# 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_spkb12583 # _entry.id spkb12583 # 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 H10 N3 O2" 156.162 HIS y HISTIDINE c1c([nH+]c[nH]1)C[C@@H](C(=O)O)N ? "L-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" "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" "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 HIS 2 1 n PHE 3 1 n ILE 4 1 n PHE 5 1 n TYR 6 1 n LEU 7 1 n ILE 8 1 n LEU 9 1 n LEU 10 1 n VAL 11 1 n SER 12 1 n ALA 13 # _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 @ 2025-07-10 16:00:23)" _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 95.11 _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 88.07 1 1 A HIS 2 2 91.34 1 2 A PHE 3 2 95.61 1 3 A ILE 4 2 96.91 1 4 A PHE 5 2 94.87 1 5 A TYR 6 2 95.93 1 6 A LEU 7 2 97.02 1 7 A ILE 8 2 97.08 1 8 A LEU 9 2 96.55 1 9 A LEU 10 2 96.43 1 10 A VAL 11 2 96.95 1 11 A SER 12 2 96.67 1 12 A ALA 13 2 93.82 1 13 # _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 HIS . 2 A 2 A 3 1 n PHE . 3 A 3 A 4 1 n ILE . 4 A 4 A 5 1 n PHE . 5 A 5 A 6 1 n TYR . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n ILE . 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 SER . 12 A 12 A 13 1 n ALA . 13 A 13 # _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 ? 7.989 -2.614 -5.819 1.00 92.12 1 A 1 ATOM 2 C CA . MET A 1 1 ? 6.694 -3.289 -5.664 1.00 94.02 1 A 1 ATOM 3 C C . MET A 1 1 ? 6.145 -3.095 -4.250 1.00 94.22 1 A 1 ATOM 4 O O . MET A 1 1 ? 5.259 -3.824 -3.809 1.00 93.43 1 A 1 ATOM 5 C CB . MET A 1 1 ? 6.838 -4.790 -5.965 1.00 90.76 1 A 1 ATOM 6 C CG . MET A 1 1 ? 7.373 -5.069 -7.358 1.00 85.11 1 A 1 ATOM 7 S SD . MET A 1 1 ? 7.586 -6.838 -7.660 1.00 81.95 1 A 1 ATOM 8 C CE . MET A 1 1 ? 8.719 -6.798 -9.030 1.00 72.98 1 A 1 ATOM 9 N N . HIS A 1 2 ? 6.679 -2.099 -3.568 1.00 96.41 2 A 1 ATOM 10 C CA . HIS A 1 2 ? 6.225 -1.817 -2.211 1.00 97.08 2 A 1 ATOM 11 C C . HIS A 1 2 ? 4.955 -0.970 -2.222 1.00 97.62 2 A 1 ATOM 12 O O . HIS A 1 2 ? 4.163 -1.000 -1.282 1.00 97.02 2 A 1 ATOM 13 C CB . HIS A 1 2 ? 7.340 -1.112 -1.438 1.00 95.66 2 A 1 ATOM 14 C CG . HIS A 1 2 ? 8.332 -2.078 -0.850 1.00 92.03 2 A 1 ATOM 15 N ND1 . HIS A 1 2 ? 9.667 -1.788 -0.695 1.00 84.39 2 A 1 ATOM 16 C CD2 . HIS A 1 2 ? 8.161 -3.334 -0.361 1.00 82.47 2 A 1 ATOM 17 C CE1 . HIS A 1 2 ? 10.275 -2.827 -0.137 1.00 84.81 2 A 1 ATOM 18 N NE2 . HIS A 1 2 ? 9.386 -3.785 0.080 1.00 85.87 2 A 1 ATOM 19 N N . PHE A 1 3 ? 4.751 -0.229 -3.307 1.00 98.03 3 A 1 ATOM 20 C CA . PHE A 1 3 ? 3.566 0.611 -3.430 1.00 98.28 3 A 1 ATOM 21 C C . PHE A 1 3 ? 2.296 -0.236 -3.458 1.00 98.51 3 A 1 ATOM 22 O O . PHE A 1 3 ? 1.217 0.239 -3.095 1.00 98.28 3 A 1 ATOM 23 C CB . PHE A 1 3 ? 3.649 1.488 -4.686 1.00 97.89 3 A 1 ATOM 24 C CG . PHE A 1 3 ? 