# 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_spkb41894 # _entry.id spkb41894 # 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 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" "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" "C4 H9 N O3" 119.119 THR y THREONINE C[C@H]([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" "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 THR 3 1 n TRP 4 1 n ILE 5 1 n LEU 6 1 n PHE 7 1 n ALA 8 1 n CYS 9 1 n LEU 10 1 n VAL 11 1 n GLY 12 1 n ALA 13 1 n ALA 14 1 n PHE 15 1 n ALA 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 @ 2025-07-08 00:25:30)" _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 95.41 _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 81.99 1 1 A GLY 2 2 95.85 1 2 A THR 3 2 95.46 1 3 A TRP 4 2 94.69 1 4 A ILE 5 2 96.68 1 5 A LEU 6 2 97.03 1 6 A PHE 7 2 96.71 1 7 A ALA 8 2 98.28 1 8 A CYS 9 2 98.19 1 9 A LEU 10 2 97.41 1 10 A VAL 11 2 97.98 1 11 A GLY 12 2 98.41 1 12 A ALA 13 2 98.51 1 13 A ALA 14 2 98.47 1 14 A PHE 15 2 94.10 1 15 A ALA 16 2 92.75 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 GLY . 2 A 2 A 3 1 n THR . 3 A 3 A 4 1 n TRP . 4 A 4 A 5 1 n ILE . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n PHE . 7 A 7 A 8 1 n ALA . 8 A 8 A 9 1 n CYS . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n VAL . 11 A 11 A 12 1 n GLY . 12 A 12 A 13 1 n ALA . 13 A 13 A 14 1 n ALA . 14 A 14 A 15 1 n PHE . 15 A 15 A 16 1 n ALA . 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 ? -4.347 6.671 11.912 1.00 87.20 1 A 1 ATOM 2 C CA . MET A 1 1 ? -3.477 5.642 11.304 1.00 88.30 1 A 1 ATOM 3 C C . MET A 1 1 ? -3.767 5.497 9.813 1.00 88.61 1 A 1 ATOM 4 O O . MET A 1 1 ? -4.917 5.327 9.422 1.00 85.00 1 A 1 ATOM 5 C CB . MET A 1 1 ? -3.715 4.294 11.985 1.00 83.76 1 A 1 ATOM 6 C CG . MET A 1 1 ? -3.243 4.308 13.429 1.00 79.52 1 A 1 ATOM 7 S SD . MET A 1 1 ? -3.571 2.744 14.247 1.00 76.93 1 A 1 ATOM 8 C CE . MET A 1 1 ? -2.749 3.046 15.805 1.00 66.63 1 A 1 ATOM 9 N N . GLY A 1 2 ? -2.731 5.580 8.996 1.00 94.46 2 A 1 ATOM 10 C CA . GLY A 1 2 ? -2.895 5.455 7.550 1.00 95.89 2 A 1 ATOM 11 C C . GLY A 1 2 ? -1.793 4.616 6.918 1.00 97.05 2 A 1 ATOM 12 O O . GLY A 1 2 ? -1.342 4.912 5.814 1.00 96.01 2 A 1 ATOM 13 N N . THR A 1 3 ? -1.363 3.591 7.623 1.00 97.02 3 A 1 ATOM 14 C CA . THR A 1 3 ? -0.298 2.712 7.137 1.00 97.47 3 A 1 ATOM 15 C C . THR A 1 3 ? -0.791 1.819 6.003 1.00 97.93 3 A 1 ATOM 16 O O . THR A 1 3 ? -0.008 1.375 5.164 1.00 97.14 3 A 1 ATOM 17 C CB . THR A 1 3 ? 