# 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_spkb38874 # _entry.id spkb38874 # 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 H9 N O4" 147.129 GLU y "GLUTAMIC ACID" C(CC(=O)O)[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 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" "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 VAL 2 1 n VAL 3 1 n ALA 4 1 n LEU 5 1 n LEU 6 1 n ALA 7 1 n VAL 8 1 n VAL 9 1 n ALA 10 1 n LEU 11 1 n SER 12 1 n LYS 13 1 n GLY 14 1 n GLU 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 @ 2025-07-08 18:08:26)" _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 90.44 _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 81.57 1 1 A VAL 2 2 94.37 1 2 A VAL 3 2 95.36 1 3 A ALA 4 2 96.44 1 4 A LEU 5 2 93.20 1 5 A LEU 6 2 93.20 1 6 A ALA 7 2 95.97 1 7 A VAL 8 2 95.44 1 8 A VAL 9 2 95.26 1 9 A ALA 10 2 95.41 1 10 A LEU 11 2 93.07 1 11 A SER 12 2 93.55 1 12 A LYS 13 2 87.70 1 13 A GLY 14 2 89.04 1 14 A GLU 15 2 77.67 1 15 A GLY 16 2 74.37 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 VAL . 2 A 2 A 3 1 n VAL . 3 A 3 A 4 1 n ALA . 4 A 4 A 5 1 n LEU . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n ALA . 7 A 7 A 8 1 n VAL . 8 A 8 A 9 1 n VAL . 9 A 9 A 10 1 n ALA . 10 A 10 A 11 1 n LEU . 11 A 11 A 12 1 n SER . 12 A 12 A 13 1 n LYS . 13 A 13 A 14 1 n GLY . 14 A 14 A 15 1 n GLU . 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 ? -12.443 2.434 -1.877 1.00 88.75 1 A 1 ATOM 2 C CA . MET A 1 1 ? -12.298 1.992 -0.472 1.00 89.34 1 A 1 ATOM 3 C C . MET A 1 1 ? -10.961 2.454 0.115 1.00 89.04 1 A 1 ATOM 4 O O . MET A 1 1 ? -9.941 2.434 -0.561 1.00 85.29 1 A 1 ATOM 5 C CB . MET A 1 1 ? -12.376 0.469 -0.386 1.00 83.03 1 A 1 ATOM 6 C CG . MET A 1 1 ? -13.783 -0.054 -0.642 1.00 76.63 1 A 1 ATOM 7 S SD . MET A 1 1 ? -14.096 -1.574 0.256 1.00 74.93 1 A 1 ATOM 8 C CE . MET A 1 1 ? -15.880 -1.501 0.398 1.00 65.53 1 A 1 ATOM 9 N N . VAL A 1 2 ? -10.979 2.860 1.377 1.00 94.96 2 A 1 ATOM 10 C CA . VAL A 1 2 ? -9.772 3.336 2.064 1.00 96.34 2 A 1 ATOM 11 C C . VAL A 1 2 ? -8.759 2.203 2.242 1.00 97.24 2 A 1 ATOM 12 O O . VAL A 1 2 ? -7.548 2.407 2.125 1.00 96.40 2 A 1 ATOM 13 C CB . VAL A 1 2 ? -10.134 3.934 3.438 1.00 94.78 2 A 1 ATOM 14 C CG1 . VAL A 1 2 ? -8.896 4.480 4.126 1.00 89.83 2 A 1 ATOM 15 C CG2 . VAL A 1 2 ? -11.167 5.047 3.280 1.00 91.07 2 A 1 ATOM 16 N N . VAL A 1 3 ? -9.251 1.011 2.521 1.00 96.59 3 A 1 ATOM 17 C CA . VAL A 1 3 ? -8.389 -0.161 2.720 1.00 96.85 3 A 1 ATOM 18 C C . VAL A 1 3 ? -7.573 -0.459 1.464 1.00 97.36 3 A 1 ATOM 19 O O . VAL A 1 3 ? -6.379 -0.774 1.537 1.00 96.57 3 A 1 ATOM 20 C CB . VAL A 1 3 ? -9.228 -1.391 3.101 1.00 95.87 3 A 1 ATOM 21 C CG1 . VAL A 1 3 ? -8.329 -2.592 3.352 1.00 91.64 3 A 1 ATOM 22 C CG2 . VAL A 1 3 ? -10.064 -1.100 4.344 