# 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_spkb24837 # _entry.id spkb24837 # 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 H15 N4 O2" 175.209 ARG y ARGININE C(C[C@@H](C(=O)O)N)CNC(=[NH2+])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" "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" "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 VAL 2 1 n ARG 3 1 n LEU 4 1 n ALA 5 1 n SER 6 1 n LEU 7 1 n ALA 8 1 n VAL 9 1 n LEU 10 1 n GLY 11 1 n SER 12 1 n VAL 13 1 n ILE 14 1 n ALA 15 1 n THR 16 1 n ALA 17 1 n SER 18 1 n ALA 19 # _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 14:18:55)" _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 91.84 _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 82.92 1 1 A VAL 2 2 89.09 1 2 A ARG 3 2 86.59 1 3 A LEU 4 2 91.88 1 4 A ALA 5 2 96.60 1 5 A SER 6 2 94.54 1 6 A LEU 7 2 93.03 1 7 A ALA 8 2 96.46 1 8 A VAL 9 2 95.63 1 9 A LEU 10 2 93.31 1 10 A GLY 11 2 95.86 1 11 A SER 12 2 93.43 1 12 A VAL 13 2 94.59 1 13 A ILE 14 2 92.28 1 14 A ALA 15 2 96.39 1 15 A THR 16 2 93.52 1 16 A ALA 17 2 94.62 1 17 A SER 18 2 90.04 1 18 A ALA 19 2 83.78 1 19 # _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 ARG . 3 A 3 A 4 1 n LEU . 4 A 4 A 5 1 n ALA . 5 A 5 A 6 1 n SER . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n ALA . 8 A 8 A 9 1 n VAL . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n GLY . 11 A 11 A 12 1 n SER . 12 A 12 A 13 1 n VAL . 13 A 13 A 14 1 n ILE . 14 A 14 A 15 1 n ALA . 15 A 15 A 16 1 n THR . 16 A 16 A 17 1 n ALA . 17 A 17 A 18 1 n SER . 18 A 18 A 19 1 n ALA . 19 A 19 # _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 ? -13.197 -4.111 0.446 1.00 88.04 1 A 1 ATOM 2 C CA . MET A 1 1 ? -12.123 -4.180 1.454 1.00 89.66 1 A 1 ATOM 3 C C . MET A 1 1 ? -10.867 -3.470 0.942 1.00 90.11 1 A 1 ATOM 4 O O . MET A 1 1 ? -9.891 -4.104 0.562 1.00 86.30 1 A 1 ATOM 5 C CB . MET A 1 1 ? -11.813 -5.638 1.766 1.00 84.27 1 A 1 ATOM 6 C CG . MET A 1 1 ? -11.377 -5.824 3.202 1.00 80.43 1 A 1 ATOM 7 S SD . MET A 1 1 ? -11.365 -7.553 3.652 1.00 77.13 1 A 1 ATOM 8 C CE . MET A 1 1 ? -10.824 -7.424 5.349 1.00 67.42 1 A 1 ATOM 9 N N . VAL A 1 2 ? -10.920 -2.152 0.919 1.00 90.50 2 A 1 ATOM 10 C CA . VAL A 1 2 ? -9.795 -1.352 0.420 1.00 92.31 2 A 1 ATOM 11 C C . VAL A 1 2 ? -8.942 -0.788 1.554 1.00 93.83 2 A 1 ATOM 12 O O . VAL A 1 2 ? -8.078 0.059 1.329 1.00 91.40 2 A 1 ATOM 13 C CB . VAL A 1 2 ? -10.318 -0.196 -0.445 1.00 89.44 