# 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_spkb38064 # _entry.id spkb38064 # 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 "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" "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" "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" "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 LYS 2 1 n LYS 3 1 n THR 4 1 n ILE 5 1 n ILE 6 1 n SER 7 1 n THR 8 1 n LEU 9 1 n VAL 10 1 n ILE 11 1 n GLY 12 1 n LEU 13 1 n VAL 14 1 n SER 15 1 n GLY 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 @ 2025-07-09 06:43:52)" _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 94.69 _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 89.49 1 1 A LYS 2 2 91.73 1 2 A LYS 3 2 92.01 1 3 A THR 4 2 96.75 1 4 A ILE 5 2 96.34 1 5 A ILE 6 2 96.23 1 6 A SER 7 2 95.67 1 7 A THR 8 2 96.29 1 8 A LEU 9 2 96.38 1 9 A VAL 10 2 97.44 1 10 A ILE 11 2 96.94 1 11 A GLY 12 2 97.61 1 12 A LEU 13 2 95.31 1 13 A VAL 14 2 96.58 1 14 A SER 15 2 93.89 1 15 A GLY 16 2 86.69 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 LYS . 2 A 2 A 3 1 n LYS . 3 A 3 A 4 1 n THR . 4 A 4 A 5 1 n ILE . 5 A 5 A 6 1 n ILE . 6 A 6 A 7 1 n SER . 7 A 7 A 8 1 n THR . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n VAL . 10 A 10 A 11 1 n ILE . 11 A 11 A 12 1 n GLY . 12 A 12 A 13 1 n LEU . 13 A 13 A 14 1 n VAL . 14 A 14 A 15 1 n SER . 15 A 15 A 16 1 n GLY . 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 ? -4.627 4.925 8.829 1.00 95.11 1 A 1 ATOM 2 C CA . MET A 1 1 ? -3.641 5.987 8.572 1.00 96.11 1 A 1 ATOM 3 C C . MET A 1 1 ? -3.402 6.140 7.072 1.00 95.85 1 A 1 ATOM 4 O O . MET A 1 1 ? -3.650 5.216 6.303 1.00 92.90 1 A 1 ATOM 5 C CB . MET A 1 1 ? -2.315 5.668 9.270 1.00 92.80 1 A 1 ATOM 6 C CG . MET A 1 1 ? -2.460 5.575 10.781 1.00 86.74 1 A 1 ATOM 7 S SD . MET A 1 1 ? -0.924 5.117 11.601 1.00 82.37 1 A 1 ATOM 8 C CE . MET A 1 1 ? -1.463 5.123 13.304 1.00 74.04 1 A 1 ATOM 9 N N . LYS A 1 2 ? -2.915 7.312 6.659 1.00 97.54 2 A 1 ATOM 10 C CA . LYS A 1 2 ? -2.665 7.588 5.238 1.00 97.68 2 A 1 ATOM 11 C C . LYS A 1 2 ? -1.619 6.641 4.653 1.00 97.79 2 A 1 ATOM 12 O O . LYS A 1 2 ? -1.742 6.189 3.516 1.00 97.14 2 A 1 ATOM 13 C CB . LYS A 1 2 ? -2.224 9.039 5.064 1.00 96.81 2 A 1 ATOM 14 C CG . LYS A 1 2 ? -3.353 10.025 5.349 1.00 92.05 2 A 1 ATOM 15 C CD . LYS A 1 2 ? -2.933 11.461 5.089 1.00 89.06 2 A 1 ATOM 16 C CE . LYS A 1 2 ? -1.980 11.972 6.150 1.00 81.73 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? -1.724 13.424 5.988 1.00 75.74 2 A 1 ATOM 18 N N . LYS A 1 3 ? -0.597 6.321 5.430 1.00 97.69 3 A 1 ATOM 19 C CA . LYS A 1 3 ? 0.470 5.425 4.976 1.00 98.11 3 A 1 ATOM 20 C C . LYS A 1 3 ? -0.049 4.007 4.731 1.00 98.31 3 A 1 ATOM 21 O O . LYS A 1 3 ? 0.458 3.299 3.863 1.00 97.86 3 A 1 ATOM 22 C CB . LYS A 1 3 ? 1.618 5.415 5.983 1.00 97.61 3 A 1 ATOM 23 C CG . LYS A 1 3 ? 2.297 6.775 6.086 1.00 92.83 3 A 1 ATOM 24 C CD . LYS A 1 3 ? 3.577 6.706 6.896 1.00 89.08 3 A 1 ATOM 25 C CE . LYS A 1 3 ? 4.269 8.061 6.923 1.00 81.98 3 A 1 ATOM 26 N NZ . LYS A 1 3 ? 5.611 7.980 7.544 1.00 74.62 3 A 1 ATOM 27 N N . THR A 1 4 ? -1.056 3.604 5.457 1.00 98.02 4 A 1 ATOM 28 C CA . THR A 1 4 ? -1.665 2.286 5.286 1.00 98.15 4 A 1 ATOM 29 C C . THR A 1 4 ? -2.332 2.186 3.915 1.00 98.24 4 A 1 ATOM 30 O O . THR A 1 4 ? -2.235 1.162 3.238 1.00 97.77 4 A 1 ATOM 31 C CB . THR A 1 4 ? -2.705 2.022 6.383 1.00 98.07 4 A 1 ATOM 32 O OG1 . THR A 1 4 ? -2.120 2.251 7.664 1.00 94.65 4 A 1 ATOM 33 C CG2 . THR A 1 4 ? -3.206 0.591 6.323 1.00 92.35 4 A 1 ATOM 34 N N . ILE A 1 5 ? -2.989 3.259 3.493 1.00 97.75 5 A 1 ATOM 35 C CA . ILE A 1 5 ? -3.645 3.309 2.191 1.00 97.79 5 A 1 ATOM 36 C C . ILE A 1 5 ? -2.606 3.219 1.077 1.00 97.67 5 A 1 ATOM 37 O O . ILE A 1 5 ? -2.773 2.470 0.110 1.00 97.17 5 A 1 ATOM 38 C CB . ILE A 1 5 ? -4.478 4.595 2.050 1.00 97.82 5 A 1 ATOM 39 C CG1 . ILE A 1 5 ? -5.582 4.631 3.119 1.00 95.91 5 A 1 ATOM 40 C CG2 . ILE A 1 5 ? -5.082 4.688 0.650 1.00 95.53 5 A 1 ATOM 41 C CD1 . ILE A 1 5 ? -6.299 5.973 3.199 1.00 91.05 5 A 1 ATOM 42 N N . ILE A 1 6 ? -1.522 3.973 1.221 1.00 98.14 6 A 1 ATOM 43 C CA . ILE A 1 6 ? -0.448 3.977 0.229 1.00 97.97 6 A 1 ATOM 44 C C . ILE A 1 6 ? 0.177 2.592 0.113 1.00 97.65 6 A 1 ATOM 45 O O . ILE A 1 6 ? 0.428 2.100 -0.988 1.00 97.23 6 A 1 ATOM 46 C CB . ILE A 1 6 ? 0.617 5.028 0.590 1.00 97.95 6 A 1 ATOM 47 C CG1 . ILE A 1 6 ? 0.004 6.443 0.618 1.00 95.86 6 A 1 ATOM 48 C CG2 . ILE A 1 6 ? 