# 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_spkb36507 # _entry.id spkb36507 # 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 H15 N4 O2" 175.209 ARG y ARGININE C(C[C@@H](C(=O)O)N)CNC(=[NH2+])N ? "L-PEPTIDE LINKING" "C4 H8 N2 O3" 132.118 ASN y ASPARAGINE C([C@@H](C(=O)O)N)C(=O)N ? "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" "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" "C5 H9 N O2" 115.130 PRO y PROLINE C1C[C@H](NC1)C(=O)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" "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 ARG 2 1 n ASN 3 1 n PRO 4 1 n VAL 5 1 n VAL 6 1 n TRP 7 1 n GLY 8 1 n MET 9 1 n ILE 10 1 n TYR 11 1 n PHE 12 1 n ALA 13 1 n VAL 14 1 n GLY 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 @ 2025-07-05 03:29:22)" _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 94.07 _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 84.29 1 1 A ARG 2 2 85.47 1 2 A ASN 3 2 93.87 1 3 A PRO 4 2 97.08 1 4 A VAL 5 2 97.30 1 5 A VAL 6 2 97.75 1 6 A TRP 7 2 96.14 1 7 A GLY 8 2 97.98 1 8 A MET 9 2 94.60 1 9 A ILE 10 2 97.10 1 10 A TYR 11 2 95.13 1 11 A PHE 12 2 95.77 1 12 A ALA 13 2 98.10 1 13 A VAL 14 2 95.77 1 14 A GLY 15 2 87.64 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 ARG . 2 A 2 A 3 1 n ASN . 3 A 3 A 4 1 n PRO . 4 A 4 A 5 1 n VAL . 5 A 5 A 6 1 n VAL . 6 A 6 A 7 1 n TRP . 7 A 7 A 8 1 n GLY . 8 A 8 A 9 1 n MET . 9 A 9 A 10 1 n ILE . 10 A 10 A 11 1 n TYR . 11 A 11 A 12 1 n PHE . 12 A 12 A 13 1 n ALA . 13 A 13 A 14 1 n VAL . 14 A 14 A 15 1 n GLY . 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 ? -8.605 3.200 13.514 1.00 89.82 1 A 1 ATOM 2 C CA . MET A 1 1 ? -7.150 3.233 13.242 1.00 90.56 1 A 1 ATOM 3 C C . MET A 1 1 ? -6.876 2.565 11.899 1.00 91.06 1 A 1 ATOM 4 O O . MET A 1 1 ? -7.560 1.612 11.543 1.00 87.50 1 A 1 ATOM 5 C CB . MET A 1 1 ? -6.387 2.515 14.361 1.00 86.70 1 A 1 ATOM 6 C CG . MET A 1 1 ? -6.474 3.292 15.673 1.00 81.43 1 A 1 ATOM 7 S SD . MET A 1 1 ? -5.642 2.450 17.042 1.00 78.49 1 A 1 ATOM 8 C CE . MET A 1 1 ? -5.872 3.656 18.345 1.00 68.75 1 A 1 ATOM 9 N N . ARG A 1 2 ? -5.913 3.067 11.127 1.00 90.48 2 A 1 ATOM 10 C CA . ARG A 1 2 ? -5.561 2.488 9.821 1.00 93.50 2 A 1 ATOM 11 C C . ARG A 1 2 ? -4.663 1.264 10.003 1.00 94.88 2 A 1 ATOM 12 O O . ARG A 1 2 ? -3.907 1.184 10.966 1.00 93.12 2 A 1 ATOM 13 C CB . ARG A 1 2 ? -4.869 