# 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_spkb10649 # _entry.id spkb10649 # 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" "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" "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" "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" "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 TRP 2 1 n GLY 3 1 n LEU 4 1 n LYS 5 1 n VAL 6 1 n LEU 7 1 n LEU 8 1 n LEU 9 1 n PRO 10 1 n VAL 11 1 n VAL 12 1 n SER 13 1 n PHE 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 @ 2025-07-08 04:50:00)" _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 90.00 _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 80.60 1 1 A TRP 2 2 82.93 1 2 A GLY 3 2 94.39 1 3 A LEU 4 2 90.67 1 4 A LYS 5 2 88.68 1 5 A VAL 6 2 93.69 1 6 A LEU 7 2 92.07 1 7 A LEU 8 2 92.92 1 8 A LEU 9 2 91.72 1 9 A PRO 10 2 94.75 1 10 A VAL 11 2 93.37 1 11 A VAL 12 2 93.71 1 12 A SER 13 2 94.47 1 13 A PHE 14 2 88.64 1 14 A ALA 15 2 88.06 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 TRP . 2 A 2 A 3 1 n GLY . 3 A 3 A 4 1 n LEU . 4 A 4 A 5 1 n LYS . 5 A 5 A 6 1 n VAL . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n PRO . 10 A 10 A 11 1 n VAL . 11 A 11 A 12 1 n VAL . 12 A 12 A 13 1 n SER . 13 A 13 A 14 1 n PHE . 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 ? -0.613 2.701 14.404 1.00 84.92 1 A 1 ATOM 2 C CA . MET A 1 1 ? 0.477 2.868 13.416 1.00 86.90 1 A 1 ATOM 3 C C . MET A 1 1 ? -0.065 3.358 12.074 1.00 87.80 1 A 1 ATOM 4 O O . MET A 1 1 ? -0.855 2.672 11.440 1.00 85.85 1 A 1 ATOM 5 C CB . MET A 1 1 ? 1.187 1.531 13.206 1.00 81.15 1 A 1 ATOM 6 C CG . MET A 1 1 ? 2.116 1.193 14.363 1.00 76.84 1 A 1 ATOM 7 S SD . MET A 1 1 ? 2.978 -0.360 14.100 1.00 74.27 1 A 1 ATOM 8 C CE . MET A 1 1 ? 4.160 -0.288 15.446 1.00 67.06 1 A 1 ATOM 9 N N . TRP A 1 2 ? 0.352 4.545 11.630 1.00 85.12 2 A 1 ATOM 10 C CA . TRP A 1 2 ? -0.090 5.127 10.361 1.00 88.14 2 A 1 ATOM 11 C C . TRP A 1 2 ? 1.114 5.456 9.469 1.00 89.99 2 A 1 ATOM 12 O O . TRP A 1 2 ? 