# 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_spkb08937 # _entry.id spkb08937 # 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 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" "C5 H9 N O2" 115.130 PRO y PROLINE C1C[C@H](NC1)C(=O)O ? "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 ARG 2 1 n LEU 3 1 n SER 4 1 n VAL 5 1 n LEU 6 1 n LEU 7 1 n SER 8 1 n LEU 9 1 n LEU 10 1 n PRO 11 1 n LEU 12 1 n ALA 13 1 n LEU 14 1 n GLY 15 # _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 13:18:12)" _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 93.95 _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 83.19 1 1 A ARG 2 2 89.38 1 2 A LEU 3 2 93.08 1 3 A SER 4 2 96.18 1 4 A VAL 5 2 96.67 1 5 A LEU 6 2 95.01 1 6 A LEU 7 2 95.39 1 7 A SER 8 2 96.85 1 8 A LEU 9 2 96.46 1 9 A LEU 10 2 95.71 1 10 A PRO 11 2 97.49 1 11 A LEU 12 2 95.74 1 12 A ALA 13 2 97.11 1 13 A LEU 14 2 94.20 1 14 A GLY 15 2 90.35 1 15 # _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 ARG . 2 A 2 A 3 1 n LEU . 3 A 3 A 4 1 n SER . 4 A 4 A 5 1 n VAL . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n SER . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n PRO . 11 A 11 A 12 1 n LEU . 12 A 12 A 13 1 n ALA . 13 A 13 A 14 1 n LEU . 14 A 14 A 15 1 n GLY . 15 A 15 # _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 ? 7.589 -7.480 3.072 1.00 89.17 1 A 1 ATOM 2 C CA . MET A 1 1 ? 6.521 -6.542 2.679 1.00 90.43 1 A 1 ATOM 3 C C . MET A 1 1 ? 7.071 -5.122 2.553 1.00 91.89 1 A 1 ATOM 4 O O . MET A 1 1 ? 7.909 -4.696 3.339 1.00 88.06 1 A 1 ATOM 5 C CB . MET A 1 1 ? 5.410 -6.547 3.724 1.00 84.81 1 A 1 ATOM 6 C CG . MET A 1 1 ? 5.913 -6.216 5.121 1.00 78.36 1 A 1 ATOM 7 S SD . MET A 1 1 ? 4.626 -6.285 6.372 1.00 76.58 1 A 1 ATOM 8 C CE . MET A 1 1 ? 4.343 -8.038 6.432 1.00 66.25 1 A 1 ATOM 9 N N . ARG A 1 2 ? 6.591 -4.391 1.580 1.00 93.95 2 A 1 ATOM 10 C CA . ARG A 1 2 ? 7.061 -3.025 1.341 1.00 95.87 2 A 1 ATOM 11 C C . ARG A 1 2 ? 6.067 -1.993 1.884 1.00 97.02 2 A 1 ATOM 12 O O . ARG A 1 2 ? 4.857 -2.215 1.877 1.00 95.98 2 A 1 ATOM 13 C CB . ARG A 1 2 ? 7.278 -2.853 -0.160 1.00 94.39 2 A 1 ATOM 14 C CG . ARG A 1 2 ? 8.455 -3.705 -0.625 1.00 90.05 2 A 1 ATOM 15 C CD . ARG A 1 2 ? 8.481 -3.862 -2.116 1.00 89.43 2 A 1 ATOM 16 N NE . ARG A 1 2 ? 9.621 -4.689 -2.521 1.00 84.98 2 A 1 ATOM 17 C CZ . ARG A 1 2 ? 