0.240 1.833 8.270 1.00 96.23 3 A 1 ATOM 18 O OG1 . THR A 1 3 ? 0.487 2.640 9.419 1.00 91.72 3 A 1 ATOM 19 C CG2 . THR A 1 3 ? 1.525 1.147 7.854 1.00 90.74 3 A 1 ATOM 20 N N . TRP A 1 4 ? -2.107 1.578 5.988 1.00 97.10 4 A 1 ATOM 21 C CA . TRP A 1 4 ? -2.700 0.741 4.947 1.00 97.41 4 A 1 ATOM 22 C C . TRP A 1 4 ? -2.493 1.353 3.570 1.00 97.96 4 A 1 ATOM 23 O O . TRP A 1 4 ? -2.450 0.646 2.568 1.00 97.64 4 A 1 ATOM 24 C CB . TRP A 1 4 ? -4.191 0.557 5.222 1.00 96.78 4 A 1 ATOM 25 C CG . TRP A 1 4 ? -4.442 -0.417 6.326 1.00 95.80 4 A 1 ATOM 26 C CD1 . TRP A 1 4 ? -5.017 -0.169 7.523 1.00 93.65 4 A 1 ATOM 27 C CD2 . TRP A 1 4 ? -4.118 -1.824 6.322 1.00 94.57 4 A 1 ATOM 28 N NE1 . TRP A 1 4 ? -5.076 -1.323 8.263 1.00 92.48 4 A 1 ATOM 29 C CE2 . TRP A 1 4 ? -4.528 -2.358 7.551 1.00 93.77 4 A 1 ATOM 30 C CE3 . TRP A 1 4 ? -3.520 -2.675 5.381 1.00 92.66 4 A 1 ATOM 31 C CZ2 . TRP A 1 4 ? -4.356 -3.705 7.865 1.00 92.98 4 A 1 ATOM 32 C CZ3 . TRP A 1 4 ? -3.352 -4.013 5.699 1.00 91.58 4 A 1 ATOM 33 C CH2 . TRP A 1 4 ? -3.767 -4.517 6.931 1.00 91.30 4 A 1 ATOM 34 N N . ILE A 1 5 ? -2.356 2.667 3.514 1.00 98.01 5 A 1 ATOM 35 C CA . ILE A 1 5 ? -2.130 3.377 2.257 1.00 98.05 5 A 1 ATOM 36 C C . ILE A 1 5 ? -0.813 2.923 1.634 1.00 98.32 5 A 1 ATOM 37 O O . ILE A 1 5 ? -0.730 2.679 0.427 1.00 98.23 5 A 1 ATOM 38 C CB . ILE A 1 5 ? -2.102 4.897 2.484 1.00 97.74 5 A 1 ATOM 39 C CG1 . ILE A 1 5 ? -3.347 5.362 3.253 1.00 96.27 5 A 1 ATOM 40 C CG2 . ILE A 1 5 ? -2.003 5.619 1.140 1.00 95.81 5 A 1 ATOM 41 C CD1 . ILE A 1 5 ? -4.643 5.026 2.546 1.00 90.98 5 A 1 ATOM 42 N N . LEU A 1 6 ? 0.206 2.826 2.467 1.00 98.28 6 A 1 ATOM 43 C CA . LEU A 1 6 ? 1.524 2.393 2.007 1.00 98.27 6 A 1 ATOM 44 C C . LEU A 1 6 ? 1.472 0.947 1.527 1.00 98.40 6 A 1 ATOM 45 O O . LEU A 1 6 ? 2.027 0.606 0.482 1.00 98.35 6 A 1 ATOM 46 C CB . LEU A 1 6 ? 2.538 2.530 3.146 1.00 98.12 6 A 1 ATOM 47 C CG . LEU A 1 6 ? 3.978 2.288 2.716 1.00 96.24 6 A 1 ATOM 48 C CD1 . LEU A 1 6 ? 4.505 3.482 1.924 1.00 94.53 6 A 1 ATOM 49 C CD2 . LEU A 1 6 ? 