# 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_spkb29827 # _entry.id spkb29827 # 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" "C4 H8 N2 O3" 132.118 ASN y ASPARAGINE C([C@@H](C(=O)O)N)C(=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" "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 PHE 3 1 n PHE 4 1 n ALA 5 1 n LEU 6 1 n ALA 7 1 n ALA 8 1 n LEU 9 1 n PHE 10 1 n ALA 11 1 n SER 12 1 n THR 13 1 n VAL 14 1 n ASN 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 @ 2025-07-12 11:19:29)" _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 86.95 _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 84.21 1 1 A LYS 2 2 84.93 1 2 A PHE 3 2 84.46 1 3 A PHE 4 2 87.40 1 4 A ALA 5 2 93.31 1 5 A LEU 6 2 88.82 1 6 A ALA 7 2 94.16 1 7 A ALA 8 2 93.37 1 8 A LEU 9 2 88.90 1 9 A PHE 10 2 87.13 1 10 A ALA 11 2 93.12 1 11 A SER 12 2 89.63 1 12 A THR 13 2 90.76 1 13 A VAL 14 2 90.05 1 14 A ASN 15 2 81.20 1 15 A SER 16 2 70.00 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 PHE . 3 A 3 A 4 1 n PHE . 4 A 4 A 5 1 n ALA . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n ALA . 7 A 7 A 8 1 n ALA . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n PHE . 10 A 10 A 11 1 n ALA . 11 A 11 A 12 1 n SER . 12 A 12 A 13 1 n THR . 13 A 13 A 14 1 n VAL . 14 A 14 A 15 1 n ASN . 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 ? -4.208 -11.426 3.705 1.00 88.16 1 A 1 ATOM 2 C CA . MET A 1 1 ? -4.291 -9.969 3.584 1.00 90.57 1 A 1 ATOM 3 C C . MET A 1 1 ? -2.913 -9.341 3.407 1.00 91.25 1 A 1 ATOM 4 O O . MET A 1 1 ? -2.709 -8.173 3.733 1.00 88.50 1 A 1 ATOM 5 C CB . MET A 1 1 ? -4.934 -9.373 4.834 1.00 85.86 1 A 1 ATOM 6 C CG . MET A 1 1 ? -6.258 -9.996 5.183 1.00 80.87 1 A 1 ATOM 7 S SD . MET A 1 1 ? -6.937 -9.271 6.681 1.00 79.33 1 A 1 ATOM 8 C CE . MET A 1 1 ? -8.377 -10.300 6.899 1.00 69.12 1 A 1 ATOM 9 N N . LYS A 1 2 ? -1.986 -10.132 2.921 1.00 91.30 2 A 1 ATOM 10 C CA . LYS A 1 2 ? -0.627 -9.636 2.715 1.00 91.94 2 A 1 ATOM 11 C C . LYS A 1 2 ? -0.610 -8.547 1.650 1.00 91.97 2 A 1 ATOM 12 O O . LYS A 1 2 ? -0.020 -7.487 1.843 1.00 91.57 2 A 1 ATOM 13 C CB . LYS A 1 2 ? 0.299 -10.792 2.312 1.00 89.77 2 A 1 ATOM 14 C CG . LYS A 1 2 ? 0.548 -11.776 3.440 1.00 83.67 2 A 1 ATOM 15 C CD . LYS A 1 2 ? 1.560 -11.243 4.442 1.00 80.92 2 A 1 ATOM 16 C CE . LYS A 1 2 ? 