2 A 1 ATOM 14 C CG1 . VAL A 1 2 ? -10.978 -0.734 -1.702 1.00 82.50 2 A 1 ATOM 15 C CG2 . VAL A 1 2 ? -11.293 0.658 0.356 1.00 83.63 2 A 1 ATOM 16 N N . ARG A 1 3 ? -9.212 -1.254 2.772 1.00 93.38 3 A 1 ATOM 17 C CA . ARG A 1 3 ? -8.449 -0.773 3.934 1.00 94.79 3 A 1 ATOM 18 C C . ARG A 1 3 ? -6.998 -1.231 3.855 1.00 95.65 3 A 1 ATOM 19 O O . ARG A 1 3 ? -6.073 -0.434 4.003 1.00 94.53 3 A 1 ATOM 20 C CB . ARG A 1 3 ? -9.087 -1.295 5.222 1.00 92.88 3 A 1 ATOM 21 C CG . ARG A 1 3 ? -10.211 -0.421 5.702 1.00 87.53 3 A 1 ATOM 22 C CD . ARG A 1 3 ? -10.571 -0.790 7.132 1.00 86.41 3 A 1 ATOM 23 N NE . ARG A 1 3 ? -9.397 -0.635 7.998 1.00 81.01 3 A 1 ATOM 24 C CZ . ARG A 1 3 ? -9.304 -1.144 9.215 1.00 79.98 3 A 1 ATOM 25 N NH1 . ARG A 1 3 ? -10.296 -1.835 9.734 1.00 72.37 3 A 1 ATOM 26 N NH2 . ARG A 1 3 ? -8.194 -0.973 9.914 1.00 73.94 3 A 1 ATOM 27 N N . LEU A 1 4 ? -6.802 -2.513 3.620 1.00 94.54 4 A 1 ATOM 28 C CA . LEU A 1 4 ? -5.459 -3.082 3.523 1.00 95.53 4 A 1 ATOM 29 C C . LEU A 1 4 ? -4.700 -2.431 2.371 1.00 96.39 4 A 1 ATOM 30 O O . LEU A 1 4 ? -3.518 -2.102 2.487 1.00 95.19 4 A 1 ATOM 31 C CB . LEU A 1 4 ? -5.550 -4.600 3.311 1.00 94.03 4 A 1 ATOM 32 C CG . LEU A 1 4 ? -4.482 -5.374 4.075 1.00 88.41 4 A 1 ATOM 33 C CD1 . LEU A 1 4 ? -3.086 -4.894 3.716 1.00 86.37 4 A 1 ATOM 34 C CD2 . LEU A 1 4 ? -4.719 -5.231 5.573 1.00 84.56 4 A 1 ATOM 35 N N . ALA A 1 5 ? -5.390 -2.251 1.258 1.00 96.47 5 A 1 ATOM 36 C CA . ALA A 1 5 ? -4.787 -1.628 0.080 1.00 96.83 5 A 1 ATOM 37 C C . ALA A 1 5 ? -4.348 -0.197 0.380 1.00 97.27 5 A 1 ATOM 38 O O . ALA A 1 5 ? -3.273 0.233 -0.036 1.00 96.46 5 A 1 ATOM 39 C CB . ALA A 1 5 ? -5.785 -1.647 -1.072 1.00 95.99 5 A 1 ATOM 40 N N . SER A 1 6 ? -5.174 0.531 1.107 1.00 95.89 6 A 1 ATOM 41 C CA . SER A 1 6 ? -4.871 1.918 1.460 1.00 96.07 6 A 1 ATOM 42 C C . SER A 1 6 ? -3.593 2.002 2.294 1.00 96.67 6 A 1 ATOM 43 O O . SER A 1 6 ? -2.698 2.795 2.007 1.00 95.80 6 A 1 ATOM 44 C CB . SER A 1 6 ? -6.038 2.527 2.236 1.00 94.71 6 A 1 ATOM 45 O OG . SER A 1 6 ? -5.789 3.885 2.487 1.00 88.07 6 A 1 ATOM 46 N N . LEU A 1 7 ? -3.515 1.169 3.319 1.00 95.54 7 A 1 ATOM 47 C CA . LEU A 1 7 ? -2.342 1.157 4.195 1.00 95.77 7 A 1 ATOM 48 C C . LEU A 1 7 ? -1.106 0.674 3.447 1.00 96.61 7 A 1 ATOM 49 O O . LEU A 1 7 ? -0.020 1.237 3.594 1.00 95.70 7 A 1 ATOM 50 C CB . LEU A 1 7 ? -2.621 0.241 5.388 1.00 94.87 7 A 1 ATOM 51 C CG . LEU A 1 7 ? -3.588 0.857 6.396 1.00 89.96 7 A 1 ATOM 52 C CD1 . LEU A 1 7 ? -4.127 -0.211 7.337 1.00 88.34 7 A 1 ATOM 53 C CD2 . LEU A 1 7 ? -2.886 1.946 7.196 1.00 87.48 7 A 1 ATOM 54 N N . ALA A 1 8 ? -1.276 -0.365 2.655 1.00 96.44 8 A 1 ATOM 55 C CA . ALA A 1 8 ? -0.168 -0.927 1.888 1.00 96.55 8 A 1 ATOM 56 C C . ALA A 1 8 ? 