# 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_spkb07871 # _entry.id spkb07871 # 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 "C6 H15 N4 O2" 175.209 ARG y ARGININE C(C[C@@H](C(=O)O)N)CNC(=[NH2+])N ? "L-PEPTIDE LINKING" "C3 H7 N O2 S" 121.158 CYS y CYSTEINE C([C@@H](C(=O)O)N)S ? "L-PEPTIDE LINKING" "C5 H9 N O4" 147.129 GLU y "GLUTAMIC ACID" C(CC(=O)O)[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" "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" # _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 ARG 2 1 n ARG 3 1 n GLU 4 1 n LEU 5 1 n PHE 6 1 n ILE 7 1 n PHE 8 1 n LEU 9 1 n LEU 10 1 n LEU 11 1 n LEU 12 1 n GLY 13 1 n GLU 14 1 n CYS 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 @ 2025-07-04 18:37:44)" _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 93.53 _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 88.12 1 1 A ARG 2 2 86.70 1 2 A ARG 3 2 90.53 1 3 A GLU 4 2 94.18 1 4 A LEU 5 2 95.63 1 5 A PHE 6 2 96.01 1 6 A ILE 7 2 97.14 1 7 A PHE 8 2 96.57 1 8 A LEU 9 2 96.52 1 9 A LEU 10 2 97.04 1 10 A LEU 11 2 96.72 1 11 A LEU 12 2 96.31 1 12 A GLY 13 2 96.45 1 13 A GLU 14 2 87.60 1 14 A CYS 15 2 90.83 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 ARG . 2 A 2 A 3 1 n ARG . 3 A 3 A 4 1 n GLU . 4 A 4 A 5 1 n LEU . 5 A 5 A 6 1 n PHE . 6 A 6 A 7 1 n ILE . 7 A 7 A 8 1 n PHE . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n LEU . 11 A 11 A 12 1 n LEU . 12 A 12 A 13 1 n GLY . 13 A 13 A 14 1 n GLU . 14 A 14 A 15 1 n CYS . 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 ? -6.345 9.612 -1.667 1.00 91.51 1 A 1 ATOM 2 C CA . MET A 1 1 ? -5.904 8.339 -1.078 1.00 93.56 1 A 1 ATOM 3 C C . MET A 1 1 ? -4.556 8.492 -0.391 1.00 94.96 1 A 1 ATOM 4 O O . MET A 1 1 ? -3.860 9.493 -0.576 1.00 94.23 1 A 1 ATOM 5 C CB . MET A 1 1 ? -5.800 7.254 -2.145 1.00 89.18 1 A 1 ATOM 6 C CG . MET A 1 1 ? -7.128 6.890 -2.763 1.00 84.46 1 A 1 ATOM 7 S SD . MET A 1 1 ? -7.021 5.557 -3.973 1.00 83.80 1 A 1 ATOM 8 C CE . MET A 1 1 ? -6.175 6.376 -5.300 1.00 73.23 1 A 1 ATOM 9 N N . ARG A 1 2 ? -4.172 7.512 0.407 1.00 93.11 2 A 1 ATOM 10 C CA . ARG A 1 2 ? -2.930 7.548 1.166 1.00 96.06 2 A 1 ATOM 11 C C . ARG A 1 2 ? -1.871 6.658 0.523 1.00 96.72 2 A 1 ATOM 12 O O . ARG A 1 2 ? -2.172 5.567 0.044 1.00 95.71 2 A 1 ATOM 13 C CB . ARG A 1 2 ? -3.185 7.095 2.598 1.00 94.25 2 A 1 ATOM 14 C CG . ARG A 1 2 ? -4.252 7.902 3.306 1.00 88.65 2 A 1 ATOM 15 C CD . ARG A 1 2 ? -4.656 7.264 4.613 1.00 87.03 2 A 1 ATOM 16 N NE . ARG A 1 2 ? -5.947 7.798 5.069 1.00 80.88 2 A 1 ATOM 17 C CZ . ARG A 1 2 ? -7.122 7.409 4.585 1.00 77.86 2 A 1 ATOM 18 N NH1 . ARG A 1 2 ? -7.194 6.464 3.651 1.00 72.54 2 A 1 ATOM 19 N NH2 . ARG A 1 2 ? -8.229 7.956 5.041 1.00 70.91 2 A 1 ATOM 20 N N . ARG A 1 3 ? -0.617 7.132 0.551 1.00 96.28 3 A 1 ATOM 21 C CA . ARG A 1 3 ? 