# 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_spkb35861 # _entry.id spkb35861 # 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" "C6 H15 N4 O2" 175.209 ARG y ARGININE C(C[C@@H](C(=O)O)N)CNC(=[NH2+])N ? "L-PEPTIDE LINKING" "C5 H10 N2 O3" 146.144 GLN y GLUTAMINE C(CC(=O)N)[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" "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" "C4 H9 N O3" 119.119 THR y THREONINE C[C@H]([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 ARG 2 1 n MET 3 1 n GLN 4 1 n LEU 5 1 n THR 6 1 n ALA 7 1 n VAL 8 1 n LEU 9 1 n ALA 10 1 n ALA 11 1 n SER 12 1 n LEU 13 1 n LEU 14 1 n ALA 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 @ 2025-07-10 04:43:28)" _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 95.32 _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 89.50 1 1 A ARG 2 2 88.86 1 2 A MET 3 2 93.19 1 3 A GLN 4 2 94.07 1 4 A LEU 5 2 96.61 1 5 A THR 6 2 97.43 1 6 A ALA 7 2 98.57 1 7 A VAL 8 2 98.15 1 8 A LEU 9 2 96.78 1 9 A ALA 10 2 98.38 1 10 A ALA 11 2 98.56 1 11 A SER 12 2 97.90 1 12 A LEU 13 2 97.41 1 13 A LEU 14 2 97.16 1 14 A ALA 15 2 97.92 1 15 A GLY 16 2 91.64 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 ARG . 2 A 2 A 3 1 n MET . 3 A 3 A 4 1 n GLN . 4 A 4 A 5 1 n LEU . 5 A 5 A 6 1 n THR . 6 A 6 A 7 1 n ALA . 7 A 7 A 8 1 n VAL . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n ALA . 10 A 10 A 11 1 n ALA . 11 A 11 A 12 1 n SER . 12 A 12 A 13 1 n LEU . 13 A 13 A 14 1 n LEU . 14 A 14 A 15 1 n ALA . 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 ? 2.856 -4.102 11.390 1.00 94.04 1 A 1 ATOM 2 C CA . MET A 1 1 ? 1.598 -3.383 11.142 1.00 94.64 1 A 1 ATOM 3 C C . MET A 1 1 ? 1.911 -2.017 10.546 1.00 95.56 1 A 1 ATOM 4 O O . MET A 1 1 ? 2.187 -1.062 11.269 1.00 94.25 1 A 1 ATOM 5 C CB . MET A 1 1 ? 0.824 -3.208 12.450 1.00 91.57 1 A 1 ATOM 6 C CG . MET A 1 1 ? 0.443 -4.542 13.064 1.00 87.12 1 A 1 ATOM 7 S SD . MET A 1 1 ? -0.413 -4.344 14.639 1.00 84.65 1 A 1 ATOM 8 C CE . MET A 1 1 ? -0.692 -6.046 15.061 1.00 74.19 1 A 1 ATOM 9 N N . ARG A 1 2 ? 1.892 -1.947 9.228 1.00 95.56 2 A 1 ATOM 10 C CA . ARG A 1 2 ? 2.205 -0.703 8.536 1.00 96.96 2 A 1 ATOM 11 C C . ARG A 1 2 ? 