9.690 -5.998 -2.323 1.00 84.71 2 A 1 ATOM 18 N NH1 . ARG A 1 2 ? 8.702 -6.645 -1.731 1.00 77.51 2 A 1 ATOM 19 N NH2 . ARG A 1 2 ? 10.754 -6.663 -2.725 1.00 79.33 2 A 1 ATOM 20 N N . LEU A 1 3 ? 6.575 -0.856 2.334 1.00 95.41 3 A 1 ATOM 21 C CA . LEU A 1 3 ? 5.741 0.210 2.897 1.00 95.85 3 A 1 ATOM 22 C C . LEU A 1 3 ? 4.735 0.733 1.875 1.00 96.85 3 A 1 ATOM 23 O O . LEU A 1 3 ? 3.562 0.936 2.189 1.00 95.92 3 A 1 ATOM 24 C CB . LEU A 1 3 ? 6.639 1.351 3.383 1.00 95.10 3 A 1 ATOM 25 C CG . LEU A 1 3 ? 7.622 0.925 4.481 1.00 91.48 3 A 1 ATOM 26 C CD1 . LEU A 1 3 ? 8.557 2.082 4.809 1.00 87.38 3 A 1 ATOM 27 C CD2 . LEU A 1 3 ? 6.862 0.491 5.730 1.00 86.62 3 A 1 ATOM 28 N N . SER A 1 4 ? 5.169 0.949 0.659 1.00 97.90 4 A 1 ATOM 29 C CA . SER A 1 4 ? 4.294 1.457 -0.405 1.00 97.91 4 A 1 ATOM 30 C C . SER A 1 4 ? 3.156 0.482 -0.703 1.00 98.07 4 A 1 ATOM 31 O O . SER A 1 4 ? 2.045 0.884 -1.042 1.00 97.38 4 A 1 ATOM 32 C CB . SER A 1 4 ? 5.105 1.693 -1.673 1.00 97.13 4 A 1 ATOM 33 O OG . SER A 1 4 ? 6.103 2.667 -1.440 1.00 88.67 4 A 1 ATOM 34 N N . VAL A 1 5 ? 3.427 -0.795 -0.585 1.00 97.67 5 A 1 ATOM 35 C CA . VAL A 1 5 ? 2.416 -1.826 -0.844 1.00 97.64 5 A 1 ATOM 36 C C . VAL A 1 5 ? 1.307 -1.779 0.206 1.00 97.78 5 A 1 ATOM 37 O O . VAL A 1 5 ? 0.120 -1.878 -0.118 1.00 97.11 5 A 1 ATOM 38 C CB . VAL A 1 5 ? 3.057 -3.225 -0.841 1.00 97.12 5 A 1 ATOM 39 C CG1 . VAL A 1 5 ? 2.003 -4.298 -1.075 1.00 94.82 5 A 1 ATOM 40 C CG2 . VAL A 1 5 ? 4.133 -3.304 -1.915 1.00 94.53 5 A 1 ATOM 41 N N . LEU A 1 6 ? 1.685 -1.636 1.466 1.00 96.87 6 A 1 ATOM 42 C CA . LEU A 1 6 ? 0.715 -1.595 2.561 1.00 96.67 6 A 1 ATOM 43 C C . LEU A 1 6 ? -0.168 -0.352 2.468 1.00 96.92 6 A 1 ATOM 44 O O . LEU A 1 6 ? -1.386 -0.432 2.632 1.00 96.63 6 A 1 ATOM 45 C CB . LEU A 1 6 ? 1.457 -1.604 3.905 1.00 96.69 6 A 1 ATOM 46 C CG . LEU A 1 6 ? 2.318 -2.852 4.115 1.00 94.24 6 A 1 ATOM 47 C CD1 . LEU A 1 6 ? 3.102 -2.726 5.421 1.00 91.04 6 A 1 ATOM 48 C CD2 . LEU A 1 6 ? 1.441 -4.101 4.156 1.00 91.05 6 A 1 ATOM 49 N N . LEU A 1 7 ? 0.426 0.794 2.200 1.00 97.23 7 A 1 ATOM 50 C CA . LEU A 1 7 ? -0.315 2.053 2.097 1.00 97.24 7 A 1 ATOM 51 C C . LEU A 1 7 ? -1.186 2.089 0.845 1.00 97.51 7 A 1 ATOM 52 O O . LEU A 1 7 ? -2.181 2.812 0.787 1.00 97.20 7 A 1 ATOM 53 C CB . LEU A 1 7 ? 0.680 3.216 2.071 1.00 97.05 7 A 1 ATOM 54 C CG . LEU A 1 7 ? 