# 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_spkb38445 # _entry.id spkb38445 # 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" "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" "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 LEU 2 1 n TRP 3 1 n PHE 4 1 n VAL 5 1 n ALA 6 1 n VAL 7 1 n CYS 8 1 n PHE 9 1 n ALA 10 1 n ILE 11 1 n ALA 12 1 n SER 13 1 n VAL 14 1 n SER 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 @ 2025-07-04 11:53:38)" _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 91.08 _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 83.19 1 1 A LEU 2 2 89.90 1 2 A TRP 3 2 92.07 1 3 A PHE 4 2 91.37 1 4 A VAL 5 2 94.46 1 5 A ALA 6 2 96.03 1 6 A VAL 7 2 95.06 1 7 A CYS 8 2 94.61 1 8 A PHE 9 2 92.11 1 9 A ALA 10 2 95.57 1 10 A ILE 11 2 92.75 1 11 A ALA 12 2 95.22 1 12 A SER 13 2 92.92 1 13 A VAL 14 2 89.95 1 14 A SER 15 2 84.94 1 15 A ALA 16 2 78.38 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 LEU . 2 A 2 A 3 1 n TRP . 3 A 3 A 4 1 n PHE . 4 A 4 A 5 1 n VAL . 5 A 5 A 6 1 n ALA . 6 A 6 A 7 1 n VAL . 7 A 7 A 8 1 n CYS . 8 A 8 A 9 1 n PHE . 9 A 9 A 10 1 n ALA . 10 A 10 A 11 1 n ILE . 11 A 11 A 12 1 n ALA . 12 A 12 A 13 1 n SER . 13 A 13 A 14 1 n VAL . 14 A 14 A 15 1 n SER . 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 ? -5.097 -10.927 4.237 1.00 89.06 1 A 1 ATOM 2 C CA . MET A 1 1 ? -5.094 -9.679 3.450 1.00 89.54 1 A 1 ATOM 3 C C . MET A 1 1 ? -3.858 -8.835 3.755 1.00 90.84 1 A 1 ATOM 4 O O . MET A 1 1 ? -3.965 -7.717 4.262 1.00 87.61 1 A 1 ATOM 5 C CB . MET A 1 1 ? -6.349 -8.869 3.751 1.00 84.57 1 A 1 ATOM 6 C CG . MET A 1 1 ? -6.679 -8.811 5.234 1.00 79.94 1 A 1 ATOM 7 S SD . MET A 1 1 ? -8.246 -7.986 5.512 1.00 76.08 1 A 1 ATOM 8 C CE . MET A 1 1 ? -8.561 -8.463 7.207 1.00 67.91 1 A 1 ATOM 9 N N . LEU A 1 2 ? -2.709 -9.383 3.450 1.00 91.20 2 A 1 ATOM 10 C CA . LEU A 1 2 ? -1.454 -8.680 3.682 1.00 93.63 2 A 1 ATOM 11 C C . LEU A 1 2 ? -1.208 -7.654 2.579 1.00 95.52 2 A 1 ATOM 12 O O . LEU A 1 2 ? -0.583 -6.617 2.783 1.00 94.06 2 A 1 ATOM 13 C CB . LEU A 1 2 ? -0.295 -9.684 3.738 1.00 91.75 2 A 1 ATOM 14 C CG . LEU A 1 2 ? 0.666 -9.442 4.898 1.00 87.37 2 A 1 ATOM 15 C CD1 . LEU A 1 2 ? 