# 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_spkb13663 # _entry.id spkb13663 # 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" "C4 H7 N O4" 133.103 ASP y "ASPARTIC ACID" C([C@@H](C(=O)O)N)C(=O)O ? "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" "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 LEU 2 1 n ARG 3 1 n LEU 4 1 n VAL 5 1 n LEU 6 1 n LEU 7 1 n LEU 8 1 n LEU 9 1 n VAL 10 1 n THR 11 1 n ASP 12 1 n PHE 13 1 n ALA 14 1 n ALA 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 @ 2025-07-09 04:06:15)" _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 94.51 _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 88.37 1 1 A LEU 2 2 95.59 1 2 A ARG 3 2 92.53 1 3 A LEU 4 2 95.78 1 4 A VAL 5 2 97.78 1 5 A LEU 6 2 95.88 1 6 A LEU 7 2 96.05 1 7 A LEU 8 2 96.58 1 8 A LEU 9 2 95.50 1 9 A VAL 10 2 97.52 1 10 A THR 11 2 96.51 1 11 A ASP 12 2 94.85 1 12 A PHE 13 2 92.88 1 13 A ALA 14 2 96.67 1 14 A ALA 15 2 95.06 1 15 A SER 16 2 87.12 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 LEU . 2 A 2 A 3 1 n ARG . 3 A 3 A 4 1 n LEU . 4 A 4 A 5 1 n VAL . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n VAL . 10 A 10 A 11 1 n THR . 11 A 11 A 12 1 n ASP . 12 A 12 A 13 1 n PHE . 13 A 13 A 14 1 n ALA . 14 A 14 A 15 1 n ALA . 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 ? -2.350 2.660 12.540 1.00 94.65 1 A 1 ATOM 2 C CA . MET A 1 1 ? -1.359 2.248 11.534 1.00 94.67 1 A 1 ATOM 3 C C . MET A 1 1 ? -2.034 1.560 10.349 1.00 95.45 1 A 1 ATOM 4 O O . MET A 1 1 ? -1.364 1.106 9.423 1.00 93.77 1 A 1 ATOM 5 C CB . MET A 1 1 ? -0.323 1.320 12.162 1.00 90.35 1 A 1 ATOM 6 C CG . MET A 1 1 ? 0.491 2.016 13.245 1.00 84.15 1 A 1 ATOM 7 S SD . MET A 1 1 ? 1.647 0.914 14.060 1.00 81.61 1 A 1 ATOM 8 C CE . MET A 1 1 ? 2.386 2.042 15.231 1.00 72.32 1 A 1 ATOM 9 N N . LEU A 1 2 ? -3.346 1.503 10.400 1.00 97.42 2 A 1 ATOM 10 C CA . LEU A 1 2 ? -4.128 0.909 9.316 1.00 97.98 2 A 1 ATOM 11 C C . LEU A 1 2 ? -3.895 1.649 8.004 1.00 98.34 2 A 1 ATOM 12 O O . LEU A 1 2 ? -3.863 1.046 6.930 1.00 97.97 2 A 1 ATOM 13 C CB . LEU A 1 2 ? -5.612 0.951 9.685 1.00 97.64 2 A 1 ATOM 14 C CG . LEU A 1 2 ? -6.254 -0.419 9.840 1.00 93.27 2 A 1 ATOM 15 C CD1 . LEU A 1 2 ? -7.663 -0.277 10.375 1.00 91.58 2 A 1 ATOM 16 C CD2 . LEU A 1 2 ? -6.258 -1.162 8.518 1.00 90.51 2 A 1 ATOM 17 N N . ARG A 