# 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_spkb33585 # _entry.id spkb33585 # 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 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" "C9 H11 N O2" 165.189 PHE y PHENYLALANINE c1ccc(cc1)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 LYS 2 1 n VAL 3 1 n LEU 4 1 n ILE 5 1 n VAL 6 1 n LEU 7 1 n LEU 8 1 n LEU 9 1 n GLY 10 1 n LEU 11 1 n ALA 12 1 n PHE 13 1 n VAL 14 1 n LEU 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 @ 2025-07-12 00:38:53)" _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 95.66 _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 88.77 1 1 A LYS 2 2 92.81 1 2 A VAL 3 2 97.03 1 3 A LEU 4 2 95.75 1 4 A ILE 5 2 97.04 1 5 A VAL 6 2 98.12 1 6 A LEU 7 2 96.80 1 7 A LEU 8 2 96.52 1 8 A LEU 9 2 96.47 1 9 A GLY 10 2 98.37 1 10 A LEU 11 2 96.06 1 11 A ALA 12 2 98.32 1 12 A PHE 13 2 96.23 1 13 A VAL 14 2 97.21 1 14 A LEU 15 2 95.41 1 15 A ALA 16 2 91.90 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 VAL . 3 A 3 A 4 1 n LEU . 4 A 4 A 5 1 n ILE . 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 GLY . 10 A 10 A 11 1 n LEU . 11 A 11 A 12 1 n ALA . 12 A 12 A 13 1 n PHE . 13 A 13 A 14 1 n VAL . 14 A 14 A 15 1 n LEU . 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 ? -14.035 4.478 3.391 1.00 93.60 1 A 1 ATOM 2 C CA . MET A 1 1 ? -12.590 4.240 3.534 1.00 94.42 1 A 1 ATOM 3 C C . MET A 1 1 ? -12.026 3.503 2.315 1.00 94.44 1 A 1 ATOM 4 O O . MET A 1 1 ? -12.707 2.685 1.703 1.00 91.79 1 A 1 ATOM 5 C CB . MET A 1 1 ? -12.321 3.423 4.794 1.00 91.10 1 A 1 ATOM 6 C CG . MET A 1 1 ? -13.000 2.064 4.795 1.00 86.72 1 A 1 ATOM 7 S SD . MET A 1 1 ? -12.745 1.141 6.314 1.00 84.13 1 A 1 ATOM 8 C CE . MET A 1 1 ? -13.893 1.972 7.396 1.00 73.94 1 A 1 ATOM 9 N N . LYS A 1 2 ? -10.774 3.788 1.969 1.00 97.25 2 A 1 ATOM 10 C CA . LYS A 1 2 ? -10.108 3.154 0.839 1.00 97.53 2 A 1 ATOM 11 C C . LYS A 1 2 ? -8.923 2.313 1.315 1.00 97.87 2 A 1 ATOM 12 O O . LYS A 1 2 ? -7.776 2.753 1.257 1.00 97.43 2 A 1 ATOM 13 C CB . LYS A 1 2 ? -9.634 4.209 -0.153 1.00 96.75 2 A 1 ATOM 14 C CG . LYS A 1 2 ? -10.727 4.681 -1.097 1.00 92.96 2 A 1 ATOM 15 C CD . LYS A 1 2 ? -11.648 5.686 -0.454 1.00 90.36 2 A 1 ATOM 16 C CE . LYS A 1 2 ? -12.678 6.193 -1.437 