1.239 -8.042 4.845 1.00 84.25 2 A 1 ATOM 16 C CD2 . LEU A 1 2 ? -0.046 -9.677 6.224 1.00 81.44 2 A 1 ATOM 17 N N . TRP A 1 3 ? -1.724 -7.974 1.400 1.00 94.85 3 A 1 ATOM 18 C CA . TRP A 1 3 ? -1.577 -7.102 0.236 1.00 95.51 3 A 1 ATOM 19 C C . TRP A 1 3 ? -2.255 -5.758 0.470 1.00 96.34 3 A 1 ATOM 20 O O . TRP A 1 3 ? -1.858 -4.747 -0.114 1.00 95.78 3 A 1 ATOM 21 C CB . TRP A 1 3 ? -2.169 -7.784 -0.993 1.00 94.57 3 A 1 ATOM 22 C CG . TRP A 1 3 ? -3.408 -8.570 -0.679 1.00 92.44 3 A 1 ATOM 23 C CD1 . TRP A 1 3 ? -3.458 -9.807 -0.127 1.00 91.11 3 A 1 ATOM 24 C CD2 . TRP A 1 3 ? -4.776 -8.177 -0.893 1.00 92.48 3 A 1 ATOM 25 N NE1 . TRP A 1 3 ? -4.773 -10.203 0.025 1.00 89.50 3 A 1 ATOM 26 C CE2 . TRP A 1 3 ? -5.601 -9.221 -0.444 1.00 91.76 3 A 1 ATOM 27 C CE3 . TRP A 1 3 ? -5.369 -7.035 -1.437 1.00 91.04 3 A 1 ATOM 28 C CZ2 . TRP A 1 3 ? -6.997 -9.148 -0.524 1.00 90.56 3 A 1 ATOM 29 C CZ3 . TRP A 1 3 ? -6.757 -6.962 -1.520 1.00 86.71 3 A 1 ATOM 30 C CH2 . TRP A 1 3 ? -7.552 -8.011 -1.062 1.00 86.34 3 A 1 ATOM 31 N N . PHE A 1 4 ? -3.261 -5.741 1.331 1.00 93.68 4 A 1 ATOM 32 C CA . PHE A 1 4 ? -3.970 -4.506 1.642 1.00 94.47 4 A 1 ATOM 33 C C . PHE A 1 4 ? -3.040 -3.492 2.294 1.00 96.18 4 A 1 ATOM 34 O O . PHE A 1 4 ? -3.079 -2.301 1.984 1.00 95.79 4 A 1 ATOM 35 C CB . PHE A 1 4 ? -5.145 -4.796 2.577 1.00 93.38 4 A 1 ATOM 36 C CG . PHE A 1 4 ? -6.471 -4.808 1.860 1.00 90.94 4 A 1 ATOM 37 C CD1 . PHE A 1 4 ? -6.803 -3.779 0.994 1.00 88.91 4 A 1 ATOM 38 C CD2 . PHE A 1 4 ? -7.377 -5.835 2.066 1.00 88.70 4 A 1 ATOM 39 C CE1 . PHE A 1 4 ? -8.020 -3.781 0.335 1.00 87.75 4 A 1 ATOM 40 C CE2 . PHE A 1 4 ? -8.597 -5.837 1.411 1.00 87.48 4 A 1 ATOM 41 C CZ . PHE A 1 4 ? -8.918 -4.812 0.543 1.00 87.79 4 A 1 ATOM 42 N N . VAL A 1 5 ? -2.210 -3.965 3.200 1.00 95.09 5 A 1 ATOM 43 C CA . VAL A 1 5 ? -1.258 -3.096 3.886 1.00 95.51 5 A 1 ATOM 44 C C . VAL A 1 5 ? -0.292 -2.480 2.885 1.00 96.44 5 A 1 ATOM 45 O O . VAL A 1 5 ? 0.005 -1.288 2.937 1.00 96.33 5 A 1 ATOM 46 C CB . VAL A 1 5 ? -0.469 -3.874 4.951 1.00 94.65 5 A 1 ATOM 47 C CG1 . VAL A 1 5 ? 0.477 -2.944 5.692 1.00 91.59 5 A 1 ATOM 48 C CG2 . VAL A 1 5 ? -1.427 -4.540 5.927 1.00 91.60 5 A 1 ATOM 49 N N . ALA A 1 6 ? 0.197 -3.305 1.986 1.00 95.43 6 A 1 ATOM 50 C CA . ALA A 1 6 ? 1.133 -2.843 0.965 1.00 96.02 6 A 1 ATOM 51 C C . ALA A 1 6 ? 