0.517 6.379 0.018 1.00 97.50 3 A 1 ATOM 22 C C . ARG A 1 3 ? 0.691 5.074 0.792 1.00 98.12 3 A 1 ATOM 23 O O . ARG A 1 3 ? 1.017 4.042 0.217 1.00 97.56 3 A 1 ATOM 24 C CB . ARG A 1 3 ? 1.775 7.245 0.101 1.00 96.66 3 A 1 ATOM 25 C CG . ARG A 1 3 ? 3.074 6.536 -0.264 1.00 92.98 3 A 1 ATOM 26 C CD . ARG A 1 3 ? 3.101 6.080 -1.708 1.00 91.24 3 A 1 ATOM 27 N NE . ARG A 1 3 ? 4.399 5.502 -2.051 1.00 86.70 3 A 1 ATOM 28 C CZ . ARG A 1 3 ? 4.686 4.892 -3.184 1.00 83.89 3 A 1 ATOM 29 N NH1 . ARG A 1 3 ? 3.760 4.761 -4.120 1.00 77.81 3 A 1 ATOM 30 N NH2 . ARG A 1 3 ? 5.897 4.407 -3.392 1.00 77.13 3 A 1 ATOM 31 N N . GLU A 1 4 ? 0.466 5.145 2.096 1.00 97.67 4 A 1 ATOM 32 C CA . GLU A 1 4 ? 0.597 3.980 2.968 1.00 98.06 4 A 1 ATOM 33 C C . GLU A 1 4 ? -0.385 2.876 2.580 1.00 98.37 4 A 1 ATOM 34 O O . GLU A 1 4 ? -0.049 1.689 2.641 1.00 98.04 4 A 1 ATOM 35 C CB . GLU A 1 4 ? 0.372 4.382 4.421 1.00 97.64 4 A 1 ATOM 36 C CG . GLU A 1 4 ? 1.409 5.355 4.966 1.00 94.09 4 A 1 ATOM 37 C CD . GLU A 1 4 ? 1.092 6.803 4.654 1.00 91.01 4 A 1 ATOM 38 O OE1 . GLU A 1 4 ? 0.155 7.069 3.878 1.00 86.34 4 A 1 ATOM 39 O OE2 . GLU A 1 4 ? 1.782 7.682 5.193 1.00 86.43 4 A 1 ATOM 40 N N . LEU A 1 5 ? -1.583 3.263 2.180 1.00 97.62 5 A 1 ATOM 41 C CA . LEU A 1 5 ? -2.603 2.304 1.772 1.00 97.89 5 A 1 ATOM 42 C C . LEU A 1 5 ? -2.150 1.564 0.518 1.00 98.19 5 A 1 ATOM 43 O O . LEU A 1 5 ? -2.295 0.348 0.407 1.00 98.18 5 A 1 ATOM 44 C CB . LEU A 1 5 ? -3.932 3.023 1.501 1.00 97.91 5 A 1 ATOM 45 C CG . LEU A 1 5 ? -5.215 2.303 1.911 1.00 94.05 5 A 1 ATOM 46 C CD1 . LEU A 1 5 ? -6.401 2.940 1.210 1.00 89.86 5 A 1 ATOM 47 C CD2 . LEU A 1 5 ? -5.169 0.816 1.637 1.00 91.38 5 A 1 ATOM 48 N N . PHE A 1 6 ? -1.587 2.319 -0.441 1.00 98.02 6 A 1 ATOM 49 C CA . PHE A 1 6 ? -1.099 1.738 -1.686 1.00 98.15 6 A 1 ATOM 50 C C . PHE A 1 6 ? 0.019 0.736 -1.419 1.00 98.29 6 A 1 ATOM 51 O O . PHE A 1 6 ? 0.035 -0.354 -1.990 1.00 98.09 6 A 1 ATOM 52 C CB . PHE A 1 6 ? -0.609 2.845 -2.620 1.00 97.94 6 A 1 ATOM 53 C CG . PHE A 1 6 ? -0.141 2.339 -3.957 1.00 96.70 6 A 1 ATOM 54 C CD1 . PHE A 1 6 ? -1.010 1.659 -4.796 1.00 94.21 6 A 1 ATOM 55 C CD2 . PHE A 1 6 ? 