4.857 2.036 3.931 1.00 94.02 6 A 1 ATOM 50 N N . PHE A 1 7 ? 0.790 0.110 2.299 1.00 98.27 7 A 1 ATOM 51 C CA . PHE A 1 7 ? 0.649 -1.300 1.951 1.00 98.21 7 A 1 ATOM 52 C C . PHE A 1 7 ? -0.088 -1.456 0.629 1.00 98.46 7 A 1 ATOM 53 O O . PHE A 1 7 ? 0.306 -2.249 -0.228 1.00 98.39 7 A 1 ATOM 54 C CB . PHE A 1 7 ? -0.110 -2.020 3.066 1.00 97.83 7 A 1 ATOM 55 C CG . PHE A 1 7 ? -0.052 -3.515 2.924 1.00 96.96 7 A 1 ATOM 56 C CD1 . PHE A 1 7 ? 1.113 -4.201 3.215 1.00 95.53 7 A 1 ATOM 57 C CD2 . PHE A 1 7 ? -1.163 -4.222 2.502 1.00 95.55 7 A 1 ATOM 58 C CE1 . PHE A 1 7 ? 1.176 -5.576 3.085 1.00 94.81 7 A 1 ATOM 59 C CE2 . PHE A 1 7 ? -1.106 -5.600 2.365 1.00 94.64 7 A 1 ATOM 60 C CZ . PHE A 1 7 ? 0.064 -6.281 2.655 1.00 95.20 7 A 1 ATOM 61 N N . ALA A 1 8 ? -1.154 -0.687 0.461 1.00 98.26 8 A 1 ATOM 62 C CA . ALA A 1 8 ? -1.943 -0.733 -0.768 1.00 98.31 8 A 1 ATOM 63 C C . ALA A 1 8 ? -1.102 -0.301 -1.964 1.00 98.47 8 A 1 ATOM 64 O O . ALA A 1 8 ? -1.201 -0.888 -3.043 1.00 98.29 8 A 1 ATOM 65 C CB . ALA A 1 8 ? -3.167 0.169 -0.627 1.00 98.05 8 A 1 ATOM 66 N N . CYS A 1 9 ? -0.281 0.717 -1.763 1.00 98.49 9 A 1 ATOM 67 C CA . CYS A 1 9 ? 0.587 1.225 -2.823 1.00 98.49 9 A 1 ATOM 68 C C . CYS A 1 9 ? 1.631 0.181 -3.209 1.00 98.54 9 A 1 ATOM 69 O O . CYS A 1 9 ? 1.931 -0.001 -4.387 1.00 98.23 9 A 1 ATOM 70 C CB . CYS A 1 9 ? 1.273 2.508 -2.356 1.00 98.29 9 A 1 ATOM 71 S SG . CYS A 1 9 ? 2.195 3.301 -3.682 1.00 97.09 9 A 1 ATOM 72 N N . LEU A 1 10 ? 2.165 -0.496 -2.208 1.00 98.50 10 A 1 ATOM 73 C CA . LEU A 1 10 ? 3.176 -1.529 -2.435 1.00 98.43 10 A 1 ATOM 74 C C . LEU A 1 10 ? 2.613 -2.668 -3.273 1.00 98.55 10 A 1 ATOM 75 O O . LEU A 1 10 ? 3.197 -3.063 -4.283 1.00 98.42 10 A 1 ATOM 76 C CB . LEU A 1 10 ? 3.669 -2.072 -1.091 1.00 98.27 10 A 1 ATOM 77 C CG . LEU A 1 10 ? 4.862 -3.014 -1.218 1.00 96.82 10 A 1 ATOM 78 C CD1 . LEU A 1 10 ? 6.146 -2.223 -1.431 1.00 95.18 10 A 1 ATOM 79 C CD2 . LEU A 1 10 ? 4.983 -3.890 0.018 1.00 95.10 10 A 1 ATOM 80 N N . VAL A 1 11 ? 1.482 -3.191 -2.848 1.00 98.55 11 A 1 ATOM 81 C CA . VAL A 1 11 ? 0.831 -4.289 -3.562 1.00 98.46 11 A 1 ATOM 82 C C . VAL A 1 11 ? 0.384 -3.836 -4.943 1.00 98.55 11 A 1 ATOM 83 O O . VAL A 1 11 ? 