1 3 ? -3.724 2.958 8.110 1.00 98.05 3 A 1 ATOM 18 C CA . ARG A 1 3 ? -3.508 3.792 6.931 1.00 98.35 3 A 1 ATOM 19 C C . ARG A 1 3 ? -2.219 3.411 6.220 1.00 98.45 3 A 1 ATOM 20 O O . ARG A 1 3 ? -2.153 3.451 4.991 1.00 98.09 3 A 1 ATOM 21 C CB . ARG A 1 3 ? -3.468 5.266 7.344 1.00 98.06 3 A 1 ATOM 22 C CG . ARG A 1 3 ? -4.804 5.743 7.882 1.00 93.95 3 A 1 ATOM 23 C CD . ARG A 1 3 ? -4.662 7.061 8.608 1.00 91.66 3 A 1 ATOM 24 N NE . ARG A 1 3 ? -5.942 7.494 9.176 1.00 88.74 3 A 1 ATOM 25 C CZ . ARG A 1 3 ? -6.065 8.184 10.299 1.00 87.66 3 A 1 ATOM 26 N NH1 . ARG A 1 3 ? -4.994 8.543 10.991 1.00 81.62 3 A 1 ATOM 27 N NH2 . ARG A 1 3 ? -7.264 8.522 10.736 1.00 83.18 3 A 1 ATOM 28 N N . LEU A 1 4 ? -1.212 3.047 6.982 1.00 98.14 4 A 1 ATOM 29 C CA . LEU A 1 4 ? 0.079 2.655 6.429 1.00 98.33 4 A 1 ATOM 30 C C . LEU A 1 4 ? -0.072 1.372 5.614 1.00 98.47 4 A 1 ATOM 31 O O . LEU A 1 4 ? 0.395 1.282 4.478 1.00 98.26 4 A 1 ATOM 32 C CB . LEU A 1 4 ? 1.098 2.458 7.561 1.00 98.16 4 A 1 ATOM 33 C CG . LEU A 1 4 ? 2.558 2.699 7.181 1.00 92.70 4 A 1 ATOM 34 C CD1 . LEU A 1 4 ? 3.063 1.667 6.195 1.00 90.93 4 A 1 ATOM 35 C CD2 . LEU A 1 4 ? 2.737 4.105 6.630 1.00 91.24 4 A 1 ATOM 36 N N . VAL A 1 5 ? -0.734 0.400 6.204 1.00 98.42 5 A 1 ATOM 37 C CA . VAL A 1 5 ? -0.966 -0.884 5.541 1.00 98.44 5 A 1 ATOM 38 C C . VAL A 1 5 ? -1.836 -0.706 4.303 1.00 98.48 5 A 1 ATOM 39 O O . VAL A 1 5 ? -1.570 -1.297 3.252 1.00 98.15 5 A 1 ATOM 40 C CB . VAL A 1 5 ? -1.628 -1.878 6.511 1.00 98.17 5 A 1 ATOM 41 C CG1 . VAL A 1 5 ? -1.877 -3.209 5.818 1.00 96.48 5 A 1 ATOM 42 C CG2 . VAL A 1 5 ? -0.763 -2.075 7.745 1.00 96.34 5 A 1 ATOM 43 N N . LEU A 1 6 ? -2.860 0.105 4.435 1.00 98.34 6 A 1 ATOM 44 C CA . LEU A 1 6 ? -3.767 0.385 3.325 1.00 98.33 6 A 1 ATOM 45 C C . LEU A 1 6 ? -3.027 1.065 2.181 1.00 98.41 6 A 1 ATOM 46 O O . LEU A 1 6 ? -3.224 0.721 1.015 1.00 98.26 6 A 1 ATOM 47 C CB . LEU A 1 6 ? -4.916 1.267 3.810 1.00 98.08 6 A 1 ATOM 48 C CG . LEU A 1 6 ? -6.014 1.483 2.777 1.00 91.91 6 A 1 ATOM 49 C CD1 . LEU A 1 6 ? -6.805 0.195 2.553 1.00 91.45 6 A 1 ATOM 50 C CD2 . LEU A 1 6 ? -6.945 2.596 3.215 1.00 92.27 6 A 1 ATOM 51 N N . LEU A 1 7 ? -2.185 2.012 2.513 1.00 98.40 7 A 1 ATOM 52 C CA . LEU A 1 7 ? -1.401 2.739 1.518 1.00 98.37 7 A 1 ATOM 53 C C . LEU A 1 7 ? -0.495 1.782 0.751 1.00 98.44 7 A 1 ATOM 54 O O . LEU A 1 7 ? -0.382 1.865 -0.471 1.00 98.21 7 A 1 ATOM 55 C CB . LEU A 1 7 ? -0.569 3.821 2.206 1.00 98.18 7 A 1 ATOM 56 C CG . LEU A 1 7 ? -0.071 4.913 1.267 1.00 92.20 7 A 1 ATOM 57 C CD1 . LEU A 1 7 ? -1.188 5.905 0.954 1.00 91.93 7 A 1 ATOM 58 C CD2 . LEU A 1 7 ? 