# 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_spkb12882 # _entry.id spkb12882 # 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" "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" "C5 H9 N O2" 115.130 PRO y PROLINE C1C[C@H](NC1)C(=O)O ? "L-PEPTIDE LINKING" "C3 H7 N O3" 105.093 SER y SERINE C([C@@H](C(=O)O)N)O ? "L-PEPTIDE LINKING" "C11 H12 N2 O2" 204.225 TRP y TRYPTOPHAN c1ccc2c(c1)c(c[nH]2)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 TRP 2 1 n PRO 3 1 n LEU 4 1 n ALA 5 1 n ALA 6 1 n ALA 7 1 n LEU 8 1 n LEU 9 1 n LEU 10 1 n GLY 11 1 n SER 12 1 n CYS 13 1 n CYS 14 1 n CYS 15 1 n GLY 16 1 n SER 17 1 n ALA 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 @ 2025-07-02 15:01:49)" _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 88.61 _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 85.37 1 1 A TRP 2 2 85.22 1 2 A PRO 3 2 93.49 1 3 A LEU 4 2 92.29 1 4 A ALA 5 2 95.46 1 5 A ALA 6 2 94.64 1 6 A ALA 7 2 93.79 1 7 A LEU 8 2 92.37 1 8 A LEU 9 2 92.48 1 9 A LEU 10 2 92.06 1 10 A GLY 11 2 93.55 1 11 A SER 12 2 90.72 1 12 A CYS 13 2 87.41 1 13 A CYS 14 2 86.76 1 14 A CYS 15 2 82.60 1 15 A GLY 16 2 86.40 1 16 A SER 17 2 81.24 1 17 A ALA 18 2 73.00 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 TRP . 2 A 2 A 3 1 n PRO . 3 A 3 A 4 1 n LEU . 4 A 4 A 5 1 n ALA . 5 A 5 A 6 1 n ALA . 6 A 6 A 7 1 n ALA . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n GLY . 11 A 11 A 12 1 n SER . 12 A 12 A 13 1 n CYS . 13 A 13 A 14 1 n CYS . 14 A 14 A 15 1 n CYS . 15 A 15 A 16 1 n GLY . 16 A 16 A 17 1 n SER . 17 A 17 A 18 1 n ALA . 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 ? -7.438 -12.290 3.754 1.00 90.66 1 A 1 ATOM 2 C CA . MET A 1 1 ? -6.225 -11.462 3.590 1.00 90.24 1 A 1 ATOM 3 C C . MET A 1 1 ? -6.472 -10.330 2.595 1.00 91.16 1 A 1 ATOM 4 O O . MET A 1 1 ? -7.245 -10.478 1.660 1.00 89.34 1 A 1 ATOM 5 C CB . MET A 1 1 ? -5.064 -12.327 3.080 1.00 86.73 1 A 1 ATOM 6 C CG . MET A 1 1 ? -4.569 -13.279 4.168 1.00 82.83 1 A 1 ATOM 7 S SD . MET A 1 1 ? -5.551 -14.778 4.229 1.00 80.17 1 A 1 ATOM 8 C CE . MET A 1 1 ? -5.729 -14.953 6.001 1.00 71.81 1 A 1 ATOM 9 N N . TRP A 1 2 ? -5.808 -9.208 2.784 1.00 90.23 2 A 1 ATOM 10 C CA . TRP A 1 2 ? -5.951 -8.023 1.938 1.00 91.37 2 A 1 ATOM 11 C C . TRP A 1 2 ? -4.589 -7.545 1.419 1.00 93.33 2 A 1 ATOM 12 O O . TRP A 1 2 ? -4.170 -6.424 1.691 1.00 92.41 2 A 1 ATOM 13 C CB . TRP A 1 2 ? -6.632 -6.918 2.740 1.00 89.05 2 A 1 ATOM 14 C CG . TRP A 1 2 ? -5.960 -6.657 4.061 1.00 85.48 2 A 1 ATOM 15 C CD1 . TRP A 1 2 ? -5.405 -7.561 4.893 1.00 82.89 2 A 1 ATOM 16 C CD2 . TRP A 1 2 ? -5.786 -5.371 4.702 1.00 84.81 2 A 1 ATOM 17 N NE1 . TRP A 1 2 ? -4.890 -6.942 6.002 1.00 81.76 2 A 1 ATOM 18 C CE2 . TRP A 1 2 ? -5.119 -5.594 5.910 1.00 83.26 2 A 1 ATOM 19 C CE3 . TRP A 1 2 ? -6.135 -4.064 4.352 1.00 81.23 2 A 1 ATOM 20 C CZ2 . TRP A 1 2 ? -4.790 -4.546 6.786 1.00 80.92 2 A 1 ATOM 21 C CZ3 . TRP A 1 2 ? -5.816 -3.019 5.222 1.00 78.41 2 A 1 ATOM 22 C CH2 . TRP A 1 2 ? -5.146 -3.266 6.421 1.00 77.98 2 A 1 ATOM 23 N N . PRO A 1 3 ? -3.903 -8.375 0.655 1.00 94.64 3 A 1 ATOM 24 C CA . PRO A 1 3 ? -2.579 -8.022 0.121 1.00 94.98 3 A 1 ATOM 25 C C . PRO A 1 3 ? -2.634 -6.905 -0.914 1.00 95.65 3 A 1 ATOM 26 O O . PRO A 1 3 ? -1.672 -6.152 -1.077 1.00 94.00 3 A 1 ATOM 27 C CB . PRO A 1 3 ? -2.092 -9.334 -0.507 1.00 92.71 3 A 1 ATOM 28 C CG . PRO A 1 3 ? -3.342 -10.075 -0.842 1.00 90.08 3 A 1 ATOM 29 C CD . PRO A 1 3 ? -4.347 -9.698 0.220 1.00 92.40 3 A 1 ATOM 30 N N . LEU A 1 4 ? -3.751 -6.778 -1.607 1.00 95.08 4 A 1 ATOM 31 C CA . LEU A 1 4 ? -3.913 -5.746 -2.627 1.00 94.88 4 A 1 ATOM 32 C C . LEU A 1 4 ? -4.285 -4.403 -2.003 1.00 95.72 4 A 1 ATOM 33 O O . LEU A 1 4 ? -3.765 -3.361 -2.398 1.00 95.65 4 A 1 ATOM 34 C CB . LEU A 1 4 ? -4.988 -6.187 -3.624 1.00 94.04 4 A 1 ATOM 35 C CG . LEU A 1 4 ? -4.979 -5.372 -4.913 1.00 89.33 4 A 1 ATOM 36 C CD1 . LEU A 1 4 ? -3.677 -5.596 -5.679 1.00 87.28 4 A 1 ATOM 37 C CD2 . LEU A 1 4 ? -6.168 -5.768 -5.779 1.00 86.31 4 A 1 ATOM 38 N N . ALA A 1 5 ? -5.176 -4.415 -1.030 1.00 95.73 5 A 1 ATOM 39 C CA . ALA A 1 5 ? -5.617 -3.187 -0.357 1.00 95.49 5 A 1 ATOM 40 C C . ALA A 1 5 ? -4.463 -2.525 0.395 1.00 95.89 5 A 1 ATOM 41 O O . ALA A 1 5 ? -4.312 -1.307 0.365 1.00 95.37 5 A 1 ATOM 42 C CB . ALA A 1 5 ? -6.755 -3.517 0.603 1.00 94.82 5 A 1 ATOM 43 N N . ALA A 1 6 ? -3.650 -3.317 1.064 1.00 95.39 6 A 1 ATOM 44 C CA . ALA A 1 6 ? -2.508 -2.796 1.822 1.00 94.66 6 A 1 ATOM 45 C C . ALA A 1 6 ? -1.453 -2.202 0.893 1.00 95.20 6 A 1 ATOM 46 O O . ALA A 1 6 ? -0.787 -1.228 1.241 1.00 94.41 6 A 1 ATOM 47 C CB . ALA A 1 6 ? -1.903 -3.920 2.654 1.00 93.55 6 A 1 ATOM 48 N N . ALA A 1 7 ? -1.299 -2.765 -0.283 1.00 94.27 7 A 1 ATOM 49 C CA . ALA A 1 7 ? -0.315 -2.290 -1.258 1.00 93.78 7 A 1 ATOM 50 C C . ALA A 1 7 ? -0.643 -0.875 -1.731 1.00 94.50 7 A 1 ATOM 51 O O . ALA A 1 7 ? 