# 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_spkb25780 # _entry.id spkb25780 # 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" "C5 H10 N2 O3" 146.144 GLN y GLUTAMINE C(CC(=O)N)[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" "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 GLN 2 1 n PHE 3 1 n THR 4 1 n THR 5 1 n ILE 6 1 n VAL 7 1 n MET 8 1 n THR 9 1 n LEU 10 1 n ALA 11 1 n ALA 12 1 n ALA 13 1 n VAL 14 1 n ALA 15 1 n VAL 16 1 n THR 17 1 n ALA 18 # _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 @ 2025-07-08 12:57:34)" _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 94.12 _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 85.66 1 1 A GLN 2 2 88.82 1 2 A PHE 3 2 90.90 1 3 A THR 4 2 93.08 1 4 A THR 5 2 94.51 1 5 A ILE 6 2 95.42 1 6 A VAL 7 2 96.34 1 7 A MET 8 2 93.04 1 8 A THR 9 2 95.93 1 9 A LEU 10 2 95.23 1 10 A ALA 11 2 97.74 1 11 A ALA 12 2 97.81 1 12 A ALA 13 2 97.85 1 13 A VAL 14 2 97.26 1 14 A ALA 15 2 98.08 1 15 A VAL 16 2 96.08 1 16 A THR 17 2 95.70 1 17 A ALA 18 2 93.16 1 18 # _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 GLN . 2 A 2 A 3 1 n PHE . 3 A 3 A 4 1 n THR . 4 A 4 A 5 1 n THR . 5 A 5 A 6 1 n ILE . 6 A 6 A 7 1 n VAL . 7 A 7 A 8 1 n MET . 8 A 8 A 9 1 n THR . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n ALA . 11 A 11 A 12 1 n ALA . 12 A 12 A 13 1 n ALA . 13 A 13 A 14 1 n VAL . 14 A 14 A 15 1 n ALA . 15 A 15 A 16 1 n VAL . 16 A 16 A 17 1 n THR . 17 A 17 A 18 1 n ALA . 18 A 18 # _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 ? -3.303 9.213 14.093 1.00 91.14 1 A 1 ATOM 2 C CA . MET A 1 1 ? -2.082 8.750 13.410 1.00 91.81 1 A 1 ATOM 3 C C . MET A 1 1 ? -2.280 7.330 12.881 1.00 92.91 1 A 1 ATOM 4 O O . MET A 1 1 ? -2.330 6.382 13.655 1.00 91.28 1 A 1 ATOM 5 C CB . MET A 1 1 ? -0.901 8.770 14.377 1.00 88.01 1 A 1 ATOM 6 C CG . MET A 1 1 ? -0.611 10.158 14.907 1.00 83.97 1 A 1 ATOM 7 S SD . MET A 1 1 ? 0.731 10.160 16.111 1.00 78.42 1 A 1 ATOM 8 C CE . MET A 1 1 ? 0.736 11.883 16.561 1.00 67.75 1 A 1 ATOM 9 N N . GLN A 1 2 ? -2.395 7.204 11.570 1.00 92.17 2 A 1 ATOM 10 C CA . GLN A 1 2 ? -2.613 5.912 10.935 1.00 94.58 2 A 1 ATOM 11 C C . GLN A 1 2 ? -1.605 5.678 9.809 1.00 95.92 2 A 1 ATOM 12 O O . GLN A 1 2 ? -1.977 5.511 8.647 1.00 94.98 2 A 1 ATOM 13 C CB . GLN A 1 2 ? -4.032 5.842 10.390 1.00 92.46 2 A 1 ATOM 14 C CG . GLN A 1 2 ? -4.396 7.016 9.512 1.00 87.54 2 A 1 ATOM 15 C CD . GLN A 1 2 ? -5.822 6.932 9.023 1.00 85.77 2 A 1 ATOM 16 O OE1 . GLN A 1 2 ? -6.153 6.066 8.226 1.00 78.52 2 A 1 ATOM 17 N NE2 . GLN A 1 2 ? -6.674 7.815 9.493 1.00 77.41 2 A 1 ATOM 18 N N . PHE A 1 3 ? -0.340 5.683 10.162 1.00 93.37 3 A 1 ATOM 19 C CA . PHE A 1 3 ? 