1.00 92.67 3 A 1 ATOM 23 N N . ALA A 1 4 ? -8.209 -0.356 0.309 1.00 96.28 4 A 1 ATOM 24 C CA . ALA A 1 4 ? -7.539 -0.611 -0.968 1.00 96.71 4 A 1 ATOM 25 C C . ALA A 1 4 ? -6.432 0.411 -1.217 1.00 97.17 4 A 1 ATOM 26 O O . ALA A 1 4 ? -5.347 0.065 -1.685 1.00 96.02 4 A 1 ATOM 27 C CB . ALA A 1 4 ? -8.561 -0.569 -2.100 1.00 96.03 4 A 1 ATOM 28 N N . LEU A 1 5 ? -6.707 1.673 -0.896 1.00 96.43 5 A 1 ATOM 29 C CA . LEU A 1 5 ? -5.730 2.748 -1.076 1.00 96.54 5 A 1 ATOM 30 C C . LEU A 1 5 ? -4.506 2.517 -0.190 1.00 97.09 5 A 1 ATOM 31 O O . LEU A 1 5 ? -3.370 2.717 -0.622 1.00 96.35 5 A 1 ATOM 32 C CB . LEU A 1 5 ? -6.380 4.098 -0.738 1.00 95.83 5 A 1 ATOM 33 C CG . LEU A 1 5 ? -5.536 5.306 -1.149 1.00 88.65 5 A 1 ATOM 34 C CD1 . LEU A 1 5 ? -5.520 5.449 -2.667 1.00 87.92 5 A 1 ATOM 35 C CD2 . LEU A 1 5 ? -6.088 6.580 -0.519 1.00 86.79 5 A 1 ATOM 36 N N . LEU A 1 6 ? -4.746 2.090 1.041 1.00 96.36 6 A 1 ATOM 37 C CA . LEU A 1 6 ? -3.661 1.822 1.987 1.00 96.28 6 A 1 ATOM 38 C C . LEU A 1 6 ? -2.751 0.711 1.472 1.00 96.80 6 A 1 ATOM 39 O O . LEU A 1 6 ? -1.526 0.788 1.594 1.00 96.06 6 A 1 ATOM 40 C CB . LEU A 1 6 ? -4.258 1.427 3.343 1.00 95.25 6 A 1 ATOM 41 C CG . LEU A 1 6 ? -4.446 2.612 4.292 1.00 88.92 6 A 1 ATOM 42 C CD1 . LEU A 1 6 ? -5.392 2.245 5.428 1.00 88.66 6 A 1 ATOM 43 C CD2 . LEU A 1 6 ? -3.099 3.040 4.862 1.00 87.29 6 A 1 ATOM 44 N N . ALA A 1 7 ? -3.343 -0.315 0.892 1.00 96.07 7 A 1 ATOM 45 C CA . ALA A 1 7 ? -2.583 -1.439 0.347 1.00 96.12 7 A 1 ATOM 46 C C . ALA A 1 7 ? -1.687 -0.989 -0.804 1.00 96.54 7 A 1 ATOM 47 O O . ALA A 1 7 ? -0.540 -1.422 -0.914 1.00 95.59 7 A 1 ATOM 48 C CB . ALA A 1 7 ? -3.545 -2.523 -0.127 1.00 95.55 7 A 1 ATOM 49 N N . VAL A 1 8 ? -2.205 -0.116 -1.661 1.00 96.34 8 A 1 ATOM 50 C CA . VAL A 1 8 ? -1.446 0.398 -2.805 1.00 96.42 8 A 1 ATOM 51 C C . VAL A 1 8 ? -0.235 1.197 -2.336 1.00 96.74 8 A 1 ATOM 52 O O . VAL A 1 8 ? 0.867 1.041 -2.866 1.00 95.59 8 A 1 ATOM 53 C CB . VAL A 1 8 ? -2.337 1.279 -3.696 1.00 95.64 8 A 1 ATOM 54 C CG1 . VAL A 1 8 ? -1.521 1.904 -4.822 1.00 93.27 8 A 1 ATOM 55 C CG2 . VAL A 1 8 ? -3.475 0.457 -4.278 1.00 94.06 8 A 1 ATOM 56 N N . VAL A 1 9 ? -0.439 2.056 -1.344 1.00 96.87 9 A 1 ATOM 57 C CA . VAL A 1 9 ? 0.646 2.880 -0.802 1.00 96.49 9 A 1 ATOM 58 C C . VAL A 1 9 ? 1.730 2.003 -0.186 1.00 96.63 9 A 1 ATOM 59 O O . VAL A 1 9 ? 2.923 2.234 -0.394 1.00 95.66 9 A 1 ATOM 60 C CB . VAL A 1 9 ? 0.110 3.863 0.251 1.00 95.71 9 A 1 ATOM 61 C CG1 . VAL A 1 9 ? 1.250 4.649 0.890 1.00 92.31 9 A 1 ATOM 62 C CG2 . VAL A 1 9 ? -0.884 4.824 -0.383 1.00 93.12 9 A 1 ATOM 63 N N . ALA A 1 10 ? 1.319 1.002 0.570 1.00 95.87 10 A 1 ATOM 64 C CA . ALA A 1 10 ? 2.260 0.092 1.220 1.00 95.60 10 A 1 ATOM 65 C C . ALA A 1 10 ? 3.074 -0.687 0.190 1.00 96.01 10 A 1 ATOM 66 O O . ALA A 1 10 ? 