0.362 0.076 0.869 1.00 97.07 8 A 1 ATOM 57 O O . ALA A 1 8 ? 1.572 0.272 0.749 1.00 96.35 8 A 1 ATOM 58 C CB . ALA A 1 8 ? -0.628 -2.199 1.185 1.00 95.89 8 A 1 ATOM 59 N N . VAL A 1 9 ? -0.538 0.704 0.141 1.00 96.45 9 A 1 ATOM 60 C CA . VAL A 1 9 ? -0.156 1.687 -0.875 1.00 96.60 9 A 1 ATOM 61 C C . VAL A 1 9 ? 0.566 2.863 -0.229 1.00 96.92 9 A 1 ATOM 62 O O . VAL A 1 9 ? 1.623 3.291 -0.696 1.00 96.32 9 A 1 ATOM 63 C CB . VAL A 1 9 ? -1.394 2.183 -1.634 1.00 96.04 9 A 1 ATOM 64 C CG1 . VAL A 1 9 ? -1.027 3.333 -2.561 1.00 93.62 9 A 1 ATOM 65 C CG2 . VAL A 1 9 ? -2.006 1.044 -2.434 1.00 93.43 9 A 1 ATOM 66 N N . LEU A 1 10 ? -0.003 3.370 0.841 1.00 95.97 10 A 1 ATOM 67 C CA . LEU A 1 10 ? 0.601 4.497 1.549 1.00 95.81 10 A 1 ATOM 68 C C . LEU A 1 10 ? 1.997 4.134 2.045 1.00 96.29 10 A 1 ATOM 69 O O . LEU A 1 10 ? 2.943 4.905 1.890 1.00 95.65 10 A 1 ATOM 70 C CB . LEU A 1 10 ? -0.283 4.899 2.732 1.00 95.30 10 A 1 ATOM 71 C CG . LEU A 1 10 ? 0.115 6.239 3.346 1.00 90.56 10 A 1 ATOM 72 C CD1 . LEU A 1 10 ? -0.231 7.383 2.397 1.00 88.88 10 A 1 ATOM 73 C CD2 . LEU A 1 10 ? -0.598 6.432 4.680 1.00 88.06 10 A 1 ATOM 74 N N . GLY A 1 11 ? 2.123 2.967 2.644 1.00 95.72 11 A 1 ATOM 75 C CA . GLY A 1 11 ? 3.415 2.505 3.147 1.00 95.31 11 A 1 ATOM 76 C C . GLY A 1 11 ? 4.430 2.361 2.033 1.00 96.30 11 A 1 ATOM 77 O O . GLY A 1 11 ? 5.601 2.711 2.191 1.00 96.10 11 A 1 ATOM 78 N N . SER A 1 12 ? 3.988 1.849 0.899 1.00 95.46 12 A 1 ATOM 79 C CA . SER A 1 12 ? 4.859 1.669 -0.262 1.00 95.54 12 A 1 ATOM 80 C C . SER A 1 12 ? 5.400 3.011 -0.742 1.00 96.26 12 A 1 ATOM 81 O O . SER A 1 12 ? 6.593 3.154 -1.007 1.00 94.60 12 A 1 ATOM 82 C CB . SER A 1 12 ? 4.093 0.988 -1.394 1.00 94.23 12 A 1 ATOM 83 O OG . SER A 1 12 ? 4.958 0.754 -2.482 1.00 84.47 12 A 1 ATOM 84 N N . VAL A 1 13 ? 4.524 3.991 -0.840 1.00 95.37 13 A 1 ATOM 85 C CA . VAL A 1 13 ? 4.917 5.329 -1.281 1.00 95.78 13 A 1 ATOM 86 C C . VAL A 1 13 ? 5.911 5.946 -0.303 1.00 96.61 13 A 1 ATOM 87 O O . VAL A 1 13 ? 6.909 6.547 -0.707 1.00 95.89 13 A 1 ATOM 88 C CB . VAL A 1 13 ? 3.688 6.240 -1.411 1.00 94.89 13 A 1 ATOM 89 C CG1 . VAL A 1 13 ? 4.109 7.650 -1.800 1.00 91.78 13 A 1 ATOM 90 C CG2 . VAL A 1 13 ? 