# 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_spkb12603 # _entry.id spkb12603 # 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 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" "C3 H7 N O3" 105.093 SER y SERINE C([C@@H](C(=O)O)N)O ? "L-PEPTIDE LINKING" "C9 H11 N O3" 181.189 TYR y TYROSINE c1cc(ccc1C[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 TYR 3 1 n LEU 4 1 n SER 5 1 n ILE 6 1 n ILE 7 1 n SER 8 1 n ILE 9 1 n VAL 10 1 n ALA 11 1 n LEU 12 1 n ALA 13 1 n LEU 14 1 n ALA 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 @ 2025-07-07 09:30:16)" _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 95.62 _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 90.14 1 1 A LYS 2 2 92.82 1 2 A TYR 3 2 95.15 1 3 A LEU 4 2 95.75 1 4 A SER 5 2 96.89 1 5 A ILE 6 2 96.87 1 6 A ILE 7 2 96.49 1 7 A SER 8 2 96.99 1 8 A ILE 9 2 96.62 1 9 A VAL 10 2 97.79 1 10 A ALA 11 2 98.35 1 11 A LEU 12 2 95.77 1 12 A ALA 13 2 98.29 1 13 A LEU 14 2 95.69 1 14 A ALA 15 2 93.75 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 LYS . 2 A 2 A 3 1 n TYR . 3 A 3 A 4 1 n LEU . 4 A 4 A 5 1 n SER . 5 A 5 A 6 1 n ILE . 6 A 6 A 7 1 n ILE . 7 A 7 A 8 1 n SER . 8 A 8 A 9 1 n ILE . 9 A 9 A 10 1 n VAL . 10 A 10 A 11 1 n ALA . 11 A 11 A 12 1 n LEU . 12 A 12 A 13 1 n ALA . 13 A 13 A 14 1 n LEU . 14 A 14 A 15 1 n ALA . 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 ? 9.623 -1.251 -4.507 1.00 94.63 1 A 1 ATOM 2 C CA . MET A 1 1 ? 9.332 0.014 -3.805 1.00 95.63 1 A 1 ATOM 3 C C . MET A 1 1 ? 8.380 -0.241 -2.642 1.00 95.68 1 A 1 ATOM 4 O O . MET A 1 1 ? 7.363 -0.905 -2.811 1.00 93.43 1 A 1 ATOM 5 C CB . MET A 1 1 ? 8.716 1.013 -4.771 1.00 92.92 1 A 1 ATOM 6 C CG . MET A 1 1 ? 9.692 1.383 -5.869 1.00 90.04 1 A 1 ATOM 7 S SD . MET A 1 1 ? 8.972 2.462 -7.102 1.00 84.69 1 A 1 ATOM 8 C CE . MET A 1 1 ? 8.463 1.262 -8.305 1.00 74.09 1 A 1 ATOM 9 N N . LYS A 1 2 ? 8.726 0.258 -1.465 1.00 96.36 2 A 1 ATOM 10 C CA . LYS A 1 2 ? 7.921 0.031 -0.264 1.00 96.94 2 A 1 ATOM 11 C C . LYS A 1 2 ? 6.712 0.964 -0.215 1.00 97.51 2 A 1 ATOM 12 O O . LYS A 1 2 ? 5.621 0.554 0.170 1.00 97.09 2 A 1 ATOM 13 C CB . LYS A 1 2 ? 