# 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_spkb16047 # _entry.id spkb16047 # 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" "C3 H7 N O2 S" 121.158 CYS y CYSTEINE C([C@@H](C(=O)O)N)S ? "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" "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" "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 SER 3 1 n ILE 4 1 n ILE 5 1 n LEU 6 1 n SER 7 1 n CYS 8 1 n PHE 9 1 n VAL 10 1 n ILE 11 1 n SER 12 1 n ALA 13 1 n ALA 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 18:25:48)" _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 93.48 _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 85.03 1 1 A LYS 2 2 86.89 1 2 A SER 3 2 93.84 1 3 A ILE 4 2 94.59 1 4 A ILE 5 2 95.20 1 5 A LEU 6 2 93.87 1 6 A SER 7 2 94.71 1 7 A CYS 8 2 95.94 1 8 A PHE 9 2 94.64 1 9 A VAL 10 2 96.21 1 10 A ILE 11 2 95.53 1 11 A SER 12 2 95.05 1 12 A ALA 13 2 96.63 1 13 A ALA 14 2 96.38 1 14 A ALA 15 2 91.58 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 SER . 3 A 3 A 4 1 n ILE . 4 A 4 A 5 1 n ILE . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n SER . 7 A 7 A 8 1 n CYS . 8 A 8 A 9 1 n PHE . 9 A 9 A 10 1 n VAL . 10 A 10 A 11 1 n ILE . 11 A 11 A 12 1 n SER . 12 A 12 A 13 1 n ALA . 13 A 13 A 14 1 n ALA . 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 ? -3.735 9.202 5.447 1.00 91.09 1 A 1 ATOM 2 C CA . MET A 1 1 ? -3.495 7.804 5.867 1.00 92.29 1 A 1 ATOM 3 C C . MET A 1 1 ? -2.431 7.169 4.977 1.00 92.80 1 A 1 ATOM 4 O O . MET A 1 1 ? -2.636 7.022 3.773 1.00 88.90 1 A 1 ATOM 5 C CB . MET A 1 1 ? -4.785 6.998 5.768 1.00 87.73 1 A 1 ATOM 6 C CG . MET A 1 1 ? -5.825 7.477 6.767 1.00 82.77 1 A 1 ATOM 7 S SD . MET A 1 1 ? -7.442 6.760 6.483 1.00 76.62 1 A 1 ATOM 8 C CE . MET A 1 1 ? -8.371 7.534 7.787 1.00 68.06 1 A 1 ATOM 9 N N . LYS A 1 2 ? -1.288 6.822 5.566 1.00 93.84 2 A 1 ATOM 10 C CA . LYS A 1 2 ? -0.163 6.268 4.813 1.00 94.58 2 A 1 ATOM 11 C C . LYS A 1 2 ? -0.206 4.745 4.763 1.00 95.21 2 A 1 ATOM 12 O O . LYS A 1 2 ? 0.279 4.139 3.809 1.00 94.15 2 A 1 ATOM 13 C CB . LYS A 1 2 ? 1.139 6.744 5.452 1.00 92.26 2 A 1 ATOM 14 C CG . LYS A 1 2 ? 1.312 8.250 5.384 1.00 85.41 2 A 1 ATOM 15 C CD . LYS A 1 2 ? 2.092 8.779 6.565 1.00 81.86 2 A 1 ATOM 16 C CE . LYS A 1 2 ? 2.008 10.292 6.628 1.00 76.08 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? 