1.004 -0.256 7.706 1.00 97.80 2 A 1 ATOM 12 O O . ARG A 1 2 ? 0.768 -0.783 6.615 1.00 96.78 2 A 1 ATOM 13 C CB . ARG A 1 2 ? 3.418 -0.897 7.628 1.00 95.42 2 A 1 ATOM 14 C CG . ARG A 1 2 ? 4.675 -1.353 8.364 1.00 90.88 2 A 1 ATOM 15 C CD . ARG A 1 2 ? 5.247 -0.252 9.241 1.00 88.66 2 A 1 ATOM 16 N NE . ARG A 1 2 ? 6.506 -0.676 9.863 1.00 83.21 2 A 1 ATOM 17 C CZ . ARG A 1 2 ? 7.233 0.085 10.673 1.00 82.24 2 A 1 ATOM 18 N NH1 . ARG A 1 2 ? 6.842 1.308 10.973 1.00 74.78 2 A 1 ATOM 19 N NH2 . ARG A 1 2 ? 8.358 -0.379 11.179 1.00 75.12 2 A 1 ATOM 20 N N . MET A 1 3 ? 0.264 0.713 8.220 1.00 96.38 3 A 1 ATOM 21 C CA . MET A 1 3 ? -0.904 1.242 7.505 1.00 97.30 3 A 1 ATOM 22 C C . MET A 1 3 ? -0.485 1.888 6.189 1.00 97.96 3 A 1 ATOM 23 O O . MET A 1 3 ? -1.243 1.897 5.218 1.00 97.11 3 A 1 ATOM 24 C CB . MET A 1 3 ? -1.633 2.262 8.381 1.00 96.65 3 A 1 ATOM 25 C CG . MET A 1 3 ? -2.251 1.632 9.611 1.00 93.34 3 A 1 ATOM 26 S SD . MET A 1 3 ? -3.569 0.469 9.229 1.00 89.06 3 A 1 ATOM 27 C CE . MET A 1 3 ? -4.846 1.594 8.692 1.00 77.70 3 A 1 ATOM 28 N N . GLN A 1 4 ? 0.743 2.412 6.158 1.00 97.79 4 A 1 ATOM 29 C CA . GLN A 1 4 ? 1.284 3.045 4.960 1.00 97.93 4 A 1 ATOM 30 C C . GLN A 1 4 ? 1.400 2.033 3.821 1.00 98.30 4 A 1 ATOM 31 O O . GLN A 1 4 ? 1.045 2.323 2.676 1.00 97.78 4 A 1 ATOM 32 C CB . GLN A 1 4 ? 2.652 3.657 5.262 1.00 97.45 4 A 1 ATOM 33 C CG . GLN A 1 4 ? 2.572 4.823 6.245 1.00 94.03 4 A 1 ATOM 34 C CD . GLN A 1 4 ? 3.947 5.340 6.628 1.00 92.30 4 A 1 ATOM 35 O OE1 . GLN A 1 4 ? 4.897 4.571 6.723 1.00 85.56 4 A 1 ATOM 36 N NE2 . GLN A 1 4 ? 4.075 6.634 6.847 1.00 85.51 4 A 1 ATOM 37 N N . LEU A 1 5 ? 1.885 0.841 4.132 1.00 98.13 5 A 1 ATOM 38 C CA . LEU A 1 5 ? 2.031 -0.215 3.134 1.00 98.31 5 A 1 ATOM 39 C C . LEU A 1 5 ? 0.666 -0.636 2.608 1.00 98.48 5 A 1 ATOM 40 O O . LEU A 1 5 ? 0.487 -0.873 1.411 1.00 98.26 5 A 1 ATOM 41 C CB . LEU A 1 5 ? 2.754 -1.419 3.745 1.00 98.17 5 A 1 ATOM 42 C CG . LEU A 1 5 ? 4.205 -1.139 4.125 1.00 95.89 5 A 1 ATOM 43 C CD1 . LEU A 1 5 ? 4.815 -2.343 4.827 1.00 93.06 5 A 1 ATOM 44 C CD2 . LEU A 1 5 ? 