8.776 0.252 0.983 1.00 95.90 2 A 1 ATOM 14 C CG . LYS A 1 2 ? 10.143 -0.389 0.903 1.00 92.52 2 A 1 ATOM 15 C CD . LYS A 1 2 ? 10.938 -0.139 2.174 1.00 90.58 2 A 1 ATOM 16 C CE . LYS A 1 2 ? 12.410 0.023 1.869 1.00 86.84 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? 13.184 0.285 3.111 1.00 81.65 2 A 1 ATOM 18 N N . TYR A 1 3 ? 6.926 2.217 -0.577 1.00 96.42 3 A 1 ATOM 19 C CA . TYR A 1 3 ? 5.865 3.218 -0.513 1.00 97.16 3 A 1 ATOM 20 C C . TYR A 1 3 ? 4.696 2.860 -1.427 1.00 97.43 3 A 1 ATOM 21 O O . TYR A 1 3 ? 3.533 3.019 -1.057 1.00 96.86 3 A 1 ATOM 22 C CB . TYR A 1 3 ? 6.431 4.588 -0.893 1.00 97.15 3 A 1 ATOM 23 C CG . TYR A 1 3 ? 7.623 4.979 -0.050 1.00 95.68 3 A 1 ATOM 24 C CD1 . TYR A 1 3 ? 7.450 5.418 1.257 1.00 93.79 3 A 1 ATOM 25 C CD2 . TYR A 1 3 ? 8.907 4.896 -0.561 1.00 93.92 3 A 1 ATOM 26 C CE1 . TYR A 1 3 ? 8.542 5.770 2.038 1.00 93.26 3 A 1 ATOM 27 C CE2 . TYR A 1 3 ? 10.010 5.245 0.216 1.00 93.72 3 A 1 ATOM 28 C CZ . TYR A 1 3 ? 9.816 5.685 1.513 1.00 94.07 3 A 1 ATOM 29 O OH . TYR A 1 3 ? 10.901 6.030 2.275 1.00 92.36 3 A 1 ATOM 30 N N . LEU A 1 4 ? 4.989 2.370 -2.608 1.00 97.98 4 A 1 ATOM 31 C CA . LEU A 1 4 ? 3.950 1.999 -3.560 1.00 97.95 4 A 1 ATOM 32 C C . LEU A 1 4 ? 3.091 0.869 -3.010 1.00 98.15 4 A 1 ATOM 33 O O . LEU A 1 4 ? 1.882 0.840 -3.219 1.00 97.73 4 A 1 ATOM 34 C CB . LEU A 1 4 ? 4.565 1.589 -4.895 1.00 97.68 4 A 1 ATOM 35 C CG . LEU A 1 4 ? 4.952 2.778 -5.777 1.00 94.92 4 A 1 ATOM 36 C CD1 . LEU A 1 4 ? 6.205 3.457 -5.250 1.00 91.19 4 A 1 ATOM 37 C CD2 . LEU A 1 4 ? 5.156 2.326 -7.217 1.00 90.42 4 A 1 ATOM 38 N N . SER A 1 5 ? 3.715 -0.038 -2.291 1.00 97.64 5 A 1 ATOM 39 C CA . SER A 1 5 ? 2.996 -1.166 -1.716 1.00 97.89 5 A 1 ATOM 40 C C . SER A 1 5 ? 2.044 -0.689 -0.624 1.00 98.18 5 A 1 ATOM 41 O O . SER A 1 5 ? 0.945 -1.216 -0.478 1.00 97.82 5 A 1 ATOM 42 C CB . SER A 1 5 ? 3.983 -2.181 -1.142 1.00 97.27 5 A 1 ATOM 43 O OG . SER A 1 5 ? 4.726 -1.615 -0.099 1.00 92.51 5 A 1 ATOM 44 N N . ILE A 1 6 ? 2.474 0.307 0.128 1.00 98.01 6 A 1 ATOM 45 C CA . ILE A 1 6 ? 1.653 0.866 1.196 1.00 98.15 6 A 1 ATOM 46 C C . ILE A 1 6 ? 