1.784 4.976 -0.400 1.00 95.10 6 A 1 ATOM 49 C CD1 . ILE A 1 6 ? -0.606 6.874 -0.713 1.00 89.91 6 A 1 ATOM 50 N N . SER A 1 7 ? 0.409 1.950 1.241 1.00 97.98 7 A 1 ATOM 51 C CA . SER A 1 7 ? 0.987 0.606 1.261 1.00 97.75 7 A 1 ATOM 52 C C . SER A 1 7 ? 0.090 -0.383 0.519 1.00 97.86 7 A 1 ATOM 53 O O . SER A 1 7 ? 0.565 -1.203 -0.262 1.00 97.52 7 A 1 ATOM 54 C CB . SER A 1 7 ? 1.193 0.148 2.703 1.00 97.20 7 A 1 ATOM 55 O OG . SER A 1 7 ? 1.794 -1.130 2.731 1.00 85.74 7 A 1 ATOM 56 N N . THR A 1 8 ? -1.206 -0.286 0.743 1.00 97.86 8 A 1 ATOM 57 C CA . THR A 1 8 ? -2.174 -1.158 0.083 1.00 97.82 8 A 1 ATOM 58 C C . THR A 1 8 ? -2.153 -0.946 -1.430 1.00 97.89 8 A 1 ATOM 59 O O . THR A 1 8 ? -2.208 -1.911 -2.199 1.00 97.32 8 A 1 ATOM 60 C CB . THR A 1 8 ? -3.584 -0.894 0.623 1.00 97.66 8 A 1 ATOM 61 O OG1 . THR A 1 8 ? -3.598 -1.077 2.033 1.00 93.54 8 A 1 ATOM 62 C CG2 . THR A 1 8 ? -4.594 -1.854 0.006 1.00 91.96 8 A 1 ATOM 63 N N . LEU A 1 9 ? -2.057 0.303 -1.854 1.00 97.81 9 A 1 ATOM 64 C CA . LEU A 1 9 ? -2.010 0.631 -3.275 1.00 97.78 9 A 1 ATOM 65 C C . LEU A 1 9 ? -0.748 0.075 -3.928 1.00 97.94 9 A 1 ATOM 66 O O . LEU A 1 9 ? -0.807 -0.469 -5.034 1.00 97.54 9 A 1 ATOM 67 C CB . LEU A 1 9 ? -2.067 2.149 -3.460 1.00 97.69 9 A 1 ATOM 68 C CG . LEU A 1 9 ? -3.429 2.767 -3.139 1.00 96.02 9 A 1 ATOM 69 C CD1 . LEU A 1 9 ? -3.332 4.285 -3.132 1.00 92.72 9 A 1 ATOM 70 C CD2 . LEU A 1 9 ? -4.476 2.328 -4.161 1.00 93.56 9 A 1 ATOM 71 N N . VAL A 1 10 ? 0.383 0.201 -3.252 1.00 98.14 10 A 1 ATOM 72 C CA . VAL A 1 10 ? 1.656 -0.297 -3.773 1.00 98.17 10 A 1 ATOM 73 C C . VAL A 1 10 ? 1.615 -1.815 -3.924 1.00 98.17 10 A 1 ATOM 74 O O . VAL A 1 10 ? 2.020 -2.357 -4.953 1.00 97.76 10 A 1 ATOM 75 C CB . VAL A 1 10 ? 2.822 0.124 -2.865 1.00 97.88 10 A 1 ATOM 76 C CG1 . VAL A 1 10 ? 4.128 -0.522 -3.308 1.00 96.00 10 A 1 ATOM 77 C CG2 . VAL A 1 10 ? 2.976 1.638 -2.882 1.00 95.94 10 A 1 ATOM 78 N N . ILE A 1 11 ? 1.119 -2.500 -2.908 1.00 98.33 11 A 1 ATOM 79 C CA . ILE A 1 11 ? 1.010 -3.960 -2.947 1.00 98.17 11 A 1 ATOM 80 C C . ILE A 1 11 ? 0.078 -4.393 -4.076 1.00 98.02 11 A 1 ATOM 81 O O . ILE A 1 11 ? 0.374 -5.338 -4.810 1.00 97.43 11 A 1 ATOM 82 C CB . ILE A 1 11 ? 