1.160 2.553 -4.374 1.00 94.31 6 A 1 ATOM 56 C CE1 . PHE A 1 6 ? -0.587 1.195 -6.032 1.00 93.81 6 A 1 ATOM 57 C CE2 . PHE A 1 6 ? 1.589 2.091 -5.613 1.00 93.27 6 A 1 ATOM 58 C CZ . PHE A 1 6 ? 0.716 1.413 -6.439 1.00 93.33 6 A 1 ATOM 59 N N . ILE A 1 7 ? 0.953 1.103 -0.550 1.00 98.14 7 A 1 ATOM 60 C CA . ILE A 1 7 ? 2.056 0.217 -0.185 1.00 98.18 7 A 1 ATOM 61 C C . ILE A 1 7 ? 1.513 -1.051 0.473 1.00 98.31 7 A 1 ATOM 62 O O . ILE A 1 7 ? 1.965 -2.160 0.179 1.00 98.17 7 A 1 ATOM 63 C CB . ILE A 1 7 ? 3.046 0.932 0.757 1.00 98.07 7 A 1 ATOM 64 C CG1 . ILE A 1 7 ? 3.755 2.065 0.004 1.00 96.81 7 A 1 ATOM 65 C CG2 . ILE A 1 7 ? 4.070 -0.053 1.315 1.00 96.66 7 A 1 ATOM 66 C CD1 . ILE A 1 7 ? 4.542 2.997 0.888 1.00 92.75 7 A 1 ATOM 67 N N . PHE A 1 8 ? 0.542 -0.888 1.350 1.00 98.00 8 A 1 ATOM 68 C CA . PHE A 1 8 ? -0.093 -2.011 2.032 1.00 98.07 8 A 1 ATOM 69 C C . PHE A 1 8 ? -0.704 -2.983 1.028 1.00 98.19 8 A 1 ATOM 70 O O . PHE A 1 8 ? -0.514 -4.197 1.131 1.00 97.99 8 A 1 ATOM 71 C CB . PHE A 1 8 ? -1.164 -1.482 2.986 1.00 97.92 8 A 1 ATOM 72 C CG . PHE A 1 8 ? -1.911 -2.562 3.721 1.00 96.97 8 A 1 ATOM 73 C CD1 . PHE A 1 8 ? -1.271 -3.353 4.661 1.00 95.35 8 A 1 ATOM 74 C CD2 . PHE A 1 8 ? -3.262 -2.764 3.483 1.00 95.53 8 A 1 ATOM 75 C CE1 . PHE A 1 8 ? -1.969 -4.336 5.348 1.00 95.03 8 A 1 ATOM 76 C CE2 . PHE A 1 8 ? -3.965 -3.747 4.168 1.00 94.43 8 A 1 ATOM 77 C CZ . PHE A 1 8 ? -3.316 -4.532 5.100 1.00 94.84 8 A 1 ATOM 78 N N . LEU A 1 9 ? -1.427 -2.439 0.051 1.00 97.84 9 A 1 ATOM 79 C CA . LEU A 1 9 ? -2.052 -3.263 -0.974 1.00 97.80 9 A 1 ATOM 80 C C . LEU A 1 9 ? -1.006 -3.985 -1.822 1.00 97.93 9 A 1 ATOM 81 O O . LEU A 1 9 ? -1.189 -5.151 -2.174 1.00 97.74 9 A 1 ATOM 82 C CB . LEU A 1 9 ? -2.952 -2.406 -1.864 1.00 97.66 9 A 1 ATOM 83 C CG . LEU A 1 9 ? -4.196 -1.851 -1.171 1.00 95.19 9 A 1 ATOM 84 C CD1 . LEU A 1 9 ? -4.902 -0.869 -2.090 1.00 93.58 9 A 1 ATOM 85 C CD2 . LEU A 1 9 ? -5.143 -2.979 -0.777 1.00 94.40 9 A 1 ATOM 86 N N . LEU A 1 10 ? 0.093 -3.297 -2.136 1.00 98.12 10 A 1 ATOM 87 C CA . LEU A 1 10 ? 1.175 -3.906 -2.902 1.00 98.02 10 A 1 ATOM 88 C C . LEU A 1 10 ? 1.795 -5.063 -2.129 1.00 98.11 10 A 1 ATOM 89 O O . LEU A 1 10 ? 2.056 -6.124 -2.698 1.00 97.76 10 A 1 ATOM 90 C CB . LEU A 1 10 ? 2.254 -2.872 -3.220 1.00 97.88 10 A 1 ATOM 91 C CG . LEU A 1 10 ? 1.905 -1.882 -4.327 1.00 96.49 10 A 1 ATOM 92 C CD1 . LEU A 1 10 ? 3.002 -0.834 -4.431 1.00 94.84 10 A 1 ATOM 93 C CD2 . LEU A 1 10 ? 