0.474 -1.819 0.045 1.00 96.76 6 A 1 ATOM 52 O O . ALA A 1 6 ? 1.071 -0.799 -0.297 1.00 96.48 6 A 1 ATOM 53 C CB . ALA A 1 6 ? 1.635 -4.029 0.153 1.00 95.47 6 A 1 ATOM 54 N N . VAL A 1 7 ? -0.758 -2.096 -0.348 1.00 95.81 7 A 1 ATOM 55 C CA . VAL A 1 7 ? -1.500 -1.194 -1.226 1.00 95.87 7 A 1 ATOM 56 C C . VAL A 1 7 ? -1.796 0.123 -0.520 1.00 96.49 7 A 1 ATOM 57 O O . VAL A 1 7 ? -1.673 1.197 -1.109 1.00 96.24 7 A 1 ATOM 58 C CB . VAL A 1 7 ? -2.817 -1.843 -1.678 1.00 95.18 7 A 1 ATOM 59 C CG1 . VAL A 1 7 ? -3.639 -0.865 -2.503 1.00 92.82 7 A 1 ATOM 60 C CG2 . VAL A 1 7 ? -2.533 -3.097 -2.484 1.00 92.98 7 A 1 ATOM 61 N N . CYS A 1 8 ? -2.184 0.042 0.737 1.00 95.28 8 A 1 ATOM 62 C CA . CYS A 1 8 ? -2.483 1.236 1.523 1.00 95.46 8 A 1 ATOM 63 C C . CYS A 1 8 ? -1.255 2.130 1.632 1.00 96.08 8 A 1 ATOM 64 O O . CYS A 1 8 ? -1.332 3.340 1.450 1.00 95.63 8 A 1 ATOM 65 C CB . CYS A 1 8 ? -2.959 0.833 2.918 1.00 94.51 8 A 1 ATOM 66 S SG . CYS A 1 8 ? -4.759 0.769 3.031 1.00 90.71 8 A 1 ATOM 67 N N . PHE A 1 9 ? -0.124 1.513 1.940 1.00 95.14 9 A 1 ATOM 68 C CA . PHE A 1 9 ? 1.121 2.259 2.070 1.00 95.13 9 A 1 ATOM 69 C C . PHE A 1 9 ? 1.521 2.864 0.731 1.00 95.93 9 A 1 ATOM 70 O O . PHE A 1 9 ? 1.994 3.999 0.663 1.00 95.79 9 A 1 ATOM 71 C CB . PHE A 1 9 ? 2.226 1.340 2.579 1.00 94.50 9 A 1 ATOM 72 C CG . PHE A 1 9 ? 3.366 2.112 3.196 1.00 91.78 9 A 1 ATOM 73 C CD1 . PHE A 1 9 ? 4.342 2.681 2.400 1.00 89.97 9 A 1 ATOM 74 C CD2 . PHE A 1 9 ? 3.443 2.267 4.573 1.00 89.88 9 A 1 ATOM 75 C CE1 . PHE A 1 9 ? 5.383 3.404 2.963 1.00 88.27 9 A 1 ATOM 76 C CE2 . PHE A 1 9 ? 4.484 2.986 5.138 1.00 88.41 9 A 1 ATOM 77 C CZ . PHE A 1 9 ? 5.454 3.558 4.336 1.00 88.44 9 A 1 ATOM 78 N N . ALA A 1 10 ? 1.325 2.102 -0.327 1.00 95.38 10 A 1 ATOM 79 C CA . ALA A 1 10 ? 1.662 2.572 -1.668 1.00 95.55 10 A 1 ATOM 80 C C . ALA A 1 10 ? 0.812 3.780 -2.046 1.00 96.27 10 A 1 ATOM 81 O O . ALA A 1 10 ? 1.322 4.775 -2.556 1.00 95.61 10 A 1 ATOM 82 C CB . ALA A 1 10 ? 