# 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_spkb33552 # _entry.id spkb33552 # 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" "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" "C3 H7 N O3" 105.093 SER y SERINE C([C@@H](C(=O)O)N)O ? "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 TRP 2 1 n LYS 3 1 n GLY 4 1 n PHE 5 1 n LEU 6 1 n CYS 7 1 n CYS 8 1 n LEU 9 1 n LEU 10 1 n VAL 11 1 n ALA 12 1 n GLY 13 1 n VAL 14 1 n THR 15 1 n SER 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 @ 2025-07-02 21:43:12)" _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 86.73 _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 79.42 1 1 A TRP 2 2 78.90 1 2 A LYS 3 2 84.01 1 3 A GLY 4 2 91.73 1 4 A PHE 5 2 86.43 1 5 A LEU 6 2 88.81 1 6 A CYS 7 2 90.59 1 7 A CYS 8 2 92.08 1 8 A LEU 9 2 90.55 1 9 A LEU 10 2 91.23 1 10 A VAL 11 2 92.73 1 11 A ALA 12 2 93.65 1 12 A GLY 13 2 93.70 1 13 A VAL 14 2 86.96 1 14 A THR 15 2 84.52 1 15 A SER 16 2 79.05 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 TRP . 2 A 2 A 3 1 n LYS . 3 A 3 A 4 1 n GLY . 4 A 4 A 5 1 n PHE . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n CYS . 7 A 7 A 8 1 n CYS . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n VAL . 11 A 11 A 12 1 n ALA . 12 A 12 A 13 1 n GLY . 13 A 13 A 14 1 n VAL . 14 A 14 A 15 1 n THR . 15 A 15 A 16 1 n SER . 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 ? -1.986 13.536 6.328 1.00 83.75 1 A 1 ATOM 2 C CA . MET A 1 1 ? -0.898 12.615 5.953 1.00 85.85 1 A 1 ATOM 3 C C . MET A 1 1 ? -1.452 11.386 5.236 1.00 87.95 1 A 1 ATOM 4 O O . MET A 1 1 ? -1.725 10.366 5.849 1.00 84.19 1 A 1 ATOM 5 C CB . MET A 1 1 ? -0.150 12.173 7.207 1.00 79.48 1 A 1 ATOM 6 C CG . MET A 1 1 ? 0.880 13.197 7.637 1.00 75.07 1 A 1 ATOM 7 S SD . MET A 1 1 ? 1.015 13.285 9.414 1.00 73.49 1 A 1 ATOM 8 C CE . MET A 1 1 ? 1.966 14.778 9.605 1.00 65.58 1 A 1 ATOM 9 N N . TRP A 1 2 ? -1.632 11.517 3.935 1.00 83.35 2 A 1 ATOM 10 C CA . TRP A 1 2 ? -2.191 10.440 3.122 1.00 86.36 2 A 1 ATOM 11 C C . TRP A 1 2 ? -1.098 9.490 2.648 1.00 89.48 2 A 1 ATOM 12 O O . TRP A 1 2 ? -1.333 8.311 2.418 1.00 86.28 2 A 1 ATOM 13 C CB . TRP A 1 2 ? -2.903 11.049 1.923 1.00 82.92 2 A 1 ATOM 14 C CG . TRP A 1 2 ? -3.552 12.365 2.235 1.00 