# 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_spkb16371 # _entry.id spkb16371 # 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" "C3 H7 N O2 S" 121.158 CYS y CYSTEINE C([C@@H](C(=O)O)N)S ? "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" "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 GLY 2 1 n ARG 3 1 n LEU 4 1 n LEU 5 1 n ALA 6 1 n LEU 7 1 n VAL 8 1 n VAL 9 1 n GLY 10 1 n ALA 11 1 n ALA 12 1 n LEU 13 1 n VAL 14 1 n SER 15 1 n SER 16 1 n ALA 17 1 n CYS 18 # _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 @ 2025-07-03 01:18:25)" _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 95.56 _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 87.74 1 1 A GLY 2 2 97.45 1 2 A ARG 3 2 92.82 1 3 A LEU 4 2 96.73 1 4 A LEU 5 2 95.75 1 5 A ALA 6 2 98.49 1 6 A LEU 7 2 96.69 1 7 A VAL 8 2 98.03 1 8 A VAL 9 2 97.69 1 9 A GLY 10 2 98.14 1 10 A ALA 11 2 98.15 1 11 A ALA 12 2 98.31 1 12 A LEU 13 2 96.71 1 13 A VAL 14 2 97.76 1 14 A SER 15 2 95.97 1 15 A SER 16 2 95.47 1 16 A ALA 17 2 95.96 1 17 A CYS 18 2 88.88 1 18 # _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 GLY . 2 A 2 A 3 1 n ARG . 3 A 3 A 4 1 n LEU . 4 A 4 A 5 1 n LEU . 5 A 5 A 6 1 n ALA . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n VAL . 8 A 8 A 9 1 n VAL . 9 A 9 A 10 1 n GLY . 10 A 10 A 11 1 n ALA . 11 A 11 A 12 1 n ALA . 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 SER . 16 A 16 A 17 1 n ALA . 17 A 17 A 18 1 n CYS . 18 A 18 # _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 ? -12.182 7.147 2.447 1.00 93.46 1 A 1 ATOM 2 C CA . MET A 1 1 ? -10.941 6.480 2.877 1.00 94.23 1 A 1 ATOM 3 C C . MET A 1 1 ? -10.204 5.867 1.689 1.00 95.19 1 A 1 ATOM 4 O O . MET A 1 1 ? -10.064 4.649 1.597 1.00 93.45 1 A 1 ATOM 5 C CB . MET A 1 1 ? -11.266 5.390 3.891 1.00 90.02 1 A 1 ATOM 6 C CG . MET A 1 1 ? -11.681 5.962 5.228 1.00 83.97 1 A 1 ATOM 7 S SD . MET A 1 1 ? -11.804 4.683 6.482 1.00 81.27 1 A 1 ATOM 8 C CE . MET A 1 1 ? -11.832 5.698 7.953 1.00 70.30 1 A 1 ATOM 9 N N . GLY A 1 2 ? -9.766 6.715 0.798 1.00 97.16 2 A 1 ATOM 10 C CA . GLY A 1 2 ? -9.045 6.240 -0.381 1.00 97.51 2 A 1 ATOM 11 C C . GLY A 1 2 ? -7.554 6.492 -0.277 1.00 97.99 2 A 1 ATOM 12 O O . GLY A 1 2 ? -6.737 5.588 -0.426 1.00 97.15 2 A 1 ATOM 13 N N . ARG A 1 3 ? -7.209 