1.914 -12.286 5.481 1.00 75.18 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? 3.031 -11.831 6.355 1.00 68.04 2 A 1 ATOM 18 N N . PHE A 1 3 ? -1.259 -8.823 0.546 1.00 87.25 3 A 1 ATOM 19 C CA . PHE A 1 3 ? -1.313 -7.868 -0.554 1.00 89.11 3 A 1 ATOM 20 C C . PHE A 1 3 ? -2.174 -6.666 -0.190 1.00 91.81 3 A 1 ATOM 21 O O . PHE A 1 3 ? -1.963 -5.561 -0.685 1.00 90.15 3 A 1 ATOM 22 C CB . PHE A 1 3 ? -1.854 -8.548 -1.809 1.00 86.77 3 A 1 ATOM 23 C CG . PHE A 1 3 ? -0.857 -9.487 -2.440 1.00 84.34 3 A 1 ATOM 24 C CD1 . PHE A 1 3 ? -0.667 -10.755 -1.934 1.00 82.41 3 A 1 ATOM 25 C CD2 . PHE A 1 3 ? -0.115 -9.082 -3.541 1.00 81.53 3 A 1 ATOM 26 C CE1 . PHE A 1 3 ? 0.255 -11.617 -2.510 1.00 79.11 3 A 1 ATOM 27 C CE2 . PHE A 1 3 ? 0.805 -9.940 -4.123 1.00 79.14 3 A 1 ATOM 28 C CZ . PHE A 1 3 ? 0.989 -11.209 -3.608 1.00 77.46 3 A 1 ATOM 29 N N . PHE A 1 4 ? -3.132 -6.888 0.675 1.00 89.25 4 A 1 ATOM 30 C CA . PHE A 1 4 ? -4.016 -5.814 1.108 1.00 90.40 4 A 1 ATOM 31 C C . PHE A 1 4 ? -3.237 -4.776 1.903 1.00 92.74 4 A 1 ATOM 32 O O . PHE A 1 4 ? -3.475 -3.576 1.790 1.00 91.95 4 A 1 ATOM 33 C CB . PHE A 1 4 ? -5.148 -6.389 1.958 1.00 89.46 4 A 1 ATOM 34 C CG . PHE A 1 4 ? -6.449 -5.663 1.741 1.00 87.20 4 A 1 ATOM 35 C CD1 . PHE A 1 4 ? -6.606 -4.357 2.167 1.00 84.04 4 A 1 ATOM 36 C CD2 . PHE A 1 4 ? -7.508 -6.291 1.102 1.00 84.79 4 A 1 ATOM 37 C CE1 . PHE A 1 4 ? -7.798 -3.678 1.960 1.00 83.68 4 A 1 ATOM 38 C CE2 . PHE A 1 4 ? -8.704 -5.618 0.896 1.00 84.18 4 A 1 ATOM 39 C CZ . PHE A 1 4 ? -8.847 -4.311 1.326 1.00 83.69 4 A 1 ATOM 40 N N . ALA A 1 5 ? -2.295 -5.257 2.707 1.00 92.39 5 A 1 ATOM 41 C CA . ALA A 1 5 ? -1.461 -4.373 3.513 1.00 93.49 5 A 1 ATOM 42 C C . ALA A 1 5 ? -0.584 -3.503 2.622 1.00 94.49 5 A 1 ATOM 43 O O . ALA A 1 5 ? -0.386 -2.321 2.893 1.00 93.32 5 A 1 ATOM 44 C CB . ALA A 1 5 ? -0.598 -5.196 4.461 1.00 92.86 5 A 1 ATOM 45 N N . LEU A 1 6 ? -0.069 -4.105 1.567 1.00 92.05 6 A 1 ATOM 46 C CA . LEU A 1 6 ? 0.772 -3.384 0.621 1.00 92.34 6 A 1 ATOM 47 C C . LEU A 1 6 ? -0.044 -2.323 -0.103 1.00 93.44 6 A 1 ATOM 48 O O . LEU A 1 6 ? 0.427 -1.213 -0.340 1.00 92.66 6 A 1 ATOM 49 C CB . LEU A 1 6 ? 1.380 -4.353 -0.393 1.00 91.18 6 A 1 ATOM 50 C CG . LEU A 1 6 ? 2.800 -3.985 -0.806 1.00 84.61 6 A 1 ATOM 51 C CD1 . LEU A 1 6 ? 