5.025 -0.789 2.889 1.00 92.57 5 A 1 ATOM 45 N N . THR A 1 6 ? -0.300 -0.723 3.504 1.00 98.61 6 A 1 ATOM 46 C CA . THR A 1 6 ? -1.662 -1.088 3.131 1.00 98.58 6 A 1 ATOM 47 C C . THR A 1 6 ? -2.249 -0.043 2.190 1.00 98.68 6 A 1 ATOM 48 O O . THR A 1 6 ? -2.946 -0.378 1.227 1.00 98.54 6 A 1 ATOM 49 C CB . THR A 1 6 ? -2.552 -1.207 4.372 1.00 98.27 6 A 1 ATOM 50 O OG1 . THR A 1 6 ? -1.972 -2.137 5.289 1.00 95.46 6 A 1 ATOM 51 C CG2 . THR A 1 6 ? -3.942 -1.683 3.992 1.00 93.85 6 A 1 ATOM 52 N N . ALA A 1 7 ? -1.952 1.226 2.459 1.00 98.60 7 A 1 ATOM 53 C CA . ALA A 1 7 ? -2.439 2.322 1.629 1.00 98.60 7 A 1 ATOM 54 C C . ALA A 1 7 ? -1.883 2.213 0.212 1.00 98.71 7 A 1 ATOM 55 O O . ALA A 1 7 ? -2.600 2.459 -0.762 1.00 98.55 7 A 1 ATOM 56 C CB . ALA A 1 7 ? -2.048 3.660 2.250 1.00 98.38 7 A 1 ATOM 57 N N . VAL A 1 8 ? -0.610 1.828 0.092 1.00 98.55 8 A 1 ATOM 58 C CA . VAL A 1 8 ? 0.027 1.663 -1.213 1.00 98.57 8 A 1 ATOM 59 C C . VAL A 1 8 ? -0.659 0.550 -1.997 1.00 98.67 8 A 1 ATOM 60 O O . VAL A 1 8 ? -0.929 0.685 -3.194 1.00 98.54 8 A 1 ATOM 61 C CB . VAL A 1 8 ? 1.525 1.357 -1.064 1.00 98.36 8 A 1 ATOM 62 C CG1 . VAL A 1 8 ? 2.159 1.053 -2.415 1.00 97.18 8 A 1 ATOM 63 C CG2 . VAL A 1 8 ? 2.232 2.534 -0.413 1.00 97.16 8 A 1 ATOM 64 N N . LEU A 1 9 ? -0.947 -0.546 -1.322 1.00 98.45 9 A 1 ATOM 65 C CA . LEU A 1 9 ? -1.616 -1.677 -1.959 1.00 98.39 9 A 1 ATOM 66 C C . LEU A 1 9 ? -3.004 -1.268 -2.438 1.00 98.57 9 A 1 ATOM 67 O O . LEU A 1 9 ? -3.433 -1.646 -3.531 1.00 98.54 9 A 1 ATOM 68 C CB . LEU A 1 9 ? -1.729 -2.838 -0.971 1.00 98.17 9 A 1 ATOM 69 C CG . LEU A 1 9 ? -0.389 -3.472 -0.605 1.00 95.34 9 A 1 ATOM 70 C CD1 . LEU A 1 9 ? -0.570 -4.505 0.496 1.00 93.39 9 A 1 ATOM 71 C CD2 . LEU A 1 9 ? 0.251 -4.116 -1.827 1.00 93.35 9 A 1 ATOM 72 N N . ALA A 1 10 ? -3.703 -0.493 -1.621 1.00 98.48 10 A 1 ATOM 73 C CA . ALA A 1 10 ? -5.033 -0.008 -1.975 1.00 98.43 10 A 1 ATOM 74 C C . ALA A 1 10 ? -4.968 0.887 -3.204 1.00 98.57 10 A 1 ATOM 75 O O . ALA A 1 10 ? -5.825 0.806 -4.090 1.00 98.36 10 A 1 ATOM 76 C CB . ALA A 1 10 ? -5.639 0.759 -0.804 1.00 98.07 10 A 1 ATOM 77 N N . ALA A 1 11 ? -3.944 1.735 -3.269 1.00 98.68 11 A 1 ATOM 78 C CA . ALA A 1 11 ? -3.759 2.628 -4.408 1.00 98.62 11 A 1 ATOM 79 C C . ALA A 1 11 ? -3.521 1.828 -5.682 1.00 98.71 11 A 1 ATOM 80 O O . ALA A 1 11 ? -4.052 2.161 -6.744 1.00 98.45 11 A 1 ATOM 81 