1.461 1.452 -2.679 1.00 95.05 10 A 1 ATOM 83 N N . ILE A 1 11 ? -0.484 3.698 -1.791 1.00 95.81 11 A 1 ATOM 84 C CA . ILE A 1 11 ? -1.402 4.791 -2.098 1.00 95.13 11 A 1 ATOM 85 C C . ILE A 1 11 ? -1.099 6.011 -1.240 1.00 95.34 11 A 1 ATOM 86 O O . ILE A 1 11 ? -1.118 7.146 -1.719 1.00 94.89 11 A 1 ATOM 87 C CB . ILE A 1 11 ? -2.857 4.353 -1.867 1.00 94.21 11 A 1 ATOM 88 C CG1 . ILE A 1 11 ? -3.219 3.192 -2.790 1.00 91.27 11 A 1 ATOM 89 C CG2 . ILE A 1 11 ? -3.804 5.526 -2.117 1.00 91.22 11 A 1 ATOM 90 C CD1 . ILE A 1 11 ? -4.524 2.525 -2.413 1.00 84.15 11 A 1 ATOM 91 N N . ALA A 1 12 ? -0.826 5.767 0.037 1.00 96.05 12 A 1 ATOM 92 C CA . ALA A 1 12 ? -0.506 6.852 0.960 1.00 95.47 12 A 1 ATOM 93 C C . ALA A 1 12 ? 0.769 7.565 0.534 1.00 95.98 12 A 1 ATOM 94 O O . ALA A 1 12 ? 0.866 8.787 0.614 1.00 94.47 12 A 1 ATOM 95 C CB . ALA A 1 12 ? -0.343 6.303 2.374 1.00 94.14 12 A 1 ATOM 96 N N . SER A 1 13 ? 1.745 6.795 0.087 1.00 96.01 13 A 1 ATOM 97 C CA . SER A 1 13 ? 3.021 7.349 -0.362 1.00 95.53 13 A 1 ATOM 98 C C . SER A 1 13 ? 2.824 8.225 -1.591 1.00 95.30 13 A 1 ATOM 99 O O . SER A 1 13 ? 3.396 9.311 -1.695 1.00 92.47 13 A 1 ATOM 100 C CB . SER A 1 13 ? 4.008 6.229 -0.682 1.00 93.83 13 A 1 ATOM 101 O OG . SER A 1 13 ? 5.271 6.760 -0.991 1.00 84.36 13 A 1 ATOM 102 N N . VAL A 1 14 ? 2.012 7.747 -2.521 1.00 93.98 14 A 1 ATOM 103 C CA . VAL A 1 14 ? 1.725 8.498 -3.743 1.00 93.40 14 A 1 ATOM 104 C C . VAL A 1 14 ? 0.816 9.687 -3.448 1.00 93.65 14 A 1 ATOM 105 O O . VAL A 1 14 ? 0.825 10.689 -4.167 1.00 89.74 14 A 1 ATOM 106 C CB . VAL A 1 14 ? 1.068 7.584 -4.792 1.00 90.70 14 A 1 ATOM 107 C CG1 . VAL A 1 14 ? 0.712 8.366 -6.043 1.00 83.65 14 A 1 ATOM 108 C CG2 . VAL A 1 14 ? 1.988 6.431 -5.132 1.00 84.55 14 A 1 ATOM 109 N N . SER A 1 15 ? 0.055 9.590 -2.366 1.00 89.95 15 A 1 ATOM 110 C CA . SER A 1 15 ? -0.890 10.641 -1.985 1.00 88.86 15 A 1 ATOM 111 C C . SER A 1 15 ? -1.896 10.893 -3.100 1.00 88.40 15 A 1 ATOM 112 O O . SER A 1 15 ? -2.064 12.025 -3.574 1.00 82.80 15 A 1 ATOM 113 C CB . SER A 1 15 ? -0.134 11.937 -1.673 1.00 84.92 15 A 1 ATOM 114 O OG . SER A 1 15 ? 0.506 11.853 -0.424 1.00 74.68 15 A 1 ATOM 115 N N . ALA A 1 16 ? -2.559 9.794 -3.493 1.00 85.37 16 A 1 ATOM 116 C CA . ALA A 1 16 ? -3.539 9.876 -4.575 1.00 82.83 16 A 1 ATOM 117 C C . ALA A 1 16 ? -4.941 10.043 -3.997 1.00 81.46 16 A 1 ATOM 118 O O . ALA A 1 16 ? -5.581 9.043 -3.662 1.00 74.68 16 A 1 ATOM 119 C CB . ALA A 1 16 ? -3.473 8.632 -5.444 1.00 75.80 16 A 1 ATOM 120 O OXT . ALA A 1 16 ? -5.398 11.184 -3.864 1.00 70.16 16 A 1 #