3.808 -4.648 0.121 1.00 82.91 6 A 1 ATOM 52 C CD2 . LEU A 1 6 ? 3.057 -4.386 -2.249 1.00 81.39 6 A 1 ATOM 53 N N . ALA A 1 7 ? -1.251 -2.688 -0.449 1.00 94.36 7 A 1 ATOM 54 C CA . ALA A 1 7 ? -2.147 -1.773 -1.148 1.00 94.50 7 A 1 ATOM 55 C C . ALA A 1 7 ? -2.524 -0.600 -0.254 1.00 94.96 7 A 1 ATOM 56 O O . ALA A 1 7 ? -2.715 0.520 -0.729 1.00 93.47 7 A 1 ATOM 57 C CB . ALA A 1 7 ? -3.401 -2.518 -1.585 1.00 93.50 7 A 1 ATOM 58 N N . ALA A 1 8 ? -2.634 -0.871 1.030 1.00 94.22 8 A 1 ATOM 59 C CA . ALA A 1 8 ? -2.985 0.161 1.999 1.00 93.42 8 A 1 ATOM 60 C C . ALA A 1 8 ? -1.903 1.231 2.056 1.00 94.05 8 A 1 ATOM 61 O O . ALA A 1 8 ? -2.198 2.422 2.137 1.00 92.37 8 A 1 ATOM 62 C CB . ALA A 1 8 ? -3.176 -0.464 3.374 1.00 92.77 8 A 1 ATOM 63 N N . LEU A 1 9 ? -0.657 0.792 2.016 1.00 92.08 9 A 1 ATOM 64 C CA . LEU A 1 9 ? 0.474 1.718 2.043 1.00 91.74 9 A 1 ATOM 65 C C . LEU A 1 9 ? 0.497 2.567 0.781 1.00 92.79 9 A 1 ATOM 66 O O . LEU A 1 9 ? 0.778 3.764 0.828 1.00 91.67 9 A 1 ATOM 67 C CB . LEU A 1 9 ? 1.785 0.947 2.178 1.00 91.11 9 A 1 ATOM 68 C CG . LEU A 1 9 ? 2.962 1.816 2.613 1.00 85.90 9 A 1 ATOM 69 C CD1 . LEU A 1 9 ? 3.497 1.358 3.964 1.00 83.10 9 A 1 ATOM 70 C CD2 . LEU A 1 9 ? 4.070 1.782 1.575 1.00 82.82 9 A 1 ATOM 71 N N . PHE A 1 10 ? 0.214 1.930 -0.330 1.00 91.84 10 A 1 ATOM 72 C CA . PHE A 1 10 ? 0.194 2.618 -1.613 1.00 90.53 10 A 1 ATOM 73 C C . PHE A 1 10 ? -0.891 3.685 -1.620 1.00 91.86 10 A 1 ATOM 74 O O . PHE A 1 10 ? -0.690 4.796 -2.111 1.00 90.67 10 A 1 ATOM 75 C CB . PHE A 1 10 ? -0.056 1.612 -2.738 1.00 89.74 10 A 1 ATOM 76 C CG . PHE A 1 10 ? 0.759 1.921 -3.975 1.00 86.65 10 A 1 ATOM 77 C CD1 . PHE A 1 10 ? 0.888 3.215 -4.433 1.00 83.85 10 A 1 ATOM 78 C CD2 . PHE A 1 10 ? 1.392 0.902 -4.673 1.00 84.48 10 A 1 ATOM 79 C CE1 . PHE A 1 10 ? 1.635 3.505 -5.564 1.00 83.25 10 A 1 ATOM 80 C CE2 . PHE A 1 10 ? 2.137 1.181 -5.809 1.00 83.03 10 A 1 ATOM 81 C CZ . PHE A 1 10 ? 2.259 2.485 -6.253 1.00 82.58 10 A 1 ATOM 82 N N . ALA A 1 11 ? -2.027 3.331 -1.077 1.00 94.02 11 A 1 ATOM 83 C CA . ALA A 1 11 ? -3.149 4.263 -1.015 1.00 93.58 11 A 1 ATOM 84 C C . ALA A 1 11 ? -2.863 5.394 -0.037 1.00 93.85 11 A 1 ATOM 85 O O . ALA A 1 11 ? -3.319 6.521 -0.228 1.00 91.42 11 A 1 ATOM 86 C CB . ALA A 1 11 ? -4.410 3.520 -0.604 1.00 92.74 11 A 1 ATOM 87 N N . SER