3.540 8.950 1.00 90.77 2 A 1 ATOM 14 C CG . ARG A 1 2 ? -5.865 4.570 8.410 1.00 85.70 2 A 1 ATOM 15 C CD . ARG A 1 2 ? -5.161 5.533 7.461 1.00 84.97 2 A 1 ATOM 16 N NE . ARG A 1 2 ? -6.113 6.447 6.813 1.00 80.34 2 A 1 ATOM 17 C CZ . ARG A 1 2 ? -5.782 7.442 6.006 1.00 78.87 2 A 1 ATOM 18 N NH1 . ARG A 1 2 ? -4.532 7.712 5.724 1.00 73.90 2 A 1 ATOM 19 N NH2 . ARG A 1 2 ? -6.714 8.178 5.465 1.00 73.59 2 A 1 ATOM 20 N N . ASN A 1 3 ? -4.721 0.346 9.035 1.00 95.96 3 A 1 ATOM 21 C CA . ASN A 1 3 ? -3.887 -0.851 9.062 1.00 96.89 3 A 1 ATOM 22 C C . ASN A 1 3 ? -2.581 -0.578 8.307 1.00 97.63 3 A 1 ATOM 23 O O . ASN A 1 3 ? -2.629 -0.211 7.134 1.00 97.12 3 A 1 ATOM 24 C CB . ASN A 1 3 ? -4.654 -2.020 8.440 1.00 95.83 3 A 1 ATOM 25 C CG . ASN A 1 3 ? -5.837 -2.451 9.285 1.00 92.88 3 A 1 ATOM 26 O OD1 . ASN A 1 3 ? -6.216 -1.826 10.253 1.00 88.53 3 A 1 ATOM 27 N ND2 . ASN A 1 3 ? -6.466 -3.546 8.917 1.00 86.12 3 A 1 ATOM 28 N N . PRO A 1 4 ? -1.416 -0.769 8.927 1.00 97.56 4 A 1 ATOM 29 C CA . PRO A 1 4 ? -0.127 -0.525 8.273 1.00 97.75 4 A 1 ATOM 30 C C . PRO A 1 4 ? 0.129 -1.477 7.103 1.00 98.18 4 A 1 ATOM 31 O O . PRO A 1 4 ? 0.827 -1.120 6.154 1.00 97.58 4 A 1 ATOM 32 C CB . PRO A 1 4 ? 0.903 -0.707 9.398 1.00 96.70 4 A 1 ATOM 33 C CG . PRO A 1 4 ? 0.216 -1.603 10.399 1.00 95.05 4 A 1 ATOM 34 C CD . PRO A 1 4 ? -1.244 -1.236 10.299 1.00 96.77 4 A 1 ATOM 35 N N . VAL A 1 5 ? -0.461 -2.659 7.123 1.00 97.97 5 A 1 ATOM 36 C CA . VAL A 1 5 ? -0.310 -3.659 6.056 1.00 98.09 5 A 1 ATOM 37 C C . VAL A 1 5 ? -0.869 -3.146 4.724 1.00 98.23 5 A 1 ATOM 38 O O . VAL A 1 5 ? -0.322 -3.442 3.663 1.00 97.76 5 A 1 ATOM 39 C CB . VAL A 1 5 ? -1.007 -4.968 6.463 1.00 97.68 5 A 1 ATOM 40 C CG1 . VAL A 1 5 ? -0.872 -6.031 5.384 1.00 95.90 5 A 1 ATOM 41 C CG2 . VAL A 1 5 ? -0.417 -5.505 7.764 1.00 95.45 5 A 1 ATOM 42 N N . VAL A 1 6 ? -1.922 -2.339 4.769 1.00 98.25 6 A 1 ATOM 43 C CA . VAL A 1 6 ? -2.545 -1.765 3.569 1.00 98.21 6 A 1 ATOM 44 C C . VAL A 1 6 ? -1.556 -0.867 2.823 1.00 98.18 6 A 1 ATOM 45 O O . VAL A 1 6 ? -1.516 -0.879 1.595 1.00 97.92 6 A 1 ATOM 46 C CB . VAL A 1 6 ? -3.814 -0.984 3.950 1.00 97.92 6 A 1 ATOM 47 C CG1 . VAL A 1 6 ? -4.438 -0.292 2.745 1.00 96.90 6 A 1 ATOM 48 C CG2 . VAL A 1 6 ? -4.847 -1.929 4.559 1.00 96.89 6 A 1 ATOM 49 N N . TRP A 1 7 ? -0.733 -0.114 3.540 1.00 97.67 7 A 1 ATOM 50 C CA . TRP A 1 7 ? 