4.571 0.932 -5.750 1.00 95.85 3 A 1 ATOM 25 C CD1 . PHE A 1 3 ? 5.922 1.246 -5.732 1.00 93.73 3 A 1 ATOM 26 C CD2 . PHE A 1 3 ? 4.081 0.111 -6.749 1.00 93.48 3 A 1 ATOM 27 C CE1 . PHE A 1 3 ? 6.780 0.753 -6.710 1.00 92.80 3 A 1 ATOM 28 C CE2 . PHE A 1 3 ? 4.933 -0.391 -7.731 1.00 92.77 3 A 1 ATOM 29 C CZ . PHE A 1 3 ? 6.279 -0.066 -7.711 1.00 92.05 3 A 1 ATOM 30 N N . ILE A 1 4 ? 2.442 -1.482 -3.874 1.00 98.27 4 A 1 ATOM 31 C CA . ILE A 1 4 ? 1.305 -2.399 -3.908 1.00 98.35 4 A 1 ATOM 32 C C . ILE A 1 4 ? 0.791 -2.624 -2.488 1.00 98.46 4 A 1 ATOM 33 O O . ILE A 1 4 ? -0.411 -2.636 -2.229 1.00 98.19 4 A 1 ATOM 34 C CB . ILE A 1 4 ? 1.706 -3.749 -4.550 1.00 98.04 4 A 1 ATOM 35 C CG1 . ILE A 1 4 ? 2.363 -3.542 -5.922 1.00 96.41 4 A 1 ATOM 36 C CG2 . ILE A 1 4 ? 0.474 -4.653 -4.681 1.00 96.06 4 A 1 ATOM 37 C CD1 . ILE A 1 4 ? 1.467 -2.836 -6.920 1.00 91.47 4 A 1 ATOM 38 N N . PHE A 1 5 ? 1.718 -2.806 -1.588 1.00 98.17 5 A 1 ATOM 39 C CA . PHE A 1 5 ? 1.376 -3.016 -0.187 1.00 98.16 5 A 1 ATOM 40 C C . PHE A 1 5 ? 0.758 -1.748 0.399 1.00 98.33 5 A 1 ATOM 41 O O . PHE A 1 5 ? -0.152 -1.810 1.219 1.00 98.23 5 A 1 ATOM 42 C CB . PHE A 1 5 ? 2.633 -3.403 0.587 1.00 97.71 5 A 1 ATOM 43 C CG . PHE A 1 5 ? 2.352 -4.352 1.718 1.00 94.91 5 A 1 ATOM 44 C CD1 . PHE A 1 5 ? 1.804 -5.598 1.469 1.00 92.24 5 A 1 ATOM 45 C CD2 . PHE A 1 5 ? 2.650 -3.994 3.022 1.00 92.53 5 A 1 ATOM 46 C CE1 . PHE A 1 5 ? 1.544 -6.476 2.508 1.00 91.69 5 A 1 ATOM 47 C CE2 . PHE A 1 5 ? 2.392 -4.868 4.071 1.00 91.39 5 A 1 ATOM 48 C CZ . PHE A 1 5 ? 1.839 -6.109 3.812 1.00 90.25 5 A 1 ATOM 49 N N . TYR A 1 6 ? 1.260 -0.606 -0.053 1.00 98.30 6 A 1 ATOM 50 C CA . TYR A 1 6 ? 0.736 0.675 0.408 1.00 98.43 6 A 1 ATOM 51 C C . TYR A 1 6 ? -0.685 0.898 -0.107 1.00 98.57 6 A 1 ATOM 52 O O . TYR A 1 6 ? -1.530 1.460 0.590 1.00 98.43 6 A 1 ATOM 53 C CB . TYR A 1 6 ? 1.646 1.802 -0.080 1.00 98.17 6 A 1 ATOM 54 C CG . TYR A 1 6 ? 2.777 2.085 0.881 1.00 96.54 6 A 1 ATOM 55 C CD1 . TYR A 1 6 ? 2.510 2.553 2.161 1.00 94.18 6 A 1 ATOM 56 C CD2 . TYR A 1 6 ? 4.097 1.888 0.504 1.00 94.60 6 A 1 ATOM 57 C CE1 . TYR A 1 6 ? 3.542 2.818 3.048 1.00 93.80 6 A 1 ATOM 58 C CE2 . TYR A 1 6 ? 5.137 2.152 1.387 1.00 93.81 6 A 1 ATOM 59 C CZ . TYR A 1 6 ? 4.851 2.619 2.657 1.00 93.89 6 A 1 ATOM 60 O OH . TYR A 1 6 ? 5.873 2.883 3.532 1.00 92.41 6 A 1 ATOM 61 N N . LEU A 1 7 ? -0.927 0.440 -1.321 1.00 98.31 7 A 1 ATOM 62 C CA . LEU A 1 7 ? -2.249 0.575 -1.922 1.00 98.35 7 A 1 ATOM 63 C C . LEU A 1 7 ? -3.271 -0.251 -1.151 1.00 98.47 7 A 1 ATOM 64 O O . LEU A 1 7 ? -4.382 0.204 -0.882 1.00 98.37 7 A 1 ATOM 65 C CB . LEU A 1 7 ? -2.191 0.115 -3.380 1.00 98.15 7 A 1 ATOM 66 C CG . LEU A 1 7 ? -2.635 1.168 -4.383 1.00 95.71 7 A 1 ATOM 67 C CD1 . LEU A 1 7 ? -2.265 0.752 -5.794 1.00 94.08 7 A 1 ATOM 68 C CD2 . LEU A 1 7 ? -4.139 1.387 -4.276 1.00 94.68 7 A 1 