C CB . ALA A 1 11 ? -2.589 3.569 -4.148 1.00 98.33 11 A 1 ATOM 82 N N . SER A 1 12 ? -2.737 0.757 -5.580 1.00 98.70 12 A 1 ATOM 83 C CA . SER A 1 12 ? -2.449 -0.109 -6.721 1.00 98.66 12 A 1 ATOM 84 C C . SER A 1 12 ? -3.723 -0.777 -7.216 1.00 98.73 12 A 1 ATOM 85 O O . SER A 1 12 ? -3.927 -0.940 -8.419 1.00 98.52 12 A 1 ATOM 86 C CB . SER A 1 12 ? -1.428 -1.174 -6.337 1.00 98.37 12 A 1 ATOM 87 O OG . SER A 1 12 ? -0.210 -0.571 -5.942 1.00 94.42 12 A 1 ATOM 88 N N . LEU A 1 13 ? -4.581 -1.158 -6.280 1.00 98.54 13 A 1 ATOM 89 C CA . LEU A 1 13 ? -5.851 -1.793 -6.611 1.00 98.51 13 A 1 ATOM 90 C C . LEU A 1 13 ? -6.734 -0.819 -7.383 1.00 98.62 13 A 1 ATOM 91 O O . LEU A 1 13 ? -7.393 -1.197 -8.358 1.00 98.32 13 A 1 ATOM 92 C CB . LEU A 1 13 ? -6.545 -2.274 -5.333 1.00 98.31 13 A 1 ATOM 93 C CG . LEU A 1 13 ? -7.720 -3.234 -5.560 1.00 96.99 13 A 1 ATOM 94 C CD1 . LEU A 1 13 ? -7.972 -4.049 -4.294 1.00 95.41 13 A 1 ATOM 95 C CD2 . LEU A 1 13 ? -8.983 -2.496 -5.942 1.00 94.58 13 A 1 ATOM 96 N N . LEU A 1 14 ? -6.755 0.441 -6.950 1.00 98.71 14 A 1 ATOM 97 C CA . LEU A 1 14 ? -7.541 1.472 -7.616 1.00 98.61 14 A 1 ATOM 98 C C . LEU A 1 14 ? -7.018 1.723 -9.018 1.00 98.64 14 A 1 ATOM 99 O O . LEU A 1 14 ? -7.798 1.964 -9.946 1.00 98.31 14 A 1 ATOM 100 C CB . LEU A 1 14 ? -7.499 2.767 -6.804 1.00 98.32 14 A 1 ATOM 101 C CG . LEU A 1 14 ? -8.240 2.684 -5.471 1.00 96.57 14 A 1 ATOM 102 C CD1 . LEU A 1 14 ? -7.989 3.939 -4.648 1.00 94.48 14 A 1 ATOM 103 C CD2 . LEU A 1 14 ? -9.731 2.499 -5.702 1.00 93.66 14 A 1 ATOM 104 N N . ALA A 1 15 ? -5.700 1.665 -9.186 1.00 98.43 15 A 1 ATOM 105 C CA . ALA A 1 15 ? -5.069 1.862 -10.490 1.00 98.20 15 A 1 ATOM 106 C C . ALA A 1 15 ? -5.451 0.745 -11.451 1.00 98.26 15 A 1 ATOM 107 O O . ALA A 1 15 ? -5.645 0.989 -12.646 1.00 97.27 15 A 1 ATOM 108 C CB . ALA A 1 15 ? -3.553 1.928 -10.330 1.00 97.46 15 A 1 ATOM 109 N N . GLY A 1 16 ? -5.578 -0.486 -10.906 1.00 96.51 16 A 1 ATOM 110 C CA . GLY A 1 16 ? -5.940 -1.649 -11.715 1.00 93.89 16 A 1 ATOM 111 C C . GLY A 1 16 ? -4.844 -2.045 -12.687 1.00 91.16 16 A 1 ATOM 112 O O . GLY A 1 16 ? -5.157 -2.692 -13.702 1.00 85.64 16 A 1 ATOM 113 O OXT . GLY A 1 16 ? -3.667 -1.768 -12.438 1.00 91.02 16 A 1 #