1.327 6.602 9.085 1.00 87.70 2 A 1 ATOM 13 C CB . TRP A 1 2 ? -0.912 6.386 10.633 1.00 86.17 2 A 1 ATOM 14 C CG . TRP A 1 2 ? -2.252 6.114 11.248 1.00 83.78 2 A 1 ATOM 15 C CD1 . TRP A 1 2 ? -2.572 6.217 12.558 1.00 82.35 2 A 1 ATOM 16 C CD2 . TRP A 1 2 ? -3.466 5.698 10.565 1.00 83.72 2 A 1 ATOM 17 N NE1 . TRP A 1 2 ? -3.903 5.896 12.744 1.00 80.10 2 A 1 ATOM 18 C CE2 . TRP A 1 2 ? -4.475 5.569 11.533 1.00 82.85 2 A 1 ATOM 19 C CE3 . TRP A 1 2 ? -3.768 5.441 9.225 1.00 80.51 2 A 1 ATOM 20 C CZ2 . TRP A 1 2 ? -5.776 5.186 11.195 1.00 79.24 2 A 1 ATOM 21 C CZ3 . TRP A 1 2 ? -5.064 5.059 8.895 1.00 76.14 2 A 1 ATOM 22 C CH2 . TRP A 1 2 ? -6.053 4.932 9.873 1.00 75.23 2 A 1 ATOM 23 N N . GLY A 1 3 ? 1.928 4.446 9.134 1.00 93.21 3 A 1 ATOM 24 C CA . GLY A 1 3 ? 3.118 4.664 8.309 1.00 94.38 3 A 1 ATOM 25 C C . GLY A 1 3 ? 3.341 3.549 7.299 1.00 95.32 3 A 1 ATOM 26 O O . GLY A 1 3 ? 4.188 3.653 6.420 1.00 94.66 3 A 1 ATOM 27 N N . LEU A 1 4 ? 2.583 2.473 7.423 1.00 93.61 4 A 1 ATOM 28 C CA . LEU A 1 4 ? 2.706 1.331 6.516 1.00 93.97 4 A 1 ATOM 29 C C . LEU A 1 4 ? 1.456 1.172 5.657 1.00 94.73 4 A 1 ATOM 30 O O . LEU A 1 4 ? 1.544 0.899 4.463 1.00 93.34 4 A 1 ATOM 31 C CB . LEU A 1 4 ? 2.945 0.058 7.335 1.00 92.88 4 A 1 ATOM 32 C CG . LEU A 1 4 ? 4.304 0.036 8.036 1.00 89.81 4 A 1 ATOM 33 C CD1 . LEU A 1 4 ? 4.360 -1.115 9.031 1.00 84.39 4 A 1 ATOM 34 C CD2 . LEU A 1 4 ? 5.429 -0.104 7.020 1.00 82.65 4 A 1 ATOM 35 N N . LYS A 1 5 ? 0.284 1.342 6.255 1.00 93.99 5 A 1 ATOM 36 C CA . LYS A 1 5 ? -0.980 1.201 5.527 1.00 94.08 5 A 1 ATOM 37 C C . LYS A 1 5 ? -1.179 2.366 4.559 1.00 94.39 5 A 1 ATOM 38 O O . LYS A 1 5 ? -1.717 2.189 3.468 1.00 94.02 5 A 1 ATOM 39 C CB . LYS A 1 5 ? -2.142 1.148 6.521 1.00 93.30 5 A 1 ATOM 40 C CG . LYS A 1 5 ? -2.097 -0.103 7.385 1.00 88.44 5 A 1 ATOM 41 C CD . LYS A 1 5 ? -3.113 -0.031 8.509 1.00 85.16 5 A 1 ATOM 42 C CE . LYS A 1 5 ? -3.010 -1.253 9.406 1.00 80.26 5 A 1 ATOM 43 N NZ . LYS A 1 5 ? -3.887 -1.104 10.598 1.00 74.48 5 A 1 ATOM 44 N N . VAL A 1 6 ? -0.740 3.541 4.951 1.00 95.13 6 A 1 ATOM 45 C CA . VAL A 1 6 ? -0.879 4.739 4.113 1.00 95.12 6 A 1 ATOM 46 C C . VAL A 1 6 ? 0.167 4.752 2.996 1.00 95.58 6 A 1 ATOM 47 O O . VAL A 1 6 ? -0.032 5.366 1.946 1.00 94.67 6 A 1 ATOM 48 C CB . VAL A 1 6 ? -0.747 6.011 4.967 1.00 94.13 6 A 1 ATOM 49 C CG1 . VAL A 1 6 ? -0.939 7.257 4.113 1.00 90.59 6 A 1 ATOM 50 C CG2 . VAL A 1 6 ? -1.768 5.994 6.094 1.00 90.60 6 A 1 ATOM 51 N N . LEU A 1 7 ? 