2.626 10.820 7.870 1.00 68.60 2 A 1 ATOM 18 N N . SER A 1 3 ? -0.790 4.128 5.772 1.00 94.03 3 A 1 ATOM 19 C CA . SER A 1 3 ? -0.887 2.671 5.840 1.00 96.03 3 A 1 ATOM 20 C C . SER A 1 3 ? -1.744 2.112 4.705 1.00 96.77 3 A 1 ATOM 21 O O . SER A 1 3 ? -1.530 0.994 4.245 1.00 95.29 3 A 1 ATOM 22 C CB . SER A 1 3 ? -1.459 2.247 7.192 1.00 94.06 3 A 1 ATOM 23 O OG . SER A 1 3 ? -2.675 2.902 7.447 1.00 86.84 3 A 1 ATOM 24 N N . ILE A 1 4 ? -2.704 2.897 4.248 1.00 95.97 4 A 1 ATOM 25 C CA . ILE A 1 4 ? -3.585 2.493 3.159 1.00 96.34 4 A 1 ATOM 26 C C . ILE A 1 4 ? -2.795 2.344 1.866 1.00 96.73 4 A 1 ATOM 27 O O . ILE A 1 4 ? -2.969 1.386 1.113 1.00 95.48 4 A 1 ATOM 28 C CB . ILE A 1 4 ? -4.718 3.515 2.953 1.00 96.08 4 A 1 ATOM 29 C CG1 . ILE A 1 4 ? -5.426 3.816 4.281 1.00 93.87 4 A 1 ATOM 30 C CG2 . ILE A 1 4 ? -5.712 2.997 1.916 1.00 93.27 4 A 1 ATOM 31 C CD1 . ILE A 1 4 ? -6.024 2.579 4.922 1.00 89.01 4 A 1 ATOM 32 N N . ILE A 1 5 ? -1.933 3.305 1.608 1.00 96.74 5 A 1 ATOM 33 C CA . ILE A 1 5 ? -1.115 3.308 0.402 1.00 96.76 5 A 1 ATOM 34 C C . ILE A 1 5 ? -0.164 2.116 0.399 1.00 96.78 5 A 1 ATOM 35 O O . ILE A 1 5 ? -0.012 1.426 -0.609 1.00 96.12 5 A 1 ATOM 36 C CB . ILE A 1 5 ? -0.312 4.614 0.294 1.00 96.70 5 A 1 ATOM 37 C CG1 . ILE A 1 5 ? -1.228 5.829 0.497 1.00 94.64 5 A 1 ATOM 38 C CG2 . ILE A 1 5 ? 0.385 4.678 -1.066 1.00 94.31 5 A 1 ATOM 39 C CD1 . ILE A 1 5 ? -2.375 5.881 -0.493 1.00 89.53 5 A 1 ATOM 40 N N . LEU A 1 6 ? 0.477 1.888 1.531 1.00 96.98 6 A 1 ATOM 41 C CA . LEU A 1 6 ? 1.430 0.789 1.672 1.00 96.96 6 A 1 ATOM 42 C C . LEU A 1 6 ? 0.746 -0.557 1.465 1.00 97.22 6 A 1 ATOM 43 O O . LEU A 1 6 ? 1.261 -1.433 0.770 1.00 96.76 6 A 1 ATOM 44 C CB . LEU A 1 6 ? 2.082 0.838 3.060 1.00 96.86 6 A 1 ATOM 45 C CG . LEU A 1 6 ? 3.596 0.995 3.047 1.00 90.64 6 A 1 ATOM 46 C CD1 . LEU A 1 6 ? 4.242 -0.126 2.256 1.00 87.27 6 A 1 ATOM 47 C CD2 . LEU A 1 6 ? 3.973 2.345 2.465 1.00 88.27 6 A 1 ATOM 48 N N . SER A 1 7 ? -0.421 -0.713 2.059 1.00 96.25 7 A 1 ATOM 49 C CA . SER A 1 7 ? -1.178 -1.957 1.963 1.00 96.31 7 A 1 ATOM 50 C C . SER A 1 7 ? -1.554 -2.265 0.515 1.00 96.99 7 A 1 ATOM 51 O O . SER A 1 7 ? -1.377 -3.387 0.042 1.00 96.51 7 A 1 ATOM 52 C CB . SER A 1 7 ? -2.435 -1.867 2.825 1.00 95.48 7 A 1 ATOM 53 O OG . SER A 1 7 ? -3.064 -3.123 2.908 1.00 86.70 7 A 1 ATOM 54 N N . CYS A 1 8 ? -2.044 -1.264 -0.184 1.00 96.04 8 A 1 ATOM 55 C CA . CYS A 1 8 ? -2.437 -1.424 -1.580 1.00 96.84 8 A 1 ATOM 56 C C . CYS A 1 8 ? -1.223 -1.718 -2.463 1.00 97.38 8 A 1 ATOM 57 O O . CYS A 1 8 ? -1.295 -2.512 -3.398 1.00 96.52 8 A 1 ATOM 58 C CB . CYS A 1 8 ? -3.148 -0.161 -2.064 1.00 96.28 8 A 1 ATOM 59 S SG . CYS A 1 8 ? -3.926 -0.393 -3.665 1.00 92.57 8 A 1 ATOM 60 N N . PHE A 1 9 ? -0.107 -1.078 -2.140 1.00 96.38 9 A 1 ATOM 61 C CA . PHE A 1 9 ? 1.128 -1.255 -2.894 1.00 96.54 9 A 1 ATOM 62 C C . PHE A 1 9 ? 1.649 -2.683 -2.763 1.00 97.17 9 A 1 ATOM 63 O O . PHE A 1 9 ? 2.064 -3.294 -3.746 1.00 96.49 9 A 1 ATOM 64 C CB . PHE A 1 9 ? 2.180 -0.263 -2.394 1.00 96.29 9 A 1 ATOM 65 C CG . PHE A 1 9 ? 3.435 -0.274 -3.225 1.00 95.31 9 A 1 ATOM 66 C CD1 . PHE A 1 9 ? 