A 1 12 ? -2.103 5.083 1.004 1.00 93.79 12 A 1 ATOM 88 C CA . SER A 1 12 ? -1.745 6.071 2.018 1.00 92.27 12 A 1 ATOM 89 C C . SER A 1 12 ? -0.871 7.168 1.425 1.00 92.81 12 A 1 ATOM 90 O O . SER A 1 12 ? -1.099 8.350 1.667 1.00 89.74 12 A 1 ATOM 91 C CB . SER A 1 12 ? -1.012 5.402 3.175 1.00 90.28 12 A 1 ATOM 92 O OG . SER A 1 12 ? -0.698 6.343 4.173 1.00 78.87 12 A 1 ATOM 93 N N . THR A 1 13 ? 0.124 6.765 0.652 1.00 93.42 13 A 1 ATOM 94 C CA . THR A 1 13 ? 1.035 7.720 0.028 1.00 93.33 13 A 1 ATOM 95 C C . THR A 1 13 ? 0.328 8.505 -1.076 1.00 93.88 13 A 1 ATOM 96 O O . THR A 1 13 ? 0.615 9.684 -1.292 1.00 91.68 13 A 1 ATOM 97 C CB . THR A 1 13 ? 2.266 7.000 -0.543 1.00 91.92 13 A 1 ATOM 98 O OG1 . THR A 1 13 ? 3.175 7.974 -1.060 1.00 85.85 13 A 1 ATOM 99 C CG2 . THR A 1 13 ? 1.893 6.044 -1.654 1.00 85.21 13 A 1 ATOM 100 N N . VAL A 1 14 ? -0.579 7.844 -1.754 1.00 93.58 14 A 1 ATOM 101 C CA . VAL A 1 14 ? -1.346 8.488 -2.820 1.00 92.93 14 A 1 ATOM 102 C C . VAL A 1 14 ? -2.368 9.452 -2.229 1.00 92.81 14 A 1 ATOM 103 O O . VAL A 1 14 ? -2.625 10.527 -2.780 1.00 90.75 14 A 1 ATOM 104 C CB . VAL A 1 14 ? -2.055 7.440 -3.690 1.00 90.78 14 A 1 ATOM 105 C CG1 . VAL A 1 14 ? -3.016 8.121 -4.656 1.00 84.07 14 A 1 ATOM 106 C CG2 . VAL A 1 14 ? -1.042 6.610 -4.453 1.00 85.46 14 A 1 ATOM 107 N N . ASN A 1 15 ? -2.933 9.049 -1.115 1.00 86.51 15 A 1 ATOM 108 C CA . ASN A 1 15 ? -3.927 9.868 -0.430 1.00 85.17 15 A 1 ATOM 109 C C . ASN A 1 15 ? -3.241 10.972 0.357 1.00 85.29 15 A 1 ATOM 110 O O . ASN A 1 15 ? -3.098 10.894 1.576 1.00 82.32 15 A 1 ATOM 111 C CB . ASN A 1 15 ? -4.766 8.999 0.503 1.00 82.17 15 A 1 ATOM 112 C CG . ASN A 1 15 ? -6.029 9.708 0.947 1.00 79.58 15 A 1 ATOM 113 O OD1 . ASN A 1 15 ? -7.104 9.492 0.403 1.00 74.47 15 A 1 ATOM 114 N ND2 . ASN A 1 15 ? -5.924 10.548 1.955 1.00 74.07 15 A 1 ATOM 115 N N . SER A 1 16 ? -2.824 12.003 -0.353 1.00 78.63 16 A 1 ATOM 116 C CA . SER A 1 16 ? -2.117 13.111 0.282 1.00 75.51 16 A 1 ATOM 117 C C . SER A 1 16 ? -3.071 14.269 0.606 1.00 71.88 16 A 1 ATOM 118 O O . SER A 1 16 ? -3.589 14.320 1.737 1.00 66.01 16 A 1 ATOM 119 C CB . SER A 1 16 ? -0.996 13.594 -0.632 1.00 67.97 16 A 1 ATOM 120 O OG . SER A 1 16 ? -0.062 14.365 0.093 1.00 65.05 16 A 1 ATOM 121 O OXT . SER A 1 16 ? -3.303 15.103 -0.267 1.00 64.92 16 A 1 #