0.724 5.489 9.182 1.00 94.69 3 A 1 ATOM 20 C C . PHE A 1 3 ? 0.827 4.029 8.754 1.00 96.41 3 A 1 ATOM 21 O O . PHE A 1 3 ? 1.216 3.722 7.630 1.00 95.93 3 A 1 ATOM 22 C CB . PHE A 1 3 ? 2.056 5.958 9.769 1.00 93.45 3 A 1 ATOM 23 C CG . PHE A 1 3 ? 3.121 6.132 8.724 1.00 90.23 3 A 1 ATOM 24 C CD1 . PHE A 1 3 ? 3.084 7.215 7.863 1.00 88.34 3 A 1 ATOM 25 C CD2 . PHE A 1 3 ? 4.146 5.215 8.605 1.00 87.78 3 A 1 ATOM 26 C CE1 . PHE A 1 3 ? 4.054 7.381 6.894 1.00 87.55 3 A 1 ATOM 27 C CE2 . PHE A 1 3 ? 5.122 5.374 7.632 1.00 86.62 3 A 1 ATOM 28 C CZ . PHE A 1 3 ? 5.076 6.458 6.778 1.00 85.55 3 A 1 ATOM 29 N N . THR A 1 4 ? 0.447 3.138 9.647 1.00 94.44 4 A 1 ATOM 30 C CA . THR A 1 4 ? 0.492 1.706 9.370 1.00 95.32 4 A 1 ATOM 31 C C . THR A 1 4 ? -0.435 1.343 8.215 1.00 96.36 4 A 1 ATOM 32 O O . THR A 1 4 ? -0.114 0.493 7.387 1.00 95.86 4 A 1 ATOM 33 C CB . THR A 1 4 ? 0.089 0.895 10.605 1.00 94.67 4 A 1 ATOM 34 O OG1 . THR A 1 4 ? 0.849 1.320 11.734 1.00 88.72 4 A 1 ATOM 35 C CG2 . THR A 1 4 ? 0.314 -0.585 10.367 1.00 86.17 4 A 1 ATOM 36 N N . THR A 1 5 ? -1.577 1.999 8.147 1.00 95.98 5 A 1 ATOM 37 C CA . THR A 1 5 ? -2.553 1.734 7.097 1.00 96.46 5 A 1 ATOM 38 C C . THR A 1 5 ? -2.027 2.178 5.736 1.00 97.08 5 A 1 ATOM 39 O O . THR A 1 5 ? -2.396 1.623 4.707 1.00 96.69 5 A 1 ATOM 40 C CB . THR A 1 5 ? -3.886 2.446 7.390 1.00 95.87 5 A 1 ATOM 41 O OG1 . THR A 1 5 ? -4.916 1.874 6.587 1.00 90.57 5 A 1 ATOM 42 C CG2 . THR A 1 5 ? -3.792 3.929 7.090 1.00 88.89 5 A 1 ATOM 43 N N . ILE A 1 6 ? -1.159 3.173 5.738 1.00 97.14 6 A 1 ATOM 44 C CA . ILE A 1 6 ? -0.572 3.688 4.508 1.00 97.25 6 A 1 ATOM 45 C C . ILE A 1 6 ? 0.300 2.630 3.852 1.00 97.78 6 A 1 ATOM 46 O O . ILE A 1 6 ? 0.216 2.381 2.650 1.00 97.65 6 A 1 ATOM 47 C CB . ILE A 1 6 ? 0.260 4.948 4.778 1.00 96.97 6 A 1 ATOM 48 C CG1 . ILE A 1 6 ? -0.587 6.025 5.461 1.00 94.34 6 A 1 ATOM 49 C CG2 . ILE A 1 6 ? 0.832 5.481 3.467 1.00 93.56 6 A 1 ATOM 50 C CD1 . ILE A 1 6 ? -1.812 6.415 4.652 1.00 88.71 6 A 1 ATOM 51 N N . VAL A 1 7 ? 1.140 2.020 4.644 1.00 96.86 7 A 1 ATOM 52 C CA . VAL A 1 7 ? 2.041 0.988 4.147 1.00 97.22 7 A 1 ATOM 53 C C . VAL A 1 7 ? 1.268 -0.262 3.743 1.00 97.65 7 A 1 ATOM 54 O O . VAL A 1 7 ? 