7.737 -0.010 1.00 98.30 3 A 1 ATOM 14 C CA . ARG A 1 3 ? -5.801 8.111 0.131 1.00 98.48 3 A 1 ATOM 15 C C . ARG A 1 3 ? -5.176 7.460 1.363 1.00 98.65 3 A 1 ATOM 16 O O . ARG A 1 3 ? -3.992 7.127 1.356 1.00 98.22 3 A 1 ATOM 17 C CB . ARG A 1 3 ? -5.671 9.631 0.229 1.00 98.06 3 A 1 ATOM 18 C CG . ARG A 1 3 ? -5.640 10.284 -1.143 1.00 95.30 3 A 1 ATOM 19 C CD . ARG A 1 3 ? -5.333 11.768 -1.025 1.00 92.90 3 A 1 ATOM 20 N NE . ARG A 1 3 ? -4.880 12.319 -2.300 1.00 88.57 3 A 1 ATOM 21 C CZ . ARG A 1 3 ? -4.457 13.571 -2.461 1.00 88.34 3 A 1 ATOM 22 N NH1 . ARG A 1 3 ? -4.458 14.420 -1.444 1.00 82.00 3 A 1 ATOM 23 N NH2 . ARG A 1 3 ? -4.033 13.980 -3.643 1.00 82.17 3 A 1 ATOM 24 N N . LEU A 1 4 ? -5.975 7.280 2.397 1.00 98.25 4 A 1 ATOM 25 C CA . LEU A 1 4 ? -5.493 6.646 3.623 1.00 98.37 4 A 1 ATOM 26 C C . LEU A 1 4 ? -5.045 5.216 3.338 1.00 98.52 4 A 1 ATOM 27 O O . LEU A 1 4 ? -4.012 4.766 3.836 1.00 98.24 4 A 1 ATOM 28 C CB . LEU A 1 4 ? -6.603 6.652 4.674 1.00 98.22 4 A 1 ATOM 29 C CG . LEU A 1 4 ? -6.930 8.045 5.210 1.00 95.91 4 A 1 ATOM 30 C CD1 . LEU A 1 4 ? -8.230 8.020 5.992 1.00 93.48 4 A 1 ATOM 31 C CD2 . LEU A 1 4 ? -5.800 8.540 6.110 1.00 92.87 4 A 1 ATOM 32 N N . LEU A 1 5 ? -5.825 4.519 2.519 1.00 98.44 5 A 1 ATOM 33 C CA . LEU A 1 5 ? -5.488 3.148 2.140 1.00 98.36 5 A 1 ATOM 34 C C . LEU A 1 5 ? -4.202 3.130 1.320 1.00 98.49 5 A 1 ATOM 35 O O . LEU A 1 5 ? -3.359 2.249 1.492 1.00 98.24 5 A 1 ATOM 36 C CB . LEU A 1 5 ? -6.638 2.542 1.334 1.00 98.02 5 A 1 ATOM 37 C CG . LEU A 1 5 ? -7.779 2.016 2.203 1.00 92.59 5 A 1 ATOM 38 C CD1 . LEU A 1 5 ? -9.048 1.855 1.375 1.00 90.92 5 A 1 ATOM 39 C CD2 . LEU A 1 5 ? -7.386 0.679 2.820 1.00 90.92 5 A 1 ATOM 40 N N . ALA A 1 6 ? -4.063 4.114 0.435 1.00 98.52 6 A 1 ATOM 41 C CA . ALA A 1 6 ? -2.870 4.224 -0.400 1.00 98.56 6 A 1 ATOM 42 C C . ALA A 1 6 ? -1.627 4.460 0.456 1.00 98.64 6 A 1 ATOM 43 O O . ALA A 1 6 ? -0.549 3.947 0.158 1.00 98.38 6 A 1 ATOM 44 C CB . ALA A 1 6 ? -3.048 5.358 -1.402 1.00 98.33 6 A 1 ATOM 45 N N . LEU A 1 7 ? -1.795 5.232 1.514 1.00 98.53 7 A 1 ATOM 46 C CA . LEU A 1 7 ? -0.693 5.519 2.428 1.00 98.53 7 A 1 ATOM 47 C C . LEU A 1 7 ? -0.249 4.259 3.161 1.00 98.65 7 A 1 ATOM 48 O O . LEU A 1 7 ? 