1.113 5.642 1.878 1.00 92.67 7 A 1 ATOM 59 N N . LEU A 1 8 ? 0.131 0.884 1.469 1.00 98.24 8 A 1 ATOM 60 C CA . LEU A 1 8 ? 1.018 -0.106 0.865 1.00 98.20 8 A 1 ATOM 61 C C . LEU A 1 8 ? 0.243 -1.021 -0.078 1.00 98.28 8 A 1 ATOM 62 O O . LEU A 1 8 ? 0.714 -1.352 -1.164 1.00 97.97 8 A 1 ATOM 63 C CB . LEU A 1 8 ? 1.696 -0.927 1.963 1.00 98.10 8 A 1 ATOM 64 C CG . LEU A 1 8 ? 2.957 -1.659 1.503 1.00 94.46 8 A 1 ATOM 65 C CD1 . LEU A 1 8 ? 4.107 -0.675 1.315 1.00 93.38 8 A 1 ATOM 66 C CD2 . LEU A 1 8 ? 3.347 -2.730 2.503 1.00 94.02 8 A 1 ATOM 67 N N . LEU A 1 9 ? -0.937 -1.410 0.341 1.00 98.11 9 A 1 ATOM 68 C CA . LEU A 1 9 ? -1.794 -2.273 -0.467 1.00 97.93 9 A 1 ATOM 69 C C . LEU A 1 9 ? -2.219 -1.581 -1.758 1.00 98.00 9 A 1 ATOM 70 O O . LEU A 1 9 ? -2.185 -2.185 -2.833 1.00 97.35 9 A 1 ATOM 71 C CB . LEU A 1 9 ? -3.024 -2.664 0.347 1.00 97.58 9 A 1 ATOM 72 C CG . LEU A 1 9 ? -3.968 -3.620 -0.369 1.00 92.66 9 A 1 ATOM 73 C CD1 . LEU A 1 9 ? -3.363 -5.019 -0.431 1.00 91.18 9 A 1 ATOM 74 C CD2 . LEU A 1 9 ? -5.310 -3.658 0.334 1.00 91.22 9 A 1 ATOM 75 N N . VAL A 1 10 ? -2.611 -0.329 -1.641 1.00 98.42 10 A 1 ATOM 76 C CA . VAL A 1 10 ? -3.051 0.451 -2.796 1.00 98.29 10 A 1 ATOM 77 C C . VAL A 1 10 ? -1.914 0.642 -3.791 1.00 98.32 10 A 1 ATOM 78 O O . VAL A 1 10 ? -2.109 0.490 -4.999 1.00 97.67 10 A 1 ATOM 79 C CB . VAL A 1 10 ? -3.606 1.817 -2.356 1.00 97.81 10 A 1 ATOM 80 C CG1 . VAL A 1 10 ? -3.925 2.684 -3.570 1.00 95.60 10 A 1 ATOM 81 C CG2 . VAL A 1 10 ? -4.852 1.644 -1.508 1.00 96.50 10 A 1 ATOM 82 N N . THR A 1 11 ? -0.741 0.970 -3.281 1.00 98.18 11 A 1 ATOM 83 C CA . THR A 1 11 ? 0.407 1.207 -4.151 1.00 98.08 11 A 1 ATOM 84 C C . THR A 1 11 ? 0.834 -0.083 -4.848 1.00 97.99 11 A 1 ATOM 85 O O . THR A 1 11 ? 1.226 -0.062 -6.013 1.00 97.08 11 A 1 ATOM 86 C CB . THR A 1 11 ? 1.582 1.829 -3.370 1.00 97.51 11 A 1 ATOM 87 O OG1 . THR A 1 11 ? 2.555 2.301 -4.309 1.00 93.29 11 A 1 ATOM 88 C CG2 . THR A 1 11 ? 2.246 0.850 -2.433 1.00 93.46 11 A 1 ATOM 89 N N . ASP A 1 12 ? 0.734 -1.200 -4.137 1.00 97.82 12 A 1 ATOM 90 C CA . ASP A 1 12 ? 