1.00 85.42 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? -13.699 7.020 -0.759 1.00 79.70 2 A 1 ATOM 18 N N . VAL A 1 3 ? -9.203 1.107 1.765 1.00 97.91 3 A 1 ATOM 19 C CA . VAL A 1 3 ? -8.163 0.199 2.244 1.00 98.17 3 A 1 ATOM 20 C C . VAL A 1 3 ? -7.231 -0.216 1.105 1.00 98.37 3 A 1 ATOM 21 O O . VAL A 1 3 ? -6.032 -0.424 1.312 1.00 97.86 3 A 1 ATOM 22 C CB . VAL A 1 3 ? -8.775 -1.057 2.889 1.00 97.71 3 A 1 ATOM 23 C CG1 . VAL A 1 3 ? -7.698 -1.874 3.574 1.00 94.93 3 A 1 ATOM 24 C CG2 . VAL A 1 3 ? -9.860 -0.687 3.882 1.00 94.29 3 A 1 ATOM 25 N N . LEU A 1 4 ? -7.787 -0.338 -0.097 1.00 98.04 4 A 1 ATOM 26 C CA . LEU A 1 4 ? -7.009 -0.725 -1.272 1.00 98.18 4 A 1 ATOM 27 C C . LEU A 1 4 ? -5.917 0.296 -1.584 1.00 98.36 4 A 1 ATOM 28 O O . LEU A 1 4 ? -4.820 -0.058 -2.015 1.00 98.17 4 A 1 ATOM 29 C CB . LEU A 1 4 ? -7.943 -0.904 -2.477 1.00 97.98 4 A 1 ATOM 30 C CG . LEU A 1 4 ? -8.775 0.323 -2.837 1.00 94.50 4 A 1 ATOM 31 C CD1 . LEU A 1 4 ? -8.112 1.111 -3.960 1.00 90.43 4 A 1 ATOM 32 C CD2 . LEU A 1 4 ? -10.178 -0.081 -3.238 1.00 90.35 4 A 1 ATOM 33 N N . ILE A 1 5 ? -6.215 1.567 -1.372 1.00 98.25 5 A 1 ATOM 34 C CA . ILE A 1 5 ? -5.261 2.647 -1.632 1.00 98.17 5 A 1 ATOM 35 C C . ILE A 1 5 ? -4.061 2.534 -0.696 1.00 98.26 5 A 1 ATOM 36 O O . ILE A 1 5 ? -2.915 2.721 -1.101 1.00 98.13 5 A 1 ATOM 37 C CB . ILE A 1 5 ? -5.927 4.026 -1.466 1.00 97.98 5 A 1 ATOM 38 C CG1 . ILE A 1 5 ? -7.150 4.168 -2.385 1.00 96.47 5 A 1 ATOM 39 C CG2 . ILE A 1 5 ? -4.918 5.141 -1.753 1.00 96.04 5 A 1 ATOM 40 C CD1 . ILE A 1 5 ? -6.811 4.141 -3.860 1.00 93.02 5 A 1 ATOM 41 N N . VAL A 1 6 ? -4.345 2.238 0.568 1.00 98.58 6 A 1 ATOM 42 C CA . VAL A 1 6 ? -3.297 2.104 1.578 1.00 98.59 6 A 1 ATOM 43 C C . VAL A 1 6 ? -2.358 0.951 1.232 1.00 98.61 6 A 1 ATOM 44 O O . VAL A 1 6 ? -1.136 1.075 1.351 1.00 98.44 6 A 1 ATOM 45 C CB . VAL A 1 6 ? -3.905 1.881 2.973 1.00 98.37 6 A 1 ATOM 46 C CG1 . VAL A 1 6 ? -2.814 1.788 4.027 1.00 97.25 6 A 1 ATOM 47 C CG2 . VAL A 1 6 ? -4.872 3.002 3.316 1.00 97.02 6 A 1 ATOM 48 N N . LEU A 1 7 ? -2.943 -0.160 0.816 1.00 98.47 7 A 1 ATOM 49 C CA . LEU A 1 7 ? -2.157 -1.335 0.448 1.00 98.41 7 A 1 ATOM 50 C C . LEU A 1 7 ? -1.287 -1.063 -0.775 1.00 98.53 7 A 1 ATOM 51 O O . LEU A 1 7 ? -0.132 -1.485 -0.833 