0.282 0.739 2.920 1.00 97.56 7 A 1 ATOM 51 C C . TRP A 1 7 ? 1.283 -0.084 2.121 1.00 97.76 7 A 1 ATOM 52 O O . TRP A 1 7 ? 1.630 0.292 1.002 1.00 97.58 7 A 1 ATOM 53 C CB . TRP A 1 7 ? 0.979 1.569 3.995 1.00 97.25 7 A 1 ATOM 54 C CG . TRP A 1 7 ? 0.184 2.772 4.381 1.00 96.74 7 A 1 ATOM 55 C CD1 . TRP A 1 7 ? -0.481 2.964 5.541 1.00 95.19 7 A 1 ATOM 56 C CD2 . TRP A 1 7 ? -0.036 3.960 3.585 1.00 96.40 7 A 1 ATOM 57 N NE1 . TRP A 1 7 ? -1.099 4.204 5.521 1.00 94.66 7 A 1 ATOM 58 C CE2 . TRP A 1 7 ? -0.848 4.846 4.330 1.00 95.90 7 A 1 ATOM 59 C CE3 . TRP A 1 7 ? 0.381 4.369 2.298 1.00 95.00 7 A 1 ATOM 60 C CZ2 . TRP A 1 7 ? -1.241 6.098 3.830 1.00 95.33 7 A 1 ATOM 61 C CZ3 . TRP A 1 7 ? -0.009 5.613 1.803 1.00 94.35 7 A 1 ATOM 62 C CH2 . TRP A 1 7 ? -0.817 6.469 2.559 1.00 94.56 7 A 1 ATOM 63 N N . GLY A 1 8 ? 1.696 -1.205 2.628 1.00 97.90 8 A 1 ATOM 64 C CA . GLY A 1 8 ? 2.601 -2.098 1.903 1.00 97.88 8 A 1 ATOM 65 C C . GLY A 1 8 ? 2.006 -2.566 0.574 1.00 98.21 8 A 1 ATOM 66 O O . GLY A 1 8 ? 2.695 -2.586 -0.444 1.00 97.94 8 A 1 ATOM 67 N N . MET A 1 9 ? 0.711 -2.883 0.558 1.00 97.92 9 A 1 ATOM 68 C CA . MET A 1 9 ? 0.018 -3.296 -0.671 1.00 97.99 9 A 1 ATOM 69 C C . MET A 1 9 ? -0.078 -2.147 -1.681 1.00 98.23 9 A 1 ATOM 70 O O . MET A 1 9 ? 0.090 -2.370 -2.876 1.00 97.80 9 A 1 ATOM 71 C CB . MET A 1 9 ? -1.383 -3.808 -0.335 1.00 97.56 9 A 1 ATOM 72 C CG . MET A 1 9 ? -1.333 -5.119 0.438 1.00 94.56 9 A 1 ATOM 73 S SD . MET A 1 9 ? -2.978 -5.799 0.735 1.00 89.93 9 A 1 ATOM 74 C CE . MET A 1 9 ? -2.526 -7.317 1.574 1.00 82.80 9 A 1 ATOM 75 N N . ILE A 1 10 ? -0.325 -0.931 -1.213 1.00 98.07 10 A 1 ATOM 76 C CA . ILE A 1 10 ? -0.409 0.245 -2.086 1.00 97.97 10 A 1 ATOM 77 C C . ILE A 1 10 ? 0.937 0.494 -2.773 1.00 98.03 10 A 1 ATOM 78 O O . ILE A 1 10 ? 0.978 0.706 -3.984 1.00 97.70 10 A 1 ATOM 79 C CB . ILE A 1 10 ? -0.870 1.476 -1.285 1.00 97.73 10 A 1 ATOM 80 C CG1 . ILE A 1 10 ? -2.332 1.308 -0.839 1.00 96.71 10 A 1 ATOM 81 C CG2 . ILE A 1 10 ? -0.735 2.756 -2.129 1.00 96.42 10 A 1 ATOM 82 C CD1 . ILE A 1 10 ? -2.746 2.287 0.250 1.00 94.18 10 A 1 ATOM 83 N N . TYR A 1 11 ? 2.031 0.449 -2.020 1.00 98.06 11 A 1 ATOM 84 C CA . TYR A 1 11 ? 3.364 0.642 -2.600 1.00 97.92 11 A 1 ATOM 85 C C . TYR A 1 11 ? 3.682 -0.420 -3.651 1.00 98.09 11 A 1 ATOM 86 O O . TYR A 1 11 ? 4.250 -0.107 -4.695 1.00 97.73 11 A 1 ATOM 87 C CB . TYR A 1 11 ? 