4.278 -0.883 0.360 1.00 94.71 10 A 1 ATOM 67 C CB . ALA A 1 10 ? 1.502 -0.870 2.124 1.00 94.84 10 A 1 ATOM 68 N N . LEU A 1 11 ? 2.421 -1.124 -0.881 1.00 96.86 11 A 1 ATOM 69 C CA . LEU A 1 11 ? 3.083 -1.887 -1.939 1.00 96.55 11 A 1 ATOM 70 C C . LEU A 1 11 ? 4.081 -1.018 -2.692 1.00 96.69 11 A 1 ATOM 71 O O . LEU A 1 11 ? 5.189 -1.453 -3.011 1.00 95.00 11 A 1 ATOM 72 C CB . LEU A 1 11 ? 2.029 -2.442 -2.899 1.00 95.93 11 A 1 ATOM 73 C CG . LEU A 1 11 ? 2.247 -3.909 -3.251 1.00 90.42 11 A 1 ATOM 74 C CD1 . LEU A 1 11 ? 0.965 -4.510 -3.815 1.00 87.11 11 A 1 ATOM 75 C CD2 . LEU A 1 11 ? 3.374 -4.070 -4.249 1.00 85.98 11 A 1 ATOM 76 N N . SER A 1 12 ? 3.697 0.225 -2.978 1.00 95.84 12 A 1 ATOM 77 C CA . SER A 1 12 ? 4.553 1.167 -3.699 1.00 95.63 12 A 1 ATOM 78 C C . SER A 1 12 ? 5.828 1.467 -2.923 1.00 95.56 12 A 1 ATOM 79 O O . SER A 1 12 ? 6.922 1.483 -3.489 1.00 93.91 12 A 1 ATOM 80 C CB . SER A 1 12 ? 3.794 2.465 -3.968 1.00 94.47 12 A 1 ATOM 81 O OG . SER A 1 12 ? 4.579 3.339 -4.741 1.00 85.86 12 A 1 ATOM 82 N N . LYS A 1 13 ? 5.699 1.703 -1.629 1.00 95.81 13 A 1 ATOM 83 C CA . LYS A 1 13 ? 6.856 2.027 -0.789 1.00 95.46 13 A 1 ATOM 84 C C . LYS A 1 13 ? 7.660 0.777 -0.444 1.00 94.62 13 A 1 ATOM 85 O O . LYS A 1 13 ? 8.882 0.834 -0.320 1.00 90.92 13 A 1 ATOM 86 C CB . LYS A 1 13 ? 6.373 2.716 0.489 1.00 93.58 13 A 1 ATOM 87 C CG . LYS A 1 13 ? 7.490 3.484 1.167 1.00 87.06 13 A 1 ATOM 88 C CD . LYS A 1 13 ? 7.001 4.239 2.381 1.00 83.20 13 A 1 ATOM 89 C CE . LYS A 1 13 ? 8.175 4.780 3.189 1.00 77.20 13 A 1 ATOM 90 N NZ . LYS A 1 13 ? 7.954 4.589 4.632 1.00 71.43 13 A 1 ATOM 91 N N . GLY A 1 14 ? 6.992 -0.340 -0.287 1.00 90.83 14 A 1 ATOM 92 C CA . GLY A 1 14 ? 7.658 -1.596 0.047 1.00 89.08 14 A 1 ATOM 93 C C . GLY A 1 14 ? 8.455 -2.170 -1.109 1.00 89.34 14 A 1 ATOM 94 O O . GLY A 1 14 ? 9.478 -2.826 -0.904 1.00 86.92 14 A 1 ATOM 95 N N . GLU A 1 15 ? 7.987 -1.926 -2.327 1.00 89.36 15 A 1 ATOM 96 C CA . GLU A 1 15 ? 8.653 -2.447 -3.527 1.00 87.41 15 A 1 ATOM 97 C C . GLU A 1 15 ? 9.457 -1.378 -4.262 1.00 86.17 15 A 1 ATOM 98 O O . GLU A 1 15 ? 10.076 -1.668 -5.285 1.00 78.41 15 A 1 ATOM 99 C CB . GLU A 1 15 ? 7.600 -3.047 -4.469 1.00 83.69 15 A 1 ATOM 100 C CG . GLU A 1 15 ? 7.117 -4.403 -4.000 1.00 75.86 15 A 1 ATOM 101 C CD . GLU A 1 15 ? 7.924 -5.523 -4.639 1.00 70.21 15 A 1 ATOM 102 O OE1 . GLU A 1 15 ? 7.558 -5.938 -5.748 1.00 62.74 15 A 1 ATOM 103 O OE2 . GLU A 1 15 ? 8.908 -5.966 -4.031 1.00 65.16 15 A 1 ATOM 104 N N . GLY A 1 16 ? 9.461 -0.165 -3.766 1.00 81.48 16 A 1 ATOM 105 C CA . GLY A 1 16 ? 10.161 0.942 -4.429 1.00 77.40 16 A 1 ATOM 106 C C . GLY A 1 16 ? 10.893 1.845 -3.449 1.00 74.76 16 A 1 ATOM 107 O O . GLY A 1 16 ? 10.827 3.069 -3.598 1.00 68.72 16 A 1 ATOM 108 O OXT . GLY A 1 16 ? 11.572 1.410 -2.572 1.00 69.48 16 A 1 #