0.537 -4.563 -5.928 1.00 98.39 11 A 1 ATOM 84 C CB . VAL A 1 11 ? -0.371 -4.814 -2.761 1.00 98.03 11 A 1 ATOM 85 C CG1 . VAL A 1 11 ? -1.065 -5.937 -3.517 1.00 96.83 11 A 1 ATOM 86 C CG2 . VAL A 1 11 ? 0.082 -5.307 -1.395 1.00 97.07 11 A 1 ATOM 87 N N . GLY A 1 12 ? -0.166 -2.627 -5.012 1.00 98.40 12 A 1 ATOM 88 C CA . GLY A 1 12 ? -0.629 -2.080 -6.281 1.00 98.29 12 A 1 ATOM 89 C C . GLY A 1 12 ? 0.508 -1.870 -7.260 1.00 98.55 12 A 1 ATOM 90 O O . GLY A 1 12 ? 0.369 -2.133 -8.455 1.00 98.39 12 A 1 ATOM 91 N N . ALA A 1 13 ? 1.647 -1.408 -6.754 1.00 98.61 13 A 1 ATOM 92 C CA . ALA A 1 13 ? 2.822 -1.167 -7.589 1.00 98.57 13 A 1 ATOM 93 C C . ALA A 1 13 ? 3.312 -2.465 -8.218 1.00 98.70 13 A 1 ATOM 94 O O . ALA A 1 13 ? 3.663 -2.500 -9.396 1.00 98.43 13 A 1 ATOM 95 C CB . ALA A 1 13 ? 3.930 -0.535 -6.755 1.00 98.25 13 A 1 ATOM 96 N N . ALA A 1 14 ? 3.337 -3.531 -7.426 1.00 98.58 14 A 1 ATOM 97 C CA . ALA A 1 14 ? 3.774 -4.836 -7.914 1.00 98.57 14 A 1 ATOM 98 C C . ALA A 1 14 ? 2.795 -5.395 -8.940 1.00 98.64 14 A 1 ATOM 99 O O . ALA A 1 14 ? 3.193 -6.068 -9.891 1.00 98.29 14 A 1 ATOM 100 C CB . ALA A 1 14 ? 3.921 -5.803 -6.742 1.00 98.29 14 A 1 ATOM 101 N N . PHE A 1 15 ? 1.513 -5.117 -8.722 1.00 97.70 15 A 1 ATOM 102 C CA . PHE A 1 15 ? 0.464 -5.589 -9.622 1.00 97.59 15 A 1 ATOM 103 C C . PHE A 1 15 ? 0.501 -4.834 -10.949 1.00 98.02 15 A 1 ATOM 104 O O . PHE A 1 15 ? 0.383 -5.435 -12.019 1.00 97.37 15 A 1 ATOM 105 C CB . PHE A 1 15 ? -0.898 -5.409 -8.958 1.00 96.61 15 A 1 ATOM 106 C CG . PHE A 1 15 ? -2.027 -5.841 -9.841 1.00 94.36 15 A 1 ATOM 107 C CD1 . PHE A 1 15 ? -2.679 -4.921 -10.645 1.00 91.43 15 A 1 ATOM 108 C CD2 . PHE A 1 15 ? -2.432 -7.167 -9.879 1.00 91.29 15 A 1 ATOM 109 C CE1 . PHE A 1 15 ? -3.716 -5.318 -11.475 1.00 90.53 15 A 1 ATOM 110 C CE2 . PHE A 1 15 ? -3.470 -7.570 -10.708 1.00 89.75 15 A 1 ATOM 111 C CZ . PHE A 1 15 ? -4.113 -6.639 -11.505 1.00 90.40 15 A 1 ATOM 112 N N . ALA A 1 16 ? 0.658 -3.525 -10.874 1.00 96.83 16 A 1 ATOM 113 C CA . ALA A 1 16 ? 0.679 -2.681 -12.068 1.00 95.57 16 A 1 ATOM 114 C C . ALA A 1 16 ? 2.076 -2.668 -12.694 1.00 94.91 16 A 1 ATOM 115 O O . ALA A 1 16 ? 2.530 -3.710 -13.191 1.00 91.10 16 A 1 ATOM 116 C CB . ALA A 1 16 ? 0.225 -1.268 -11.706 1.00 92.83 16 A 1 ATOM 117 O OXT . ALA A 1 16 ? 2.732 -1.634 -12.697 1.00 85.25 16 A 1 #