4.420 0.608 -1.491 1.00 97.39 11 A 1 ATOM 88 C CG . TYR A 1 11 ? 4.485 1.900 -0.714 1.00 95.58 11 A 1 ATOM 89 C CD1 . TYR A 1 11 ? 4.888 3.087 -1.350 1.00 93.82 11 A 1 ATOM 90 C CD2 . TYR A 1 11 ? 4.154 1.934 0.645 1.00 93.34 11 A 1 ATOM 91 C CE1 . TYR A 1 11 ? 4.940 4.285 -0.637 1.00 92.54 11 A 1 ATOM 92 C CE2 . TYR A 1 11 ? 4.203 3.134 1.360 1.00 92.44 11 A 1 ATOM 93 C CZ . TYR A 1 11 ? 4.593 4.305 0.715 1.00 92.88 11 A 1 ATOM 94 O OH . TYR A 1 11 ? 4.635 5.483 1.410 1.00 91.78 11 A 1 ATOM 95 N N . PHE A 1 12 ? 3.282 -1.657 -3.421 1.00 97.90 12 A 1 ATOM 96 C CA . PHE A 1 12 ? 3.523 -2.742 -4.370 1.00 97.96 12 A 1 ATOM 97 C C . PHE A 1 12 ? 2.650 -2.605 -5.626 1.00 98.28 12 A 1 ATOM 98 O O . PHE A 1 12 ? 3.098 -2.916 -6.728 1.00 97.87 12 A 1 ATOM 99 C CB . PHE A 1 12 ? 3.265 -4.077 -3.667 1.00 97.48 12 A 1 ATOM 100 C CG . PHE A 1 12 ? 3.886 -5.237 -4.397 1.00 96.29 12 A 1 ATOM 101 C CD1 . PHE A 1 12 ? 3.165 -5.932 -5.370 1.00 94.06 12 A 1 ATOM 102 C CD2 . PHE A 1 12 ? 5.204 -5.604 -4.120 1.00 93.98 12 A 1 ATOM 103 C CE1 . PHE A 1 12 ? 3.759 -6.991 -6.066 1.00 93.16 12 A 1 ATOM 104 C CE2 . PHE A 1 12 ? 5.800 -6.663 -4.813 1.00 93.04 12 A 1 ATOM 105 C CZ . PHE A 1 12 ? 5.077 -7.356 -5.787 1.00 93.47 12 A 1 ATOM 106 N N . ALA A 1 13 ? 1.415 -2.124 -5.471 1.00 98.21 13 A 1 ATOM 107 C CA . ALA A 1 13 ? 0.490 -1.963 -6.595 1.00 98.25 13 A 1 ATOM 108 C C . ALA A 1 13 ? 0.855 -0.769 -7.483 1.00 98.35 13 A 1 ATOM 109 O O . ALA A 1 13 ? 0.666 -0.826 -8.698 1.00 97.81 13 A 1 ATOM 110 C CB . ALA A 1 13 ? -0.931 -1.819 -6.041 1.00 97.88 13 A 1 ATOM 111 N N . VAL A 1 14 ? 1.351 0.314 -6.902 1.00 98.08 14 A 1 ATOM 112 C CA . VAL A 1 14 ? 1.713 1.532 -7.646 1.00 97.80 14 A 1 ATOM 113 C C . VAL A 1 14 ? 3.102 1.409 -8.278 1.00 97.69 14 A 1 ATOM 114 O O . VAL A 1 14 ? 3.340 1.960 -9.357 1.00 96.29 14 A 1 ATOM 115 C CB . VAL A 1 14 ? 1.632 2.761 -6.721 1.00 96.79 14 A 1 ATOM 116 C CG1 . VAL A 1 14 ? 2.099 4.036 -7.413 1.00 91.62 14 A 1 ATOM 117 C CG2 . VAL A 1 14 ? 0.195 2.979 -6.245 1.00 92.11 14 A 1 ATOM 118 N N . GLY A 1 15 ? 4.012 0.698 -7.634 1.00 94.00 15 A 1 ATOM 119 C CA . GLY A 1 15 ? 5.378 0.514 -8.122 1.00 90.27 15 A 1 ATOM 120 C C . GLY A 1 15 ? 5.480 -0.402 -9.328 1.00 87.32 15 A 1 ATOM 121 O O . GLY A 1 15 ? 4.512 -1.117 -9.644 1.00 81.51 15 A 1 ATOM 122 O OXT . GLY A 1 15 ? 6.565 -0.395 -9.973 1.00 85.12 15 A 1 #