78.96 2 A 1 ATOM 15 C CD1 . TRP A 1 2 ? -2.946 13.561 2.379 1.00 76.11 2 A 1 ATOM 16 C CD2 . TRP A 1 2 ? -4.964 12.595 2.456 1.00 79.76 2 A 1 ATOM 17 N NE1 . TRP A 1 2 ? -3.880 14.526 2.676 1.00 74.16 2 A 1 ATOM 18 C CE2 . TRP A 1 2 ? -5.131 13.961 2.729 1.00 79.30 2 A 1 ATOM 19 C CE3 . TRP A 1 2 ? -6.085 11.766 2.433 1.00 74.26 2 A 1 ATOM 20 C CZ2 . TRP A 1 2 ? -6.383 14.510 2.976 1.00 74.68 2 A 1 ATOM 21 C CZ3 . TRP A 1 2 ? -7.337 12.316 2.679 1.00 69.66 2 A 1 ATOM 22 C CH2 . TRP A 1 2 ? -7.479 13.678 2.952 1.00 69.31 2 A 1 ATOM 23 N N . LYS A 1 3 ? 0.095 10.005 2.508 1.00 91.30 3 A 1 ATOM 24 C CA . LYS A 1 3 ? 1.235 9.202 2.056 1.00 91.51 3 A 1 ATOM 25 C C . LYS A 1 3 ? 1.543 8.082 3.045 1.00 91.94 3 A 1 ATOM 26 O O . LYS A 1 3 ? 2.010 7.015 2.654 1.00 89.66 3 A 1 ATOM 27 C CB . LYS A 1 3 ? 2.456 10.098 1.885 1.00 89.83 3 A 1 ATOM 28 C CG . LYS A 1 3 ? 2.874 10.236 0.435 1.00 83.52 3 A 1 ATOM 29 C CD . LYS A 1 3 ? 3.930 9.216 0.071 1.00 80.40 3 A 1 ATOM 30 C CE . LYS A 1 3 ? 4.700 9.613 -1.177 1.00 73.35 3 A 1 ATOM 31 N NZ . LYS A 1 3 ? 6.031 8.951 -1.219 1.00 64.62 3 A 1 ATOM 32 N N . GLY A 1 4 ? 1.275 8.332 4.316 1.00 90.69 4 A 1 ATOM 33 C CA . GLY A 1 4 ? 1.520 7.335 5.355 1.00 91.34 4 A 1 ATOM 34 C C . GLY A 1 4 ? 0.714 6.074 5.124 1.00 93.51 4 A 1 ATOM 35 O O . GLY A 1 4 ? 1.252 4.970 5.095 1.00 91.36 4 A 1 ATOM 36 N N . PHE A 1 5 ? -0.603 6.244 4.946 1.00 86.57 5 A 1 ATOM 37 C CA . PHE A 1 5 ? -1.492 5.109 4.706 1.00 88.73 5 A 1 ATOM 38 C C . PHE A 1 5 ? -1.200 4.468 3.355 1.00 91.81 5 A 1 ATOM 39 O O . PHE A 1 5 ? -1.160 3.249 3.231 1.00 90.92 5 A 1 ATOM 40 C CB . PHE A 1 5 ? -2.941 5.578 4.750 1.00 88.52 5 A 1 ATOM 41 C CG . PHE A 1 5 ? -3.890 4.537 4.231 1.00 86.28 5 A 1 ATOM 42 C CD1 . PHE A 1 5 ? -4.058 3.343 4.908 1.00 83.91 5 A 1 ATOM 43 C CD2 . PHE A 1 5 ? -4.601 4.753 3.061 1.00 84.26 5 A 1 ATOM 44 C CE1 . PHE A 1 5 ? -4.932 2.380 4.426 1.00 83.14 5 A 1 ATOM 45 C CE2 . PHE A 1 5 ? -5.474 3.788 2.578 1.00 82.95 5 A 1 ATOM 46 C CZ . PHE A 1 5 ? -5.638 2.604 3.263 1.00 83.60 5 A 1 ATOM 47 N N . LEU A 1 6 ? -1.018 5.297 2.343 1.00 91.11 6 A 1 ATOM 48 C CA . LEU A 1 6 ? -0.735 4.808 0.997 1.00 91.66 6 A 1 ATOM 49 C C . LEU A 1 6 ? 0.580 4.044 0.969 1.00 93.12 6 A 1 ATOM 50 O O . LEU A 1 6 ? 