1.00 98.45 7 A 1 ATOM 52 C CB . LEU A 1 7 ? -3.081 -2.523 0.178 1.00 98.28 7 A 1 ATOM 53 C CG . LEU A 1 7 ? -3.332 -3.407 1.397 1.00 95.13 7 A 1 ATOM 54 C CD1 . LEU A 1 7 ? -4.535 -2.914 2.185 1.00 93.14 7 A 1 ATOM 55 C CD2 . LEU A 1 7 ? -3.528 -4.853 0.984 1.00 93.96 7 A 1 ATOM 56 N N . LEU A 1 8 ? -1.851 -0.356 -1.749 1.00 98.25 8 A 1 ATOM 57 C CA . LEU A 1 8 ? -1.129 -0.026 -2.975 1.00 98.12 8 A 1 ATOM 58 C C . LEU A 1 8 ? 0.105 0.816 -2.676 1.00 98.20 8 A 1 ATOM 59 O O . LEU A 1 8 ? 1.195 0.547 -3.187 1.00 98.12 8 A 1 ATOM 60 C CB . LEU A 1 8 ? -2.055 0.728 -3.932 1.00 97.87 8 A 1 ATOM 61 C CG . LEU A 1 8 ? -3.044 -0.157 -4.688 1.00 94.71 8 A 1 ATOM 62 C CD1 . LEU A 1 8 ? -4.188 0.667 -5.249 1.00 93.43 8 A 1 ATOM 63 C CD2 . LEU A 1 8 ? -2.336 -0.903 -5.810 1.00 93.48 8 A 1 ATOM 64 N N . LEU A 1 9 ? -0.074 1.829 -1.850 1.00 98.23 9 A 1 ATOM 65 C CA . LEU A 1 9 ? 1.022 2.718 -1.483 1.00 98.08 9 A 1 ATOM 66 C C . LEU A 1 9 ? 2.066 1.986 -0.647 1.00 98.21 9 A 1 ATOM 67 O O . LEU A 1 9 ? 3.269 2.182 -0.829 1.00 97.94 9 A 1 ATOM 68 C CB . LEU A 1 9 ? 0.476 3.917 -0.710 1.00 97.72 9 A 1 ATOM 69 C CG . LEU A 1 9 ? -0.366 4.881 -1.541 1.00 94.96 9 A 1 ATOM 70 C CD1 . LEU A 1 9 ? -1.151 5.812 -0.640 1.00 93.41 9 A 1 ATOM 71 C CD2 . LEU A 1 9 ? 0.523 5.679 -2.486 1.00 93.25 9 A 1 ATOM 72 N N . GLY A 1 10 ? 1.587 1.156 0.271 1.00 98.34 10 A 1 ATOM 73 C CA . GLY A 1 10 ? 2.484 0.390 1.127 1.00 98.34 10 A 1 ATOM 74 C C . GLY A 1 10 ? 3.301 -0.623 0.353 1.00 98.49 10 A 1 ATOM 75 O O . GLY A 1 10 ? 4.510 -0.746 0.551 1.00 98.29 10 A 1 ATOM 76 N N . LEU A 1 11 ? 2.635 -1.352 -0.533 1.00 98.12 11 A 1 ATOM 77 C CA . LEU A 1 11 ? 3.300 -2.362 -1.352 1.00 98.08 11 A 1 ATOM 78 C C . LEU A 1 11 ? 4.350 -1.734 -2.256 1.00 98.26 11 A 1 ATOM 79 O O . LEU A 1 11 ? 5.466 -2.245 -2.376 1.00 97.93 11 A 1 ATOM 80 C CB . LEU A 1 11 ? 2.269 -3.112 -2.202 1.00 97.72 11 A 1 ATOM 81 C CG . LEU A 1 11 ? 2.809 -4.361 -2.894 1.00 94.52 11 A 1 ATOM 82 C CD1 . LEU A 1 11 ? 2.968 -5.493 -1.891 1.00 91.76 11 A 1 ATOM 83 C CD2 . LEU A 1 11 ? 1.892 -4.786 -4.029 1.00 92.08 11 A 1 ATOM 84 N N . ALA A 1 12 ? 3.990 -0.640 -2.909 1.00 98.41 12 A 1 ATOM 85 C CA . ALA A 1 12 ? 4.903 0.067 -3.806 1.00 98.43 12 A 1 ATOM 86 C C . ALA A 1 12 ? 