0.946 3.972 3.256 1.00 98.48 7 A 1 ATOM 49 C CB . LEU A 1 7 ? -1.127 6.591 3.429 1.00 98.38 7 A 1 ATOM 50 C CG . LEU A 1 7 ? -0.713 8.006 3.023 1.00 94.89 7 A 1 ATOM 51 C CD1 . LEU A 1 7 ? -1.551 9.047 3.760 1.00 92.84 7 A 1 ATOM 52 C CD2 . LEU A 1 7 ? 0.763 8.221 3.321 1.00 93.22 7 A 1 ATOM 53 N N . VAL A 1 8 ? -1.216 3.521 3.663 1.00 98.54 8 A 1 ATOM 54 C CA . VAL A 1 8 ? -0.927 2.288 4.396 1.00 98.56 8 A 1 ATOM 55 C C . VAL A 1 8 ? -0.331 1.238 3.470 1.00 98.60 8 A 1 ATOM 56 O O . VAL A 1 8 ? 0.703 0.636 3.777 1.00 98.43 8 A 1 ATOM 57 C CB . VAL A 1 8 ? -2.199 1.742 5.066 1.00 98.38 8 A 1 ATOM 58 C CG1 . VAL A 1 8 ? -1.911 0.435 5.790 1.00 96.88 8 A 1 ATOM 59 C CG2 . VAL A 1 8 ? -2.758 2.765 6.049 1.00 96.84 8 A 1 ATOM 60 N N . VAL A 1 9 ? -0.989 1.021 2.342 1.00 98.44 9 A 1 ATOM 61 C CA . VAL A 1 9 ? -0.530 0.029 1.368 1.00 98.39 9 A 1 ATOM 62 C C . VAL A 1 9 ? 0.826 0.430 0.798 1.00 98.48 9 A 1 ATOM 63 O O . VAL A 1 9 ? 1.713 -0.413 0.628 1.00 98.31 9 A 1 ATOM 64 C CB . VAL A 1 9 ? -1.554 -0.136 0.237 1.00 98.02 9 A 1 ATOM 65 C CG1 . VAL A 1 9 ? -1.038 -1.095 -0.827 1.00 95.96 9 A 1 ATOM 66 C CG2 . VAL A 1 9 ? -2.876 -0.641 0.790 1.00 96.25 9 A 1 ATOM 67 N N . GLY A 1 10 ? 0.979 1.716 0.513 1.00 98.03 10 A 1 ATOM 68 C CA . GLY A 1 10 ? 2.236 2.223 -0.025 1.00 97.97 10 A 1 ATOM 69 C C . GLY A 1 10 ? 3.386 2.008 0.938 1.00 98.31 10 A 1 ATOM 70 O O . GLY A 1 10 ? 4.460 1.551 0.548 1.00 98.24 10 A 1 ATOM 71 N N . ALA A 1 11 ? 3.155 2.323 2.194 1.00 98.32 11 A 1 ATOM 72 C CA . ALA A 1 11 ? 4.177 2.138 3.222 1.00 98.25 11 A 1 ATOM 73 C C . ALA A 1 11 ? 4.526 0.666 3.387 1.00 98.40 11 A 1 ATOM 74 O O . ALA A 1 11 ? 5.692 0.313 3.566 1.00 97.97 11 A 1 ATOM 75 C CB . ALA A 1 11 ? 3.680 2.712 4.542 1.00 97.80 11 A 1 ATOM 76 N N . ALA A 1 12 ? 3.513 -0.191 3.323 1.00 98.45 12 A 1 ATOM 77 C CA . ALA A 1 12 ? 3.720 -1.629 3.450 1.00 98.40 12 A 1 ATOM 78 C C . ALA A 1 12 ? 4.560 -2.160 2.295 1.00 98.51 12 A 1 ATOM 79 O O . ALA A 1 12 ? 5.441 -2.997 2.494 1.00 98.08 12 A 1 ATOM 80 C CB . ALA A 1 12 ? 2.373 -2.343 3.494 1.00 98.12 12 A 1 ATOM 81 N N . LEU A 1 13 ? 4.289 -1.670 1.087 1.00 98.52 13 A 1 ATOM 82 C CA . LEU A 1 13 ? 5.030 -2.085 -0.102 1.00 98.46 13 A 1 ATOM 83 C C . LEU A 1 13 ? 6.490 -1.665 -0.001 1.00 98.56 13 A 1 ATOM 84 O O . LEU A 1 13 ? 7.393 -2.446 -0.311 1.00 98.28 13 A 1 ATOM 85 C CB . LEU A 1 13 ? 