1.580 -0.909 2.745 1.00 97.67 7 A 1 ATOM 55 C CB . VAL A 1 7 ? 3.094 0.620 5.204 1.00 96.55 7 A 1 ATOM 56 C CG1 . VAL A 1 7 ? 4.049 -0.436 4.662 1.00 94.40 7 A 1 ATOM 57 C CG2 . VAL A 1 7 ? 3.865 1.858 5.641 1.00 94.00 7 A 1 ATOM 58 N N . MET A 1 8 ? 0.260 -0.594 4.520 1.00 97.31 8 A 1 ATOM 59 C CA . MET A 1 8 ? -0.547 -1.778 4.256 1.00 97.31 8 A 1 ATOM 60 C C . MET A 1 8 ? -1.427 -1.592 3.024 1.00 97.74 8 A 1 ATOM 61 O O . MET A 1 8 ? -1.603 -2.510 2.228 1.00 97.55 8 A 1 ATOM 62 C CB . MET A 1 8 ? -1.415 -2.097 5.471 1.00 96.96 8 A 1 ATOM 63 C CG . MET A 1 8 ? -1.847 -3.554 5.511 1.00 92.83 8 A 1 ATOM 64 S SD . MET A 1 8 ? -0.503 -4.633 5.994 1.00 86.63 8 A 1 ATOM 65 C CE . MET A 1 8 ? -1.352 -6.213 6.025 1.00 78.01 8 A 1 ATOM 66 N N . THR A 1 9 ? -1.968 -0.400 2.880 1.00 96.70 9 A 1 ATOM 67 C CA . THR A 1 9 ? -2.854 -0.099 1.761 1.00 97.00 9 A 1 ATOM 68 C C . THR A 1 9 ? -2.101 -0.075 0.435 1.00 97.67 9 A 1 ATOM 69 O O . THR A 1 9 ? -2.482 -0.753 -0.518 1.00 97.45 9 A 1 ATOM 70 C CB . THR A 1 9 ? -3.549 1.255 1.961 1.00 96.60 9 A 1 ATOM 71 O OG1 . THR A 1 9 ? -4.308 1.236 3.166 1.00 93.74 9 A 1 ATOM 72 C CG2 . THR A 1 9 ? -4.469 1.567 0.794 1.00 92.37 9 A 1 ATOM 73 N N . LEU A 1 10 ? -1.046 0.705 0.367 1.00 97.37 10 A 1 ATOM 74 C CA . LEU A 1 10 ? -0.270 0.820 -0.862 1.00 97.31 10 A 1 ATOM 75 C C . LEU A 1 10 ? 0.425 -0.495 -1.196 1.00 97.82 10 A 1 ATOM 76 O O . LEU A 1 10 ? 0.577 -0.849 -2.367 1.00 97.66 10 A 1 ATOM 77 C CB . LEU A 1 10 ? 0.752 1.956 -0.733 1.00 96.73 10 A 1 ATOM 78 C CG . LEU A 1 10 ? 1.895 1.696 0.247 1.00 91.70 10 A 1 ATOM 79 C CD1 . LEU A 1 10 ? 3.074 1.051 -0.459 1.00 91.46 10 A 1 ATOM 80 C CD2 . LEU A 1 10 ? 2.329 2.995 0.906 1.00 91.83 10 A 1 ATOM 81 N N . ALA A 1 11 ? 0.840 -1.215 -0.179 1.00 97.78 11 A 1 ATOM 82 C CA . ALA A 1 11 ? 1.509 -2.494 -0.376 1.00 97.79 11 A 1 ATOM 83 C C . ALA A 1 11 ? 0.560 -3.511 -0.989 1.00 98.12 11 A 1 ATOM 84 O O . ALA A 1 11 ? 0.949 -4.310 -1.840 1.00 97.80 11 A 1 ATOM 85 C CB . ALA A 1 11 ? 2.043 -3.017 0.953 1.00 97.22 11 A 1 ATOM 86 N N . ALA A 1 12 ? -0.691 -3.479 -0.562 1.00 98.02 12 A 1 ATOM 87 C CA . ALA A 1 12 ? -1.698 -4.398 -1.073 1.00 97.93 12 A 1 ATOM 88 C C . ALA A 1 12 ? -1.992 -4.123 -2.540 1.00 98.20 12 A 1 ATOM 89 O O . ALA A 1 12 ? -2.121 -5.048 -3.340 1.00 97.59 12 A 1 ATOM 90 C CB . ALA A 1 12 ? -2.976 -4.274 -0.248 1.00 97.31 12 A 1 ATOM 91 N N . ALA A 1 13 ? -2.096 -2.852 -2.894 1.00 98.05 