0.402 1.503 0.609 1.00 98.29 6 A 1 ATOM 47 O O . ILE A 1 6 ? -0.695 1.380 1.155 1.00 98.03 6 A 1 ATOM 48 C CB . ILE A 1 6 ? 2.445 1.911 1.997 1.00 98.07 6 A 1 ATOM 49 C CG1 . ILE A 1 6 ? 3.654 1.249 2.662 1.00 96.31 6 A 1 ATOM 50 C CG2 . ILE A 1 6 ? 1.551 2.556 3.052 1.00 95.94 6 A 1 ATOM 51 C CD1 . ILE A 1 6 ? 4.616 2.242 3.267 1.00 92.15 6 A 1 ATOM 52 N N . ILE A 1 7 ? 0.576 2.184 -0.498 1.00 98.04 7 A 1 ATOM 53 C CA . ILE A 1 7 ? -0.543 2.829 -1.175 1.00 97.92 7 A 1 ATOM 54 C C . ILE A 1 7 ? -1.540 1.772 -1.625 1.00 98.04 7 A 1 ATOM 55 O O . ILE A 1 7 ? -2.755 1.984 -1.594 1.00 97.96 7 A 1 ATOM 56 C CB . ILE A 1 7 ? -0.046 3.642 -2.380 1.00 97.90 7 A 1 ATOM 57 C CG1 . ILE A 1 7 ? 0.895 4.753 -1.906 1.00 96.10 7 A 1 ATOM 58 C CG2 . ILE A 1 7 ? -1.231 4.243 -3.138 1.00 95.35 7 A 1 ATOM 59 C CD1 . ILE A 1 7 ? 1.610 5.453 -3.040 1.00 90.61 7 A 1 ATOM 60 N N . SER A 1 8 ? -1.026 0.644 -2.016 1.00 98.25 8 A 1 ATOM 61 C CA . SER A 1 8 ? -1.868 -0.459 -2.459 1.00 98.24 8 A 1 ATOM 62 C C . SER A 1 8 ? -2.735 -0.963 -1.307 1.00 98.43 8 A 1 ATOM 63 O O . SER A 1 8 ? -3.878 -1.362 -1.508 1.00 98.30 8 A 1 ATOM 64 C CB . SER A 1 8 ? -0.999 -1.593 -2.994 1.00 97.91 8 A 1 ATOM 65 O OG . SER A 1 8 ? -1.801 -2.630 -3.494 1.00 90.80 8 A 1 ATOM 66 N N . ILE A 1 9 ? -2.180 -0.928 -0.102 1.00 97.60 9 A 1 ATOM 67 C CA . ILE A 1 9 ? -2.908 -1.356 1.085 1.00 97.75 9 A 1 ATOM 68 C C . ILE A 1 9 ? -4.106 -0.450 1.318 1.00 98.11 9 A 1 ATOM 69 O O . ILE A 1 9 ? -5.192 -0.904 1.683 1.00 97.75 9 A 1 ATOM 70 C CB . ILE A 1 9 ? -1.997 -1.333 2.320 1.00 97.41 9 A 1 ATOM 71 C CG1 . ILE A 1 9 ? -0.788 -2.255 2.114 1.00 95.96 9 A 1 ATOM 72 C CG2 . ILE A 1 9 ? -2.784 -1.759 3.558 1.00 95.60 9 A 1 ATOM 73 C CD1 . ILE A 1 9 ? -1.189 -3.691 1.838 1.00 92.80 9 A 1 ATOM 74 N N . VAL A 1 10 ? -3.895 0.840 1.118 1.00 98.32 10 A 1 ATOM 75 C CA . VAL A 1 10 ? -4.964 1.814 1.293 1.00 98.35 10 A 1 ATOM 76 C C . VAL A 1 10 ? -6.068 1.555 0.283 1.00 98.47 10 A 1 ATOM 77 O O . VAL A 1 10 ? -7.254 1.636 0.602 1.00 98.27 10 A 1 ATOM 78 C CB . VAL A 1 10 ? -4.442 3.245 1.121 1.00 98.07 10 A 1 ATOM 79 C CG1 . VAL A 1 10 ? -5.571 4.250 1.298 1.00 96.55 10 A 1 ATOM 80 C CG2 . VAL A 1 10 ? -3.330 3.516 2.120 1.00 96.47 