0.514 -4.503 -1.595 1.00 97.92 11 A 1 ATOM 83 C CG1 . ILE A 1 11 ? 1.557 -4.235 -0.499 1.00 96.44 11 A 1 ATOM 84 C CG2 . ILE A 1 11 ? 0.228 -6.004 -1.692 1.00 96.17 11 A 1 ATOM 85 C CD1 . ILE A 1 11 ? 1.018 -4.447 0.910 1.00 93.03 11 A 1 ATOM 86 N N . GLY A 1 12 ? -1.032 -3.697 -4.221 1.00 97.91 12 A 1 ATOM 87 C CA . GLY A 1 12 ? -1.984 -3.998 -5.283 1.00 97.60 12 A 1 ATOM 88 C C . GLY A 1 12 ? -1.388 -3.794 -6.667 1.00 97.79 12 A 1 ATOM 89 O O . GLY A 1 12 ? -1.633 -4.586 -7.578 1.00 97.12 12 A 1 ATOM 90 N N . LEU A 1 13 ? -0.595 -2.747 -6.825 1.00 97.87 13 A 1 ATOM 91 C CA . LEU A 1 13 ? 0.053 -2.439 -8.101 1.00 97.83 13 A 1 ATOM 92 C C . LEU A 1 13 ? 1.093 -3.492 -8.465 1.00 98.00 13 A 1 ATOM 93 O O . LEU A 1 13 ? 1.173 -3.923 -9.619 1.00 97.01 13 A 1 ATOM 94 C CB . LEU A 1 13 ? 0.710 -1.055 -8.023 1.00 97.40 13 A 1 ATOM 95 C CG . LEU A 1 13 ? 1.358 -0.597 -9.332 1.00 94.09 13 A 1 ATOM 96 C CD1 . LEU A 1 13 ? 0.304 -0.392 -10.413 1.00 89.90 13 A 1 ATOM 97 C CD2 . LEU A 1 13 ? 2.126 0.698 -9.111 1.00 90.35 13 A 1 ATOM 98 N N . VAL A 1 14 ? 1.898 -3.905 -7.494 1.00 97.95 14 A 1 ATOM 99 C CA . VAL A 1 14 ? 2.945 -4.906 -7.723 1.00 97.85 14 A 1 ATOM 100 C C . VAL A 1 14 ? 2.347 -6.293 -7.915 1.00 97.86 14 A 1 ATOM 101 O O . VAL A 1 14 ? 2.797 -7.061 -8.772 1.00 96.84 14 A 1 ATOM 102 C CB . VAL A 1 14 ? 3.952 -4.912 -6.559 1.00 97.14 14 A 1 ATOM 103 C CG1 . VAL A 1 14 ? 4.975 -6.025 -6.723 1.00 94.05 14 A 1 ATOM 104 C CG2 . VAL A 1 14 ? 4.667 -3.575 -6.475 1.00 94.36 14 A 1 ATOM 105 N N . SER A 1 15 ? 1.349 -6.620 -7.133 1.00 97.27 15 A 1 ATOM 106 C CA . SER A 1 15 ? 0.712 -7.935 -7.189 1.00 96.82 15 A 1 ATOM 107 C C . SER A 1 15 ? -0.164 -8.086 -8.431 1.00 96.57 15 A 1 ATOM 108 O O . SER A 1 15 ? -0.206 -9.159 -9.038 1.00 92.89 15 A 1 ATOM 109 C CB . SER A 1 15 ? -0.122 -8.159 -5.931 1.00 94.85 15 A 1 ATOM 110 O OG . SER A 1 15 ? -0.689 -9.447 -5.938 1.00 84.94 15 A 1 ATOM 111 N N . GLY A 1 16 ? -0.871 -7.019 -8.787 1.00 92.75 16 A 1 ATOM 112 C CA . GLY A 1 16 ? -1.772 -7.028 -9.939 1.00 90.22 16 A 1 ATOM 113 C C . GLY A 1 16 ? -1.032 -6.900 -11.255 1.00 87.16 16 A 1 ATOM 114 O O . GLY A 1 16 ? -1.224 -7.757 -12.132 1.00 78.03 16 A 1 ATOM 115 O OXT . GLY A 1 16 ? -0.279 -5.922 -11.404 1.00 85.27 16 A 1 #