1.285 4.067 3.209 1.00 94.72 7 A 1 ATOM 52 C CA . LEU A 1 7 ? 2.361 4.021 2.219 1.00 94.45 7 A 1 ATOM 53 C C . LEU A 1 7 ? 2.348 2.711 1.432 1.00 95.39 7 A 1 ATOM 54 O O . LEU A 1 7 ? 3.129 2.542 0.497 1.00 94.68 7 A 1 ATOM 55 C CB . LEU A 1 7 ? 3.708 4.188 2.928 1.00 94.12 7 A 1 ATOM 56 C CG . LEU A 1 7 ? 3.930 5.585 3.505 1.00 89.99 7 A 1 ATOM 57 C CD1 . LEU A 1 7 ? 5.085 5.570 4.500 1.00 86.53 7 A 1 ATOM 58 C CD2 . LEU A 1 7 ? 4.233 6.575 2.387 1.00 86.68 7 A 1 ATOM 59 N N . LEU A 1 8 ? 1.472 1.800 1.795 1.00 94.85 8 A 1 ATOM 60 C CA . LEU A 1 8 ? 1.387 0.506 1.119 1.00 94.95 8 A 1 ATOM 61 C C . LEU A 1 8 ? 0.327 0.520 0.027 1.00 95.56 8 A 1 ATOM 62 O O . LEU A 1 8 ? 0.545 0.005 -1.066 1.00 95.01 8 A 1 ATOM 63 C CB . LEU A 1 8 ? 1.071 -0.587 2.146 1.00 94.54 8 A 1 ATOM 64 C CG . LEU A 1 8 ? 2.316 -1.131 2.850 1.00 91.31 8 A 1 ATOM 65 C CD1 . LEU A 1 8 ? 1.920 -1.895 4.110 1.00 88.48 8 A 1 ATOM 66 C CD2 . LEU A 1 8 ? 3.095 -2.044 1.922 1.00 88.69 8 A 1 ATOM 67 N N . LEU A 1 9 ? -0.814 1.108 0.319 1.00 94.92 9 A 1 ATOM 68 C CA . LEU A 1 9 ? -1.912 1.169 -0.648 1.00 94.66 9 A 1 ATOM 69 C C . LEU A 1 9 ? -1.522 1.933 -1.920 1.00 95.25 9 A 1 ATOM 70 O O . LEU A 1 9 ? -1.660 1.401 -3.023 1.00 94.31 9 A 1 ATOM 71 C CB . LEU A 1 9 ? -3.136 1.819 0.007 1.00 93.97 9 A 1 ATOM 72 C CG . LEU A 1 9 ? -4.443 1.505 -0.717 1.00 89.29 9 A 1 ATOM 73 C CD1 . LEU A 1 9 ? -4.967 0.136 -0.297 1.00 85.95 9 A 1 ATOM 74 C CD2 . LEU A 1 9 ? -5.489 2.571 -0.400 1.00 85.40 9 A 1 ATOM 75 N N . PRO A 1 10 ? -1.047 3.179 -1.811 1.00 95.74 10 A 1 ATOM 76 C CA . PRO A 1 10 ? -0.683 3.975 -2.992 1.00 95.22 10 A 1 ATOM 77 C C . PRO A 1 10 ? 0.590 3.497 -3.676 1.00 95.82 10 A 1 ATOM 78 O O . PRO A 1 10 ? 0.690 3.534 -4.901 1.00 94.57 10 A 1 ATOM 79 C CB . PRO A 1 10 ? -0.496 5.389 -2.425 1.00 93.84 10 A 1 ATOM 80 C CG . PRO A 1 10 ? -0.129 5.182 -0.997 1.00 92.83 10 A 1 ATOM 81 C CD . PRO A 1 10 ? -0.838 3.917 -0.559 1.00 95.23 10 A 1 ATOM 82 N N . VAL A 1 11 ? 1.568 3.053 -2.920 1.00 95.31 11 A 1 ATOM 83 C CA . VAL A 1 11 ? 2.843 2.592 -3.477 1.00 94.86 11 A 1 ATOM 84 C C . VAL A 1 11 ? 2.683 1.254 -4.192 1.00 95.34 11 A 1 ATOM 85 O O . VAL A 1 11 ? 