0.715 3.029 0.295 1.00 92.08 6 A 1 ATOM 51 C CB . LEU A 1 6 ? -0.680 5.992 0.023 1.00 91.61 6 A 1 ATOM 52 C CG . LEU A 1 6 ? -1.606 5.835 -1.173 1.00 86.92 6 A 1 ATOM 53 C CD1 . LEU A 1 6 ? -1.240 4.590 -1.971 1.00 82.20 6 A 1 ATOM 54 C CD2 . LEU A 1 6 ? -3.045 5.754 -0.692 1.00 81.75 6 A 1 ATOM 55 N N . CYS A 1 7 ? 1.550 4.537 1.702 1.00 92.99 7 A 1 ATOM 56 C CA . CYS A 1 7 ? 2.864 3.895 1.768 1.00 92.94 7 A 1 ATOM 57 C C . CYS A 1 7 ? 2.752 2.514 2.403 1.00 94.28 7 A 1 ATOM 58 O O . CYS A 1 7 ? 3.335 1.549 1.920 1.00 91.79 7 A 1 ATOM 59 C CB . CYS A 1 7 ? 3.821 4.764 2.579 1.00 90.48 7 A 1 ATOM 60 S SG . CYS A 1 7 ? 5.491 4.095 2.589 1.00 81.06 7 A 1 ATOM 61 N N . CYS A 1 8 ? 1.994 2.428 3.486 1.00 92.87 8 A 1 ATOM 62 C CA . CYS A 1 8 ? 1.809 1.155 4.175 1.00 93.39 8 A 1 ATOM 63 C C . CYS A 1 8 ? 0.967 0.202 3.337 1.00 94.76 8 A 1 ATOM 64 O O . CYS A 1 8 ? 1.244 -0.988 3.267 1.00 92.54 8 A 1 ATOM 65 C CB . CYS A 1 8 ? 1.137 1.389 5.523 1.00 91.47 8 A 1 ATOM 66 S SG . CYS A 1 8 ? 2.251 1.059 6.904 1.00 87.47 8 A 1 ATOM 67 N N . LEU A 1 9 ? -0.074 0.743 2.709 1.00 92.05 9 A 1 ATOM 68 C CA . LEU A 1 9 ? -0.957 -0.063 1.869 1.00 93.00 9 A 1 ATOM 69 C C . LEU A 1 9 ? -0.223 -0.589 0.644 1.00 94.79 9 A 1 ATOM 70 O O . LEU A 1 9 ? -0.370 -1.749 0.273 1.00 94.08 9 A 1 ATOM 71 C CB . LEU A 1 9 ? -2.149 0.784 1.434 1.00 92.59 9 A 1 ATOM 72 C CG . LEU A 1 9 ? -3.223 -0.026 0.724 1.00 88.07 9 A 1 ATOM 73 C CD1 . LEU A 1 9 ? -4.046 -0.809 1.733 1.00 85.03 9 A 1 ATOM 74 C CD2 . LEU A 1 9 ? -4.116 0.894 -0.085 1.00 84.77 9 A 1 ATOM 75 N N . LEU A 1 10 ? 0.557 0.269 0.017 1.00 94.03 10 A 1 ATOM 76 C CA . LEU A 1 10 ? 1.312 -0.118 -1.174 1.00 93.65 10 A 1 ATOM 77 C C . LEU A 1 10 ? 2.380 -1.144 -0.837 1.00 94.71 10 A 1 ATOM 78 O O . LEU A 1 10 ? 2.528 -2.153 -1.525 1.00 93.74 10 A 1 ATOM 79 C CB . LEU A 1 10 ? 1.957 1.121 -1.794 1.00 93.43 10 A 1 ATOM 80 C CG . LEU A 1 10 ? 1.234 1.615 -3.042 1.00 90.00 10 A 1 ATOM 81 C CD1 . LEU A 1 10 ? 1.693 3.027 -3.390 1.00 85.26 10 A 1 ATOM 82 C CD2 . LEU A 1 10 ? 1.505 0.674 -4.203 1.00 85.04 10 A 1 ATOM 83 N N . VAL A 1 11 ? 3.125 -0.888 0.215 1.00 94.78 11 A 1 ATOM 84 C CA . VAL A 1 11 ? 4.190 -1.797 0.630 1.00 94.14 11 A 1 ATOM 85 C C . VAL A 1 11 ? 3.610 -3.088 1.185 1.00 94.66 11 A 1 ATOM 86 O O . VAL A 1 11 ? 