0.258 -0.087 -2.010 1.00 93.17 7 A 1 ATOM 52 C CB . ALA A 1 7 ? -0.273 -3.246 -2.444 1.00 93.24 7 A 1 ATOM 53 N N . LEU A 1 8 ? -1.919 -0.542 -1.803 1.00 94.39 8 A 1 ATOM 54 C CA . LEU A 1 8 ? -2.355 0.788 -2.242 1.00 93.61 8 A 1 ATOM 55 C C . LEU A 1 8 ? -1.919 1.863 -1.251 1.00 94.41 8 A 1 ATOM 56 O O . LEU A 1 8 ? -1.462 2.933 -1.649 1.00 93.78 8 A 1 ATOM 57 C CB . LEU A 1 8 ? -3.878 0.791 -2.383 1.00 93.52 8 A 1 ATOM 58 C CG . LEU A 1 8 ? -4.351 0.203 -3.711 1.00 90.72 8 A 1 ATOM 59 C CD1 . LEU A 1 8 ? -5.829 -0.155 -3.625 1.00 89.12 8 A 1 ATOM 60 C CD2 . LEU A 1 8 ? -4.126 1.195 -4.839 1.00 89.39 8 A 1 ATOM 61 N N . LEU A 1 9 ? -2.039 1.585 0.028 1.00 93.82 9 A 1 ATOM 62 C CA . LEU A 1 9 ? -1.663 2.540 1.072 1.00 93.20 9 A 1 ATOM 63 C C . LEU A 1 9 ? -0.156 2.785 1.071 1.00 94.24 9 A 1 ATOM 64 O O . LEU A 1 9 ? 0.298 3.928 1.110 1.00 93.95 9 A 1 ATOM 65 C CB . LEU A 1 9 ? -2.102 2.005 2.437 1.00 93.11 9 A 1 ATOM 66 C CG . LEU A 1 9 ? -3.609 1.769 2.546 1.00 91.00 9 A 1 ATOM 67 C CD1 . LEU A 1 9 ? -3.929 1.038 3.836 1.00 90.23 9 A 1 ATOM 68 C CD2 . LEU A 1 9 ? -4.361 3.094 2.494 1.00 90.26 9 A 1 ATOM 69 N N . LEU A 1 10 ? 0.615 1.721 1.012 1.00 94.03 10 A 1 ATOM 70 C CA . LEU A 1 10 ? 2.075 1.827 1.009 1.00 93.34 10 A 1 ATOM 71 C C . LEU A 1 10 ? 2.591 2.344 -0.328 1.00 94.10 10 A 1 ATOM 72 O O . LEU A 1 10 ? 3.524 3.147 -0.372 1.00 93.39 10 A 1 ATOM 73 C CB . LEU A 1 10 ? 2.670 0.453 1.314 1.00 92.79 10 A 1 ATOM 74 C CG . LEU A 1 10 ? 2.503 0.040 2.778 1.00 90.57 10 A 1 ATOM 75 C CD1 . LEU A 1 10 ? 2.708 -1.460 2.921 1.00 89.37 10 A 1 ATOM 76 C CD2 . LEU A 1 10 ? 3.495 0.793 3.650 1.00 88.91 10 A 1 ATOM 77 N N . GLY A 1 11 ? 1.993 1.908 -1.408 1.00 93.88 11 A 1 ATOM 78 C CA . GLY A 1 11 ? 2.400 2.341 -2.742 1.00 93.34 11 A 1 ATOM 79 C C . GLY A 1 11 ? 2.135 3.812 -2.991 1.00 94.13 11 A 1 ATOM 80 O O . GLY A 1 11 ? 2.923 4.489 -3.650 1.00 92.85 11 A 1 ATOM 81 N N . SER A 1 12 ? 1.043 4.331 -2.463 1.00 93.37 12 A 1 ATOM 82 C CA . SER A 1 12 ? 0.669 5.737 -2.634 1.00 92.83 12 A 1 ATOM 83 C C . SER A 1 12 ? 1.627 6.660 -1.889 1.00 92.72 12 A 1 ATOM 84 O O . SER A 1 12 ? 