10 A 1 ATOM 81 N N . ALA A 1 11 ? -5.673 1.252 -0.928 1.00 98.43 11 A 1 ATOM 82 C CA . ALA A 1 11 ? -6.636 0.969 -1.986 1.00 98.42 11 A 1 ATOM 83 C C . ALA A 1 11 ? -7.434 -0.286 -1.653 1.00 98.53 11 A 1 ATOM 84 O O . ALA A 1 11 ? -8.616 -0.388 -1.979 1.00 98.22 11 A 1 ATOM 85 C CB . ALA A 1 11 ? -5.909 0.796 -3.311 1.00 98.15 11 A 1 ATOM 86 N N . LEU A 1 12 ? -6.790 -1.222 -0.997 1.00 98.36 12 A 1 ATOM 87 C CA . LEU A 1 12 ? -7.443 -2.462 -0.603 1.00 98.15 12 A 1 ATOM 88 C C . LEU A 1 12 ? -8.491 -2.190 0.468 1.00 98.35 12 A 1 ATOM 89 O O . LEU A 1 12 ? -9.536 -2.837 0.508 1.00 97.91 12 A 1 ATOM 90 C CB . LEU A 1 12 ? -6.402 -3.443 -0.070 1.00 97.54 12 A 1 ATOM 91 C CG . LEU A 1 12 ? -6.968 -4.823 0.243 1.00 93.39 12 A 1 ATOM 92 C CD1 . LEU A 1 12 ? -7.480 -5.486 -1.024 1.00 90.97 12 A 1 ATOM 93 C CD2 . LEU A 1 12 ? -5.909 -5.690 0.903 1.00 91.49 12 A 1 ATOM 94 N N . ALA A 1 13 ? -8.207 -1.237 1.338 1.00 98.37 13 A 1 ATOM 95 C CA . ALA A 1 13 ? -9.126 -0.869 2.406 1.00 98.39 13 A 1 ATOM 96 C C . ALA A 1 13 ? -10.387 -0.225 1.843 1.00 98.53 13 A 1 ATOM 97 O O . ALA A 1 13 ? -11.455 -0.294 2.451 1.00 98.10 13 A 1 ATOM 98 C CB . ALA A 1 13 ? -8.441 0.090 3.371 1.00 98.05 13 A 1 ATOM 99 N N . LEU A 1 14 ? -10.260 0.399 0.692 1.00 98.07 14 A 1 ATOM 100 C CA . LEU A 1 14 ? -11.391 1.051 0.040 1.00 98.04 14 A 1 ATOM 101 C C . LEU A 1 14 ? -12.387 0.022 -0.464 1.00 98.16 14 A 1 ATOM 102 O O . LEU A 1 14 ? -13.582 0.301 -0.570 1.00 97.46 14 A 1 ATOM 103 C CB . LEU A 1 14 ? -10.892 1.902 -1.127 1.00 97.38 14 A 1 ATOM 104 C CG . LEU A 1 14 ? -10.081 3.116 -0.686 1.00 94.29 14 A 1 ATOM 105 C CD1 . LEU A 1 14 ? -9.400 3.766 -1.884 1.00 91.36 14 A 1 ATOM 106 C CD2 . LEU A 1 14 ? -10.991 4.118 0.007 1.00 90.78 14 A 1 ATOM 107 N N . ALA A 1 15 ? -11.892 -1.154 -0.784 1.00 97.37 15 A 1 ATOM 108 C CA . ALA A 1 15 ? -12.732 -2.219 -1.295 1.00 96.49 15 A 1 ATOM 109 C C . ALA A 1 15 ? -13.634 -2.782 -0.197 1.00 95.62 15 A 1 ATOM 110 O O . ALA A 1 15 ? -13.233 -2.780 0.977 1.00 93.01 15 A 1 ATOM 111 C CB . ALA A 1 15 ? -11.876 -3.320 -1.903 1.00 94.34 15 A 1 ATOM 112 O OXT . ALA A 1 15 ? -14.738 -3.242 -0.502 1.00 85.66 15 A 1 #