4.501 -1.087 -2.875 1.00 92.07 9 A 1 ATOM 67 C CD2 . PHE A 1 9 ? 3.529 0.521 -4.351 1.00 93.09 9 A 1 ATOM 68 C CE1 . PHE A 1 9 ? 5.654 -1.110 -3.645 1.00 92.20 9 A 1 ATOM 69 C CE2 . PHE A 1 9 ? 4.684 0.502 -5.128 1.00 92.45 9 A 1 ATOM 70 C CZ . PHE A 1 9 ? 5.742 -0.314 -4.772 1.00 93.00 9 A 1 ATOM 71 N N . VAL A 1 10 ? 1.626 -3.202 -1.555 1.00 97.30 10 A 1 ATOM 72 C CA . VAL A 1 10 ? 2.100 -4.561 -1.296 1.00 97.38 10 A 1 ATOM 73 C C . VAL A 1 10 ? 1.242 -5.585 -2.033 1.00 97.55 10 A 1 ATOM 74 O O . VAL A 1 10 ? 1.756 -6.538 -2.619 1.00 96.66 10 A 1 ATOM 75 C CB . VAL A 1 10 ? 2.101 -4.869 0.210 1.00 96.67 10 A 1 ATOM 76 C CG1 . VAL A 1 10 ? 2.505 -6.314 0.465 1.00 93.86 10 A 1 ATOM 77 C CG2 . VAL A 1 10 ? 3.053 -3.930 0.934 1.00 94.02 10 A 1 ATOM 78 N N . ILE A 1 11 ? -0.059 -5.390 -1.997 1.00 97.25 11 A 1 ATOM 79 C CA . ILE A 1 11 ? -0.992 -6.296 -2.660 1.00 97.03 11 A 1 ATOM 80 C C . ILE A 1 11 ? -0.767 -6.297 -4.168 1.00 97.30 11 A 1 ATOM 81 O O . ILE A 1 11 ? -0.766 -7.351 -4.808 1.00 96.65 11 A 1 ATOM 82 C CB . ILE A 1 11 ? -2.442 -5.899 -2.346 1.00 96.48 11 A 1 ATOM 83 C CG1 . ILE A 1 11 ? -2.721 -6.046 -0.849 1.00 94.86 11 A 1 ATOM 84 C CG2 . ILE A 1 11 ? -3.410 -6.769 -3.149 1.00 94.53 11 A 1 ATOM 85 C CD1 . ILE A 1 11 ? -4.006 -5.384 -0.414 1.00 90.15 11 A 1 ATOM 86 N N . SER A 1 12 ? -0.571 -5.120 -4.723 1.00 96.99 12 A 1 ATOM 87 C CA . SER A 1 12 ? -0.340 -4.975 -6.157 1.00 96.96 12 A 1 ATOM 88 C C . SER A 1 12 ? 0.946 -5.674 -6.585 1.00 97.35 12 A 1 ATOM 89 O O . SER A 1 12 ? 1.000 -6.313 -7.635 1.00 96.80 12 A 1 ATOM 90 C CB . SER A 1 12 ? -0.271 -3.498 -6.534 1.00 96.04 12 A 1 ATOM 91 O OG . SER A 1 12 ? -0.208 -3.356 -7.933 1.00 86.14 12 A 1 ATOM 92 N N . ALA A 1 13 ? 1.987 -5.549 -5.767 1.00 96.87 13 A 1 ATOM 93 C CA . ALA A 1 13 ? 3.276 -6.168 -6.061 1.00 96.92 13 A 1 ATOM 94 C C . ALA A 1 13 ? 3.224 -7.684 -5.897 1.00 97.31 13 A 1 ATOM 95 O O . ALA A 1 13 ? 3.909 -8.417 -6.609 1.00 96.31 13 A 1 ATOM 96 C CB . ALA A 1 13 ? 4.351 -5.581 -5.151 1.00 95.76 13 A 1 ATOM 97 N N . ALA A 1 14 ? 2.427 -8.148 -4.955 1.00 96.84 14 A 1 ATOM 98 C CA . ALA A 1 14 ? 2.296 -9.578 -4.684 1.00 96.77 14 A 1 ATOM 99 C C . ALA A 1 14 ? 1.316 -10.257 -5.637 1.00 97.11 14 A 1 ATOM 100 O O . ALA A 1 14 ? 1.298 -11.483 -5.752 1.00 95.75 14 A 1 ATOM 101 C CB . ALA A 1 14 ? 1.856 -9.793 -3.236 1.00 95.41 14 A 1 ATOM 102 N N . ALA A 1 15 ? 0.497 -9.476 -6.320 1.00 96.09 15 A 1 ATOM 103 C CA . ALA A 1 15 ? -0.511 -9.990 -7.231 1.00 94.86 15 A 1 ATOM 104 C C . ALA A 1 15 ? 0.111 -10.731 -8.418 1.00 94.26 15 A 1 ATOM 105 O O . ALA A 1 15 ? 1.343 -10.719 -8.570 1.00 90.28 15 A 1 ATOM 106 C CB . ALA A 1 15 ? -1.389 -8.835 -7.719 1.00 91.20 15 A 1 ATOM 107 O OXT . ALA A 1 15 ? -0.633 -11.348 -9.197 1.00 82.76 15 A 1 #