1.081 -2.499 -4.704 1.00 97.86 12 A 1 ATOM 91 C C . ASP A 1 12 ? 0.103 -2.880 -5.809 1.00 97.95 12 A 1 ATOM 92 O O . ASP A 1 12 ? 0.495 -3.375 -6.869 1.00 97.16 12 A 1 ATOM 93 C CB . ASP A 1 12 ? 1.073 -3.564 -3.610 1.00 97.16 12 A 1 ATOM 94 C CG . ASP A 1 12 ? 1.731 -4.848 -4.069 1.00 92.01 12 A 1 ATOM 95 O OD1 . ASP A 1 12 ? 2.380 -4.842 -5.128 1.00 89.56 12 A 1 ATOM 96 O OD2 . ASP A 1 12 ? 1.602 -5.861 -3.356 1.00 89.29 12 A 1 ATOM 97 N N . PHE A 1 13 ? -1.165 -2.637 -5.563 1.00 97.06 13 A 1 ATOM 98 C CA . PHE A 1 13 ? -2.210 -2.916 -6.540 1.00 97.00 13 A 1 ATOM 99 C C . PHE A 1 13 ? -2.049 -2.050 -7.785 1.00 97.21 13 A 1 ATOM 100 O O . PHE A 1 13 ? -2.241 -2.520 -8.909 1.00 96.21 13 A 1 ATOM 101 C CB . PHE A 1 13 ? -3.581 -2.674 -5.913 1.00 96.46 13 A 1 ATOM 102 C CG . PHE A 1 13 ? -4.715 -3.072 -6.822 1.00 93.53 13 A 1 ATOM 103 C CD1 . PHE A 1 13 ? -5.038 -4.406 -6.999 1.00 90.71 13 A 1 ATOM 104 C CD2 . PHE A 1 13 ? -5.440 -2.107 -7.493 1.00 89.94 13 A 1 ATOM 105 C CE1 . PHE A 1 13 ? -6.074 -4.779 -7.835 1.00 88.25 13 A 1 ATOM 106 C CE2 . PHE A 1 13 ? -6.480 -2.476 -8.341 1.00 88.18 13 A 1 ATOM 107 C CZ . PHE A 1 13 ? -6.795 -3.809 -8.508 1.00 87.10 13 A 1 ATOM 108 N N . ALA A 1 14 ? -1.705 -0.792 -7.575 1.00 97.59 14 A 1 ATOM 109 C CA . ALA A 1 14 ? -1.512 0.145 -8.681 1.00 97.21 14 A 1 ATOM 110 C C . ALA A 1 14 ? -0.284 -0.216 -9.507 1.00 96.94 14 A 1 ATOM 111 O O . ALA A 1 14 ? -0.254 0.007 -10.718 1.00 95.22 14 A 1 ATOM 112 C CB . ALA A 1 14 ? -1.382 1.566 -8.144 1.00 96.37 14 A 1 ATOM 113 N N . ALA A 1 15 ? 0.724 -0.750 -8.838 1.00 97.01 15 A 1 ATOM 114 C CA . ALA A 1 15 ? 1.961 -1.135 -9.509 1.00 96.02 15 A 1 ATOM 115 C C . ALA A 1 15 ? 1.779 -2.399 -10.338 1.00 95.34 15 A 1 ATOM 116 O O . ALA A 1 15 ? 2.493 -2.613 -11.319 1.00 92.13 15 A 1 ATOM 117 C CB . ALA A 1 15 ? 3.072 -1.329 -8.485 1.00 94.81 15 A 1 ATOM 118 N N . SER A 1 16 ? 0.828 -3.215 -9.932 1.00 94.07 16 A 1 ATOM 119 C CA . SER A 1 16 ? 0.549 -4.470 -10.623 1.00 92.56 16 A 1 ATOM 120 C C . SER A 1 16 ? -0.270 -4.243 -11.896 1.00 89.15 16 A 1 ATOM 121 O O . SER A 1 16 ? -0.527 -5.207 -12.628 1.00 82.44 16 A 1 ATOM 122 C CB . SER A 1 16 ? -0.171 -5.438 -9.694 1.00 88.65 16 A 1 ATOM 123 O OG . SER A 1 16 ? -0.261 -6.704 -10.302 1.00 82.18 16 A 1 ATOM 124 O OXT . SER A 1 16 ? -0.678 -3.078 -12.155 1.00 80.82 16 A 1 #