2.725 5.676 -2.444 1.00 91.79 13 A 1 ATOM 91 N N . ILE A 1 14 ? 5.640 5.787 0.974 1.00 95.41 14 A 1 ATOM 92 C CA . ILE A 1 14 ? 6.514 6.327 2.012 1.00 94.75 14 A 1 ATOM 93 C C . ILE A 1 14 ? 7.893 5.687 1.935 1.00 95.21 14 A 1 ATOM 94 O O . ILE A 1 14 ? 8.916 6.369 2.042 1.00 94.63 14 A 1 ATOM 95 C CB . ILE A 1 14 ? 5.907 6.088 3.399 1.00 94.10 14 A 1 ATOM 96 C CG1 . ILE A 1 14 ? 4.623 6.905 3.561 1.00 90.89 14 A 1 ATOM 97 C CG2 . ILE A 1 14 ? 6.913 6.485 4.485 1.00 89.65 14 A 1 ATOM 98 C CD1 . ILE A 1 14 ? 3.784 6.439 4.737 1.00 83.62 14 A 1 ATOM 99 N N . ALA A 1 15 ? 7.920 4.377 1.759 1.00 96.85 15 A 1 ATOM 100 C CA . ALA A 1 15 ? 9.184 3.650 1.664 1.00 96.54 15 A 1 ATOM 101 C C . ALA A 1 15 ? 9.998 4.145 0.474 1.00 96.95 15 A 1 ATOM 102 O O . ALA A 1 15 ? 11.213 4.314 0.567 1.00 95.90 15 A 1 ATOM 103 C CB . ALA A 1 15 ? 8.910 2.158 1.530 1.00 95.70 15 A 1 ATOM 104 N N . THR A 1 16 ? 9.332 4.373 -0.641 1.00 96.35 16 A 1 ATOM 105 C CA . THR A 1 16 ? 9.998 4.857 -1.851 1.00 95.76 16 A 1 ATOM 106 C C . THR A 1 16 ? 10.520 6.276 -1.648 1.00 96.15 16 A 1 ATOM 107 O O . THR A 1 16 ? 11.642 6.603 -2.042 1.00 95.41 16 A 1 ATOM 108 C CB . THR A 1 16 ? 9.025 4.844 -3.033 1.00 94.53 16 A 1 ATOM 109 O OG1 . THR A 1 16 ? 8.484 3.536 -3.185 1.00 88.91 16 A 1 ATOM 110 C CG2 . THR A 1 16 ? 9.741 5.233 -4.316 1.00 87.56 16 A 1 ATOM 111 N N . ALA A 1 17 ? 9.711 7.116 -1.040 1.00 95.48 17 A 1 ATOM 112 C CA . ALA A 1 17 ? 10.088 8.505 -0.786 1.00 94.76 17 A 1 ATOM 113 C C . ALA A 1 17 ? 11.166 8.604 0.288 1.00 95.45 17 A 1 ATOM 114 O O . ALA A 1 17 ? 11.930 9.565 0.322 1.00 94.18 17 A 1 ATOM 115 C CB . ALA A 1 17 ? 8.856 9.301 -0.363 1.00 93.25 17 A 1 ATOM 116 N N . SER A 1 18 ? 11.228 7.606 1.162 1.00 94.19 18 A 1 ATOM 117 C CA . SER A 1 18 ? 12.212 7.588 2.250 1.00 93.28 18 A 1 ATOM 118 C C . SER A 1 18 ? 13.636 7.598 1.708 1.00 92.49 18 A 1 ATOM 119 O O . SER A 1 18 ? 14.545 8.140 2.338 1.00 89.11 18 A 1 ATOM 120 C CB . SER A 1 18 ? 12.014 6.347 3.117 1.00 90.86 18 A 1 ATOM 121 O OG . SER A 1 18 ? 12.917 6.354 4.200 1.00 80.32 18 A 1 ATOM 122 N N . ALA A 1 19 ? 13.837 7.011 0.548 1.00 89.89 19 A 1 ATOM 123 C CA . ALA A 1 19 ? 15.160 6.939 -0.077 1.00 87.55 19 A 1 ATOM 124 C C . ALA A 1 19 ? 15.622 8.317 -0.540 1.00 85.79 19 A 1 ATOM 125 O O . ALA A 1 19 ? 16.627 8.407 -1.253 1.00 81.72 19 A 1 ATOM 126 C CB . ALA A 1 19 ? 15.111 5.965 -1.247 1.00 81.86 19 A 1 ATOM 127 O OXT . ALA A 1 19 ? 14.980 9.332 -0.176 1.00 75.88 19 A 1 #