4.389 -1.472 -1.348 1.00 98.19 13 A 1 ATOM 86 C CG . LEU A 1 13 ? 3.563 -2.461 -2.159 1.00 95.18 13 A 1 ATOM 87 C CD1 . LEU A 1 13 ? 2.629 -1.728 -3.107 1.00 93.46 13 A 1 ATOM 88 C CD2 . LEU A 1 13 ? 4.475 -3.396 -2.937 1.00 93.06 13 A 1 ATOM 89 N N . VAL A 1 14 ? 6.718 -0.439 0.435 1.00 98.61 14 A 1 ATOM 90 C CA . VAL A 1 14 ? 8.076 0.076 0.597 1.00 98.53 14 A 1 ATOM 91 C C . VAL A 1 14 ? 8.828 -0.737 1.639 1.00 98.57 14 A 1 ATOM 92 O O . VAL A 1 14 ? 10.005 -1.061 1.453 1.00 98.30 14 A 1 ATOM 93 C CB . VAL A 1 14 ? 8.048 1.553 1.004 1.00 98.14 14 A 1 ATOM 94 C CG1 . VAL A 1 14 ? 9.451 2.054 1.312 1.00 95.73 14 A 1 ATOM 95 C CG2 . VAL A 1 14 ? 7.425 2.389 -0.094 1.00 96.45 14 A 1 ATOM 96 N N . SER A 1 15 ? 8.151 -1.073 2.715 1.00 98.46 15 A 1 ATOM 97 C CA . SER A 1 15 ? 8.755 -1.867 3.782 1.00 98.31 15 A 1 ATOM 98 C C . SER A 1 15 ? 9.063 -3.283 3.309 1.00 98.34 15 A 1 ATOM 99 O O . SER A 1 15 ? 10.060 -3.878 3.719 1.00 97.62 15 A 1 ATOM 100 C CB . SER A 1 15 ? 7.819 -1.915 4.984 1.00 97.74 15 A 1 ATOM 101 O OG . SER A 1 15 ? 8.456 -2.535 6.075 1.00 85.34 15 A 1 ATOM 102 N N . SER A 1 16 ? 8.206 -3.812 2.437 1.00 98.12 16 A 1 ATOM 103 C CA . SER A 1 16 ? 8.373 -5.165 1.909 1.00 97.88 16 A 1 ATOM 104 C C . SER A 1 16 ? 9.474 -5.228 0.860 1.00 97.92 16 A 1 ATOM 105 O O . SER A 1 16 ? 10.259 -6.178 0.828 1.00 96.41 16 A 1 ATOM 106 C CB . SER A 1 16 ? 7.057 -5.656 1.309 1.00 96.87 16 A 1 ATOM 107 O OG . SER A 1 16 ? 7.149 -7.020 0.984 1.00 85.59 16 A 1 ATOM 108 N N . ALA A 1 17 ? 9.528 -4.223 -0.012 1.00 97.32 17 A 1 ATOM 109 C CA . ALA A 1 17 ? 10.518 -4.176 -1.091 1.00 96.60 17 A 1 ATOM 110 C C . ALA A 1 17 ? 11.722 -3.307 -0.740 1.00 96.33 17 A 1 ATOM 111 O O . ALA A 1 17 ? 12.792 -3.455 -1.334 1.00 93.80 17 A 1 ATOM 112 C CB . ALA A 1 17 ? 9.857 -3.678 -2.374 1.00 95.74 17 A 1 ATOM 113 N N . CYS A 1 18 ? 11.531 -2.404 0.231 1.00 95.69 18 A 1 ATOM 114 C CA . CYS A 1 18 ? 12.576 -1.459 0.656 1.00 94.13 18 A 1 ATOM 115 C C . CYS A 1 18 ? 13.149 -0.690 -0.531 1.00 92.42 18 A 1 ATOM 116 O O . CYS A 1 18 ? 14.373 -0.534 -0.635 1.00 87.47 18 A 1 ATOM 117 C CB . CYS A 1 18 ? 13.693 -2.218 1.386 1.00 89.90 18 A 1 ATOM 118 S SG . CYS A 1 18 ? 13.219 -2.712 3.061 1.00 81.82 18 A 1 ATOM 119 O OXT . CYS A 1 18 ? 12.352 -0.190 -1.381 1.00 80.70 18 A 1 #