1.740 -2.601 -5.661 1.00 95.07 10 A 1 ATOM 94 N N . LEU A 1 11 ? 2.034 -4.862 -0.844 1.00 97.79 11 A 1 ATOM 95 C CA . LEU A 1 11 ? 2.614 -5.900 -0.003 1.00 97.74 11 A 1 ATOM 96 C C . LEU A 1 11 ? 1.709 -7.124 0.050 1.00 97.88 11 A 1 ATOM 97 O O . LEU A 1 11 ? 2.193 -8.256 -0.027 1.00 97.38 11 A 1 ATOM 98 C CB . LEU A 1 11 ? 2.863 -5.366 1.407 1.00 97.56 11 A 1 ATOM 99 C CG . LEU A 1 11 ? 4.005 -4.359 1.519 1.00 96.26 11 A 1 ATOM 100 C CD1 . LEU A 1 11 ? 4.027 -3.747 2.906 1.00 94.46 11 A 1 ATOM 101 C CD2 . LEU A 1 11 ? 5.339 -5.023 1.213 1.00 94.68 11 A 1 ATOM 102 N N . LEU A 1 12 ? 0.405 -6.901 0.160 1.00 97.93 12 A 1 ATOM 103 C CA . LEU A 1 12 ? -0.554 -7.997 0.178 1.00 97.80 12 A 1 ATOM 104 C C . LEU A 1 12 ? -0.528 -8.763 -1.142 1.00 97.70 12 A 1 ATOM 105 O O . LEU A 1 12 ? -0.577 -9.993 -1.154 1.00 96.65 12 A 1 ATOM 106 C CB . LEU A 1 12 ? -1.965 -7.469 0.437 1.00 97.39 12 A 1 ATOM 107 C CG . LEU A 1 12 ? -2.240 -6.975 1.852 1.00 95.98 12 A 1 ATOM 108 C CD1 . LEU A 1 12 ? -3.630 -6.352 1.905 1.00 93.69 12 A 1 ATOM 109 C CD2 . LEU A 1 12 ? -2.134 -8.116 2.854 1.00 93.34 12 A 1 ATOM 110 N N . GLY A 1 13 ? -0.438 -8.033 -2.235 1.00 96.92 13 A 1 ATOM 111 C CA . GLY A 1 13 ? -0.402 -8.645 -3.555 1.00 96.53 13 A 1 ATOM 112 C C . GLY A 1 13 ? 0.880 -9.397 -3.848 1.00 96.72 13 A 1 ATOM 113 O O . GLY A 1 13 ? 0.880 -10.353 -4.630 1.00 95.62 13 A 1 ATOM 114 N N . GLU A 1 14 ? 1.986 -8.969 -3.238 1.00 95.26 14 A 1 ATOM 115 C CA . GLU A 1 14 ? 3.284 -9.600 -3.451 1.00 94.15 14 A 1 ATOM 116 C C . GLU A 1 14 ? 3.575 -10.727 -2.465 1.00 93.49 14 A 1 ATOM 117 O O . GLU A 1 14 ? 4.630 -11.359 -2.544 1.00 88.32 14 A 1 ATOM 118 C CB . GLU A 1 14 ? 4.400 -8.551 -3.377 1.00 92.17 14 A 1 ATOM 119 C CG . GLU A 1 14 ? 4.307 -7.463 -4.444 1.00 85.93 14 A 1 ATOM 120 C CD . GLU A 1 14 ? 4.381 -8.034 -5.857 1.00 83.12 14 A 1 ATOM 121 O OE1 . GLU A 1 14 ? 5.168 -8.964 -6.085 1.00 77.83 14 A 1 ATOM 122 O OE2 . GLU A 1 14 ? 3.650 -7.536 -6.728 1.00 78.17 14 A 1 ATOM 123 N N . CYS A 1 15 ? 2.643 -10.988 -1.567 1.00 94.51 15 A 1 ATOM 124 C CA . CYS A 1 15 ? 2.821 -12.046 -0.574 1.00 94.39 15 A 1 ATOM 125 C C . CYS A 1 15 ? 2.595 -13.425 -1.197 1.00 93.84 15 A 1 ATOM 126 O O . CYS A 1 15 ? 3.326 -14.364 -0.855 1.00 90.94 15 A 1 ATOM 127 C CB . CYS A 1 15 ? 1.871 -11.834 0.608 1.00 91.70 15 A 1 ATOM 128 S SG . CYS A 1 15 ? 2.412 -10.538 1.743 1.00 86.71 15 A 1 ATOM 129 O OXT . CYS A 1 15 ? 1.669 -13.587 -2.026 1.00 83.70 15 A 1 #