ATOM 69 N N . ILE A 1 8 ? -2.890 -1.459 -0.819 1.00 98.23 8 A 1 ATOM 70 C CA . ILE A 1 8 ? -3.770 -2.352 -0.076 1.00 98.15 8 A 1 ATOM 71 C C . ILE A 1 8 ? -4.009 -1.802 1.329 1.00 98.26 8 A 1 ATOM 72 O O . ILE A 1 8 ? -5.109 -1.910 1.874 1.00 98.02 8 A 1 ATOM 73 C CB . ILE A 1 8 ? -3.166 -3.769 -0.000 1.00 97.88 8 A 1 ATOM 74 C CG1 . ILE A 1 8 ? -3.008 -4.371 -1.396 1.00 96.61 8 A 1 ATOM 75 C CG2 . ILE A 1 8 ? -4.049 -4.671 0.860 1.00 96.62 8 A 1 ATOM 76 C CD1 . ILE A 1 8 ? -2.050 -5.538 -1.435 1.00 92.84 8 A 1 ATOM 77 N N . LEU A 1 9 ? -2.983 -1.216 1.883 1.00 98.18 9 A 1 ATOM 78 C CA . LEU A 1 9 ? -3.072 -0.653 3.225 1.00 98.05 9 A 1 ATOM 79 C C . LEU A 1 9 ? -4.036 0.527 3.249 1.00 98.18 9 A 1 ATOM 80 O O . LEU A 1 9 ? -4.793 0.708 4.201 1.00 97.98 9 A 1 ATOM 81 C CB . LEU A 1 9 ? -1.679 -0.223 3.681 1.00 97.71 9 A 1 ATOM 82 C CG . LEU A 1 9 ? -1.430 -0.395 5.174 1.00 94.90 9 A 1 ATOM 83 C CD1 . LEU A 1 9 ? 0.055 -0.496 5.455 1.00 93.61 9 A 1 ATOM 84 C CD2 . LEU A 1 9 ? -2.028 0.772 5.950 1.00 93.75 9 A 1 ATOM 85 N N . LEU A 1 10 ? -4.007 1.315 2.201 1.00 98.31 10 A 1 ATOM 86 C CA . LEU A 1 10 ? -4.879 2.476 2.097 1.00 98.24 10 A 1 ATOM 87 C C . LEU A 1 10 ? -6.330 2.058 1.924 1.00 98.27 10 A 1 ATOM 88 O O . LEU A 1 10 ? -7.235 2.669 2.494 1.00 97.89 10 A 1 ATOM 89 C CB . LEU A 1 10 ? -4.428 3.333 0.918 1.00 97.93 10 A 1 ATOM 90 C CG . LEU A 1 10 ? -5.020 4.727 0.926 1.00 94.22 10 A 1 ATOM 91 C CD1 . LEU A 1 10 ? -3.958 5.744 0.558 1.00 93.04 10 A 1 ATOM 92 C CD2 . LEU A 1 10 ? -6.185 4.810 -0.037 1.00 93.56 10 A 1 ATOM 93 N N . VAL A 1 11 ? -6.550 1.033 1.128 1.00 98.26 11 A 1 ATOM 94 C CA . VAL A 1 11 ? -7.902 0.529 0.890 1.00 98.12 11 A 1 ATOM 95 C C . VAL A 1 11 ? -8.452 -0.153 2.135 1.00 98.20 11 A 1 ATOM 96 O O . VAL A 1 11 ? -9.653 -0.099 2.405 1.00 97.57 11 A 1 ATOM 97 C CB . VAL A 1 11 ? -7.904 -0.456 -0.294 1.00 97.45 11 A 1 ATOM 98 C CG1 . VAL A 1 11 ? -9.288 -1.042 -0.501 1.00 94.51 11 A 1 ATOM 99 C CG2 . VAL A 1 11 ? -7.435 0.237 -1.554 1.00 94.57 11 A 1 ATOM 100 N N . SER A 1 12 ? -7.582 -0.789 2.857 1.00 98.22 12 A 1 ATOM 101 C CA . SER A 1 12 ? -7.975 -1.496 4.072 1.00 98.09 12 A 1 ATOM 102 C C . SER A 1 12 ? -8.269 -0.526 5.217 1.00 97.94 12 A 1 ATOM 103 O O . SER A 1 12 ? -8.981 -0.860 6.161 1.00 96.34 12 A 1 ATOM 104 C CB . SER A 1 12 ? -6.869 -2.472 4.480 1.00 97.32 12 A 1 ATOM 105 O OG . SER A 1 12 ? -7.391 -3.555 5.189 1.00 92.10 12 A 1 ATOM 106 N N . ALA A 1 13 ? -7.731 0.665 5.110 1.00 97.11 13 A 1 ATOM 107 C CA . ALA A 1 13 ? -7.902 1.670 6.144 1.00 96.20 13 A 1 ATOM 108 C C . ALA A 1 13 ? -9.241 2.393 6.020 1.00 95.26 13 A 1 ATOM 109 O O . ALA A 1 13 ? -9.806 2.436 4.915 1.00 92.80 13 A 1 ATOM 110 C CB . ALA A 1 13 ? -6.751 2.661 6.097 1.00 94.63 13 A 1 ATOM 111 O OXT . ALA A 1 13 ? -9.716 2.941 7.014 1.00 86.91 13 A 1 #