2.107 7.648 -2.443 1.00 89.47 12 A 1 ATOM 85 C CB . SER A 1 12 ? -0.756 5.959 -2.130 1.00 91.50 12 A 1 ATOM 86 O OG . SER A 1 12 ? -1.153 7.283 -2.377 1.00 84.42 12 A 1 ATOM 87 N N . CYS A 1 13 ? 1.918 6.357 -0.639 1.00 91.12 13 A 1 ATOM 88 C CA . CYS A 1 13 ? 2.819 7.170 0.182 1.00 89.67 13 A 1 ATOM 89 C C . CYS A 1 13 ? 4.275 7.017 -0.256 1.00 89.83 13 A 1 ATOM 90 O O . CYS A 1 13 ? 5.053 7.968 -0.206 1.00 84.99 13 A 1 ATOM 91 C CB . CYS A 1 13 ? 2.671 6.769 1.654 1.00 86.77 13 A 1 ATOM 92 S SG . CYS A 1 13 ? 3.532 7.917 2.743 1.00 82.09 13 A 1 ATOM 93 N N . CYS A 1 14 ? 4.641 5.825 -0.680 1.00 89.31 14 A 1 ATOM 94 C CA . CYS A 1 14 ? 6.013 5.542 -1.106 1.00 88.59 14 A 1 ATOM 95 C C . CYS A 1 14 ? 6.381 6.315 -2.372 1.00 89.11 14 A 1 ATOM 96 O O . CYS A 1 14 ? 7.506 6.797 -2.514 1.00 85.33 14 A 1 ATOM 97 C CB . CYS A 1 14 ? 6.177 4.039 -1.343 1.00 86.09 14 A 1 ATOM 98 S SG . CYS A 1 14 ? 7.903 3.587 -1.564 1.00 82.11 14 A 1 ATOM 99 N N . CYS A 1 15 ? 5.438 6.447 -3.284 1.00 85.44 15 A 1 ATOM 100 C CA . CYS A 1 15 ? 5.690 7.147 -4.549 1.00 85.09 15 A 1 ATOM 101 C C . CYS A 1 15 ? 4.404 7.752 -5.113 1.00 86.71 15 A 1 ATOM 102 O O . CYS A 1 15 ? 3.924 7.357 -6.176 1.00 81.30 15 A 1 ATOM 103 C CB . CYS A 1 15 ? 6.299 6.163 -5.553 1.00 81.39 15 A 1 ATOM 104 S SG . CYS A 1 15 ? 7.006 7.020 -6.969 1.00 75.68 15 A 1 ATOM 105 N N . GLY A 1 16 ? 3.859 8.733 -4.400 1.00 86.26 16 A 1 ATOM 106 C CA . GLY A 1 16 ? 2.617 9.374 -4.834 1.00 85.87 16 A 1 ATOM 107 C C . GLY A 1 16 ? 2.438 10.754 -4.223 1.00 87.57 16 A 1 ATOM 108 O O . GLY A 1 16 ? 1.327 11.136 -3.862 1.00 85.91 16 A 1 ATOM 109 N N . SER A 1 17 ? 3.538 11.490 -4.091 1.00 84.66 17 A 1 ATOM 110 C CA . SER A 1 17 ? 3.499 12.832 -3.496 1.00 84.45 17 A 1 ATOM 111 C C . SER A 1 17 ? 4.546 13.748 -4.131 1.00 84.69 17 A 1 ATOM 112 O O . SER A 1 17 ? 4.995 14.714 -3.519 1.00 79.65 17 A 1 ATOM 113 C CB . SER A 1 17 ? 3.731 12.733 -1.990 1.00 81.11 17 A 1 ATOM 114 O OG . SER A 1 17 ? 3.373 13.941 -1.362 1.00 72.85 17 A 1 ATOM 115 N N . ALA A 1 18 ? 4.929 13.457 -5.363 1.00 78.86 18 A 1 ATOM 116 C CA . ALA A 1 18 ? 5.952 14.235 -6.071 1.00 77.08 18 A 1 ATOM 117 C C . ALA A 1 18 ? 5.540 14.461 -7.524 1.00 75.98 18 A 1 ATOM 118 O O . ALA A 1 18 ? 6.328 15.021 -8.294 1.00 69.97 18 A 1 ATOM 119 C CB . ALA A 1 18 ? 7.290 13.509 -5.996 1.00 69.93 18 A 1 ATOM 120 O OXT . ALA A 1 18 ? 4.426 14.078 -7.916 1.00 66.16 18 A 1 #