6.098 0.632 -3.048 1.00 98.52 12 A 1 ATOM 87 O O . ALA A 1 12 ? 7.224 0.614 -3.543 1.00 98.15 12 A 1 ATOM 88 C CB . ALA A 1 12 ? 4.166 1.185 -4.528 1.00 98.09 12 A 1 ATOM 89 N N . PHE A 1 13 ? 5.839 1.126 -1.850 1.00 98.30 13 A 1 ATOM 90 C CA . PHE A 1 13 ? 6.887 1.701 -1.012 1.00 98.25 13 A 1 ATOM 91 C C . PHE A 1 13 ? 7.906 0.647 -0.598 1.00 98.38 13 A 1 ATOM 92 O O . PHE A 1 13 ? 9.114 0.885 -0.642 1.00 97.98 13 A 1 ATOM 93 C CB . PHE A 1 13 ? 6.266 2.339 0.226 1.00 97.87 13 A 1 ATOM 94 C CG . PHE A 1 13 ? 7.213 3.253 0.961 1.00 96.52 13 A 1 ATOM 95 C CD1 . PHE A 1 13 ? 7.452 4.537 0.496 1.00 94.81 13 A 1 ATOM 96 C CD2 . PHE A 1 13 ? 7.850 2.824 2.113 1.00 94.80 13 A 1 ATOM 97 C CE1 . PHE A 1 13 ? 8.318 5.385 1.166 1.00 93.86 13 A 1 ATOM 98 C CE2 . PHE A 1 13 ? 8.725 3.668 2.791 1.00 93.74 13 A 1 ATOM 99 C CZ . PHE A 1 13 ? 8.957 4.949 2.316 1.00 93.99 13 A 1 ATOM 100 N N . VAL A 1 14 ? 7.413 -0.516 -0.189 1.00 98.23 14 A 1 ATOM 101 C CA . VAL A 1 14 ? 8.283 -1.617 0.232 1.00 98.15 14 A 1 ATOM 102 C C . VAL A 1 14 ? 9.085 -2.163 -0.945 1.00 98.24 14 A 1 ATOM 103 O O . VAL A 1 14 ? 10.276 -2.461 -0.814 1.00 97.63 14 A 1 ATOM 104 C CB . VAL A 1 14 ? 7.467 -2.752 0.874 1.00 97.53 14 A 1 ATOM 105 C CG1 . VAL A 1 14 ? 8.363 -3.930 1.225 1.00 95.47 14 A 1 ATOM 106 C CG2 . VAL A 1 14 ? 6.751 -2.255 2.110 1.00 95.21 14 A 1 ATOM 107 N N . LEU A 1 15 ? 8.430 -2.305 -2.086 1.00 97.74 15 A 1 ATOM 108 C CA . LEU A 1 15 ? 9.078 -2.815 -3.292 1.00 97.63 15 A 1 ATOM 109 C C . LEU A 1 15 ? 10.138 -1.852 -3.808 1.00 97.74 15 A 1 ATOM 110 O O . LEU A 1 15 ? 11.187 -2.278 -4.301 1.00 97.26 15 A 1 ATOM 111 C CB . LEU A 1 15 ? 8.034 -3.066 -4.380 1.00 97.07 15 A 1 ATOM 112 C CG . LEU A 1 15 ? 7.128 -4.270 -4.124 1.00 94.59 15 A 1 ATOM 113 C CD1 . LEU A 1 15 ? 5.893 -4.210 -5.005 1.00 91.17 15 A 1 ATOM 114 C CD2 . LEU A 1 15 ? 7.893 -5.561 -4.373 1.00 90.10 15 A 1 ATOM 115 N N . ALA A 1 16 ? 9.862 -0.568 -3.710 1.00 96.09 16 A 1 ATOM 116 C CA . ALA A 1 16 ? 10.778 0.469 -4.179 1.00 94.82 16 A 1 ATOM 117 C C . ALA A 1 16 ? 12.017 0.547 -3.291 1.00 94.04 16 A 1 ATOM 118 O O . ALA A 1 16 ? 11.925 1.052 -2.164 1.00 90.64 16 A 1 ATOM 119 C CB . ALA A 1 16 ? 10.072 1.812 -4.230 1.00 91.92 16 A 1 ATOM 120 O OXT . ALA A 1 16 ? 13.085 0.096 -3.723 1.00 83.92 16 A 1 #