 ? 5.323 -2.344 -2.538 1.00 95.51 13 A 1 ATOM 94 C CD1 . LEU A 1 13 ? 4.929 -3.050 -1.248 1.00 92.09 13 A 1 ATOM 95 C CD2 . LEU A 1 13 ? 6.837 -2.365 -2.700 1.00 91.16 13 A 1 ATOM 96 N N . VAL A 1 14 ? 3.093 -3.297 -6.443 1.00 98.27 14 A 1 ATOM 97 C CA . VAL A 1 14 ? 2.620 -4.115 -7.560 1.00 98.08 14 A 1 ATOM 98 C C . VAL A 1 14 ? 3.000 -3.475 -8.890 1.00 98.12 14 A 1 ATOM 99 O O . VAL A 1 14 ? 3.466 -4.159 -9.808 1.00 97.49 14 A 1 ATOM 100 C CB . VAL A 1 14 ? 1.098 -4.321 -7.484 1.00 97.25 14 A 1 ATOM 101 C CG1 . VAL A 1 14 ? 0.585 -5.023 -8.737 1.00 94.62 14 A 1 ATOM 102 C CG2 . VAL A 1 14 ? 0.743 -5.145 -6.258 1.00 94.93 14 A 1 ATOM 103 N N . SER A 1 15 ? 2.812 -2.179 -9.009 1.00 97.50 15 A 1 ATOM 104 C CA . SER A 1 15 ? 3.152 -1.444 -10.229 1.00 97.32 15 A 1 ATOM 105 C C . SER A 1 15 ? 4.663 -1.412 -10.444 1.00 97.27 15 A 1 ATOM 106 O O . SER A 1 15 ? 5.127 -1.392 -11.586 1.00 94.97 15 A 1 ATOM 107 C CB . SER A 1 15 ? 2.599 -0.022 -10.161 1.00 95.63 15 A 1 ATOM 108 O OG . SER A 1 15 ? 1.183 -0.053 -10.091 1.00 88.76 15 A 1 ATOM 109 N N . GLY A 1 16 ? 5.408 -1.436 -9.331 1.00 95.15 16 A 1 ATOM 110 C CA . GLY A 1 16 ? 6.868 -1.462 -9.382 1.00 93.30 16 A 1 ATOM 111 C C . GLY A 1 16 ? 7.452 -0.147 -9.871 1.00 91.32 16 A 1 ATOM 112 O O . GLY A 1 16 ? 7.771 -0.041 -11.057 1.00 85.18 16 A 1 ATOM 113 O OXT . GLY A 1 16 ? 7.673 0.725 -9.016 1.00 89.62 16 A 1 #