13 A 1 ATOM 92 C CA . ALA A 1 13 ? -2.376 -2.458 -4.270 1.00 97.97 13 A 1 ATOM 93 C C . ALA A 1 13 ? -1.243 -2.859 -5.205 1.00 98.25 13 A 1 ATOM 94 O O . ALA A 1 13 ? -1.477 -3.350 -6.308 1.00 97.66 13 A 1 ATOM 95 C CB . ALA A 1 13 ? -2.609 -0.953 -4.338 1.00 97.32 13 A 1 ATOM 96 N N . VAL A 1 14 ? -0.019 -2.656 -4.769 1.00 98.20 14 A 1 ATOM 97 C CA . VAL A 1 14 ? 1.155 -3.002 -5.563 1.00 98.14 14 A 1 ATOM 98 C C . VAL A 1 14 ? 1.293 -4.511 -5.711 1.00 98.36 14 A 1 ATOM 99 O O . VAL A 1 14 ? 1.671 -5.016 -6.769 1.00 98.07 14 A 1 ATOM 100 C CB . VAL A 1 14 ? 2.430 -2.428 -4.928 1.00 97.42 14 A 1 ATOM 101 C CG1 . VAL A 1 14 ? 3.655 -2.858 -5.718 1.00 95.23 14 A 1 ATOM 102 C CG2 . VAL A 1 14 ? 2.345 -0.915 -4.859 1.00 95.37 14 A 1 ATOM 103 N N . ALA A 1 15 ? 0.978 -5.224 -4.651 1.00 98.34 15 A 1 ATOM 104 C CA . ALA A 1 15 ? 1.068 -6.679 -4.655 1.00 98.25 15 A 1 ATOM 105 C C . ALA A 1 15 ? 0.085 -7.290 -5.644 1.00 98.32 15 A 1 ATOM 106 O O . ALA A 1 15 ? 0.391 -8.285 -6.303 1.00 97.72 15 A 1 ATOM 107 C CB . ALA A 1 15 ? 0.805 -7.222 -3.255 1.00 97.76 15 A 1 ATOM 108 N N . VAL A 1 16 ? -1.102 -6.705 -5.754 1.00 97.84 16 A 1 ATOM 109 C CA . VAL A 1 16 ? -2.125 -7.192 -6.674 1.00 97.60 16 A 1 ATOM 110 C C . VAL A 1 16 ? -1.731 -6.919 -8.122 1.00 97.89 16 A 1 ATOM 111 O O . VAL A 1 16 ? -1.967 -7.740 -9.015 1.00 97.27 16 A 1 ATOM 112 C CB . VAL A 1 16 ? -3.489 -6.545 -6.376 1.00 96.41 16 A 1 ATOM 113 C CG1 . VAL A 1 16 ? -4.527 -6.987 -7.397 1.00 92.84 16 A 1 ATOM 114 C CG2 . VAL A 1 16 ? -3.952 -6.902 -4.973 1.00 92.71 16 A 1 ATOM 115 N N . THR A 1 17 ? -1.150 -5.756 -8.348 1.00 97.42 17 A 1 ATOM 116 C CA . THR A 1 17 ? -0.729 -5.366 -9.689 1.00 97.34 17 A 1 ATOM 117 C C . THR A 1 17 ? 0.477 -6.175 -10.155 1.00 97.42 17 A 1 ATOM 118 O O . THR A 1 17 ? 0.588 -6.536 -11.329 1.00 96.36 17 A 1 ATOM 119 C CB . THR A 1 17 ? -0.378 -3.875 -9.741 1.00 96.29 17 A 1 ATOM 120 O OG1 . THR A 1 17 ? -1.498 -3.100 -9.315 1.00 92.73 17 A 1 ATOM 121 C CG2 . THR A 1 17 ? 0.003 -3.461 -11.153 1.00 92.37 17 A 1 ATOM 122 N N . ALA A 1 18 ? 1.384 -6.440 -9.232 1.00 96.91 18 A 1 ATOM 123 C CA . ALA A 1 18 ? 2.601 -7.168 -9.546 1.00 95.59 18 A 1 ATOM 124 C C . ALA A 1 18 ? 2.388 -8.674 -9.465 1.00 94.59 18 A 1 ATOM 125 O O . ALA A 1 18 ? 1.511 -9.122 -8.714 1.00 92.15 18 A 1 ATOM 126 C CB . ALA A 1 18 ? 3.727 -6.736 -8.608 1.00 93.39 18 A 1 ATOM 127 O OXT . ALA A 1 18 ? 3.105 -9.408 -10.148 1.00 86.32 18 A 1 #