3.246 1.045 -5.267 1.00 94.07 11 A 1 ATOM 86 C CB . VAL A 1 11 ? 3.897 2.469 -2.366 1.00 93.79 11 A 1 ATOM 87 C CG1 . VAL A 1 11 ? 5.209 1.943 -2.932 1.00 89.94 11 A 1 ATOM 88 C CG2 . VAL A 1 11 ? 4.123 3.822 -1.710 1.00 90.25 11 A 1 ATOM 89 N N . VAL A 1 12 ? 1.922 0.350 -3.613 1.00 95.82 12 A 1 ATOM 90 C CA . VAL A 1 12 ? 1.705 -0.977 -4.201 1.00 95.06 12 A 1 ATOM 91 C C . VAL A 1 12 ? 0.904 -0.869 -5.494 1.00 95.47 12 A 1 ATOM 92 O O . VAL A 1 12 ? 1.109 -1.645 -6.426 1.00 94.55 12 A 1 ATOM 93 C CB . VAL A 1 12 ? 0.971 -1.890 -3.205 1.00 94.02 12 A 1 ATOM 94 C CG1 . VAL A 1 12 ? 0.602 -3.218 -3.855 1.00 90.55 12 A 1 ATOM 95 C CG2 . VAL A 1 12 ? 1.850 -2.141 -1.990 1.00 90.51 12 A 1 ATOM 96 N N . SER A 1 13 ? 0.007 0.082 -5.577 1.00 96.12 13 A 1 ATOM 97 C CA . SER A 1 13 ? -0.824 0.280 -6.767 1.00 95.99 13 A 1 ATOM 98 C C . SER A 1 13 ? 0.029 0.672 -7.976 1.00 96.18 13 A 1 ATOM 99 O O . SER A 1 13 ? -0.298 0.348 -9.114 1.00 94.95 13 A 1 ATOM 100 C CB . SER A 1 13 ? -1.863 1.368 -6.502 1.00 94.83 13 A 1 ATOM 101 O OG . SER A 1 13 ? -2.758 1.456 -7.587 1.00 88.76 13 A 1 ATOM 102 N N . PHE A 1 14 ? 1.121 1.368 -7.739 1.00 93.58 14 A 1 ATOM 103 C CA . PHE A 1 14 ? 2.018 1.801 -8.817 1.00 93.00 14 A 1 ATOM 104 C C . PHE A 1 14 ? 2.990 0.688 -9.217 1.00 94.30 14 A 1 ATOM 105 O O . PHE A 1 14 ? 3.450 0.637 -10.356 1.00 92.37 14 A 1 ATOM 106 C CB . PHE A 1 14 ? 2.796 3.033 -8.359 1.00 90.99 14 A 1 ATOM 107 C CG . PHE A 1 14 ? 3.459 3.746 -9.499 1.00 88.37 14 A 1 ATOM 108 C CD1 . PHE A 1 14 ? 2.731 4.604 -10.311 1.00 85.64 14 A 1 ATOM 109 C CD2 . PHE A 1 14 ? 4.806 3.557 -9.764 1.00 85.34 14 A 1 ATOM 110 C CE1 . PHE A 1 14 ? 3.338 5.260 -11.373 1.00 84.33 14 A 1 ATOM 111 C CE2 . PHE A 1 14 ? 5.422 4.211 -10.832 1.00 83.11 14 A 1 ATOM 112 C CZ . PHE A 1 14 ? 4.684 5.063 -11.635 1.00 84.05 14 A 1 ATOM 113 N N . ALA A 1 15 ? 3.291 -0.200 -8.289 1.00 92.89 15 A 1 ATOM 114 C CA . ALA A 1 15 ? 4.222 -1.298 -8.539 1.00 91.11 15 A 1 ATOM 115 C C . ALA A 1 15 ? 3.701 -2.603 -7.933 1.00 90.04 15 A 1 ATOM 116 O O . ALA A 1 15 ? 2.988 -2.558 -6.928 1.00 86.62 15 A 1 ATOM 117 C CB . ALA A 1 15 ? 5.590 -0.963 -7.962 1.00 87.11 15 A 1 ATOM 118 O OXT . ALA A 1 15 ? 4.019 -3.690 -8.420 1.00 80.56 15 A 1 #