4.101 -4.176 0.887 1.00 93.28 11 A 1 ATOM 87 C CB . VAL A 1 11 ? 5.082 -1.134 1.688 1.00 92.70 11 A 1 ATOM 88 C CG1 . VAL A 1 11 ? 6.181 -2.086 2.124 1.00 89.21 11 A 1 ATOM 89 C CG2 . VAL A 1 11 ? 5.700 0.140 1.124 1.00 90.35 11 A 1 ATOM 90 N N . ALA A 1 12 ? 2.576 -2.970 1.990 1.00 94.21 12 A 1 ATOM 91 C CA . ALA A 1 12 ? 1.942 -4.143 2.589 1.00 94.01 12 A 1 ATOM 92 C C . ALA A 1 12 ? 1.174 -4.942 1.545 1.00 95.12 12 A 1 ATOM 93 O O . ALA A 1 12 ? 1.148 -6.166 1.582 1.00 92.94 12 A 1 ATOM 94 C CB . ALA A 1 12 ? 1.003 -3.706 3.704 1.00 91.99 12 A 1 ATOM 95 N N . GLY A 1 13 ? 0.538 -4.243 0.615 1.00 93.89 13 A 1 ATOM 96 C CA . GLY A 1 13 ? -0.222 -4.905 -0.440 1.00 93.80 13 A 1 ATOM 97 C C . GLY A 1 13 ? 0.673 -5.645 -1.408 1.00 94.63 13 A 1 ATOM 98 O O . GLY A 1 13 ? 0.353 -6.743 -1.853 1.00 92.48 13 A 1 ATOM 99 N N . VAL A 1 14 ? 1.801 -5.055 -1.738 1.00 90.69 14 A 1 ATOM 100 C CA . VAL A 1 14 ? 2.753 -5.664 -2.666 1.00 90.32 14 A 1 ATOM 101 C C . VAL A 1 14 ? 3.654 -6.657 -1.948 1.00 91.55 14 A 1 ATOM 102 O O . VAL A 1 14 ? 4.531 -7.271 -2.548 1.00 87.40 14 A 1 ATOM 103 C CB . VAL A 1 14 ? 3.605 -4.583 -3.337 1.00 87.00 14 A 1 ATOM 104 C CG1 . VAL A 1 14 ? 4.565 -5.198 -4.340 1.00 79.97 14 A 1 ATOM 105 C CG2 . VAL A 1 14 ? 2.706 -3.579 -4.032 1.00 81.81 14 A 1 ATOM 106 N N . THR A 1 15 ? 3.420 -6.833 -0.675 1.00 90.35 15 A 1 ATOM 107 C CA . THR A 1 15 ? 4.241 -7.731 0.140 1.00 88.75 15 A 1 ATOM 108 C C . THR A 1 15 ? 4.435 -9.068 -0.560 1.00 87.92 15 A 1 ATOM 109 O O . THR A 1 15 ? 3.535 -9.583 -1.222 1.00 82.28 15 A 1 ATOM 110 C CB . THR A 1 15 ? 3.588 -7.959 1.506 1.00 85.20 15 A 1 ATOM 111 O OG1 . THR A 1 15 ? 4.537 -8.576 2.382 1.00 79.28 15 A 1 ATOM 112 C CG2 . THR A 1 15 ? 2.378 -8.864 1.390 1.00 77.89 15 A 1 ATOM 113 N N . SER A 1 16 ? 5.613 -9.625 -0.405 1.00 87.25 16 A 1 ATOM 114 C CA . SER A 1 16 ? 5.931 -10.896 -1.050 1.00 84.97 16 A 1 ATOM 115 C C . SER A 1 16 ? 6.009 -12.014 -0.023 1.00 82.44 16 A 1 ATOM 116 O O . SER A 1 16 ? 6.958 -12.029 0.767 1.00 75.30 16 A 1 ATOM 117 C CB . SER A 1 16 ? 7.255 -10.790 -1.784 1.00 79.04 16 A 1 ATOM 118 O OG . SER A 1 16 ? 7.260 -9.692 -2.654 1.00 71.67 16 A 1 ATOM 119 O OXT . SER A 1 16 ? 5.117 -12.880 -0.020 1.00 72.65 16 A 1 #