1.476 3.349 3.374 1.00 94.41 7 A 1 ATOM 55 C CD1 . LEU A 1 7 ? 2.551 4.414 3.210 1.00 90.88 7 A 1 ATOM 56 C CD2 . LEU A 1 7 ? 0.546 3.712 4.523 1.00 91.57 7 A 1 ATOM 57 N N . SER A 1 8 ? -0.834 1.324 -0.147 1.00 97.86 8 A 1 ATOM 58 C CA . SER A 1 8 ? -1.581 1.286 -1.407 1.00 97.70 8 A 1 ATOM 59 C C . SER A 1 8 ? -2.876 0.487 -1.283 1.00 97.94 8 A 1 ATOM 60 O O . SER A 1 8 ? -3.719 0.504 -2.177 1.00 97.19 8 A 1 ATOM 61 C CB . SER A 1 8 ? -0.713 0.672 -2.503 1.00 96.95 8 A 1 ATOM 62 O OG . SER A 1 8 ? -1.399 0.659 -3.728 1.00 93.46 8 A 1 ATOM 63 N N . LEU A 1 9 ? -3.052 -0.217 -0.177 1.00 97.47 9 A 1 ATOM 64 C CA . LEU A 1 9 ? -4.241 -1.044 0.024 1.00 97.58 9 A 1 ATOM 65 C C . LEU A 1 9 ? -5.447 -0.197 0.433 1.00 97.88 9 A 1 ATOM 66 O O . LEU A 1 9 ? -6.565 -0.422 -0.037 1.00 97.28 9 A 1 ATOM 67 C CB . LEU A 1 9 ? -3.957 -2.094 1.106 1.00 97.33 9 A 1 ATOM 68 C CG . LEU A 1 9 ? -2.806 -3.039 0.748 1.00 96.41 9 A 1 ATOM 69 C CD1 . LEU A 1 9 ? -2.521 -3.975 1.917 1.00 93.90 9 A 1 ATOM 70 C CD2 . LEU A 1 9 ? -3.165 -3.856 -0.493 1.00 93.86 9 A 1 ATOM 71 N N . LEU A 1 10 ? -5.241 0.778 1.311 1.00 97.48 10 A 1 ATOM 72 C CA . LEU A 1 10 ? -6.319 1.642 1.792 1.00 97.49 10 A 1 ATOM 73 C C . LEU A 1 10 ? -6.959 2.456 0.665 1.00 97.90 10 A 1 ATOM 74 O O . LEU A 1 10 ? -8.190 2.502 0.560 1.00 97.48 10 A 1 ATOM 75 C CB . LEU A 1 10 ? -5.776 2.576 2.878 1.00 97.01 10 A 1 ATOM 76 C CG . LEU A 1 10 ? -5.252 1.833 4.107 1.00 94.92 10 A 1 ATOM 77 C CD1 . LEU A 1 10 ? -4.682 2.837 5.105 1.00 91.70 10 A 1 ATOM 78 C CD2 . LEU A 1 10 ? -6.374 1.023 4.747 1.00 91.69 10 A 1 ATOM 79 N N . PRO A 1 11 ? -6.179 3.113 -0.170 1.00 98.02 11 A 1 ATOM 80 C CA . PRO A 1 11 ? -6.718 3.939 -1.269 1.00 97.92 11 A 1 ATOM 81 C C . PRO A 1 11 ? -7.676 3.164 -2.164 1.00 98.13 11 A 1 ATOM 82 O O . PRO A 1 11 ? -8.661 3.712 -2.662 1.00 97.45 11 A 1 ATOM 83 C CB . PRO A 1 11 ? -5.465 4.360 -2.045 1.00 97.09 11 A 1 ATOM 84 C CG . PRO A 1 11 ? -4.382 4.325 -1.014 1.00 96.33 11 A 1 ATOM 85 C CD . PRO A 1 11 ? -4.740 3.166 -0.102 1.00 97.51 11 A 1 ATOM 86 N N . LEU A 1 12 ? -7.412 1.891 -2.373 1.00 97.73 12 A 1 ATOM 87 C CA . LEU A 1 12 ? -8.250 1.053 -3.228 1.00 97.52 12 A 1 ATOM 88 C C . LEU A 1 12 ? -9.613 0.812 -2.587 1.00 97.84 12 A 1 ATOM 89 O O . LEU A 1 12 ? -10.630 0.747 -3.280 1.00 96.61 12 A 1 ATOM 90 C CB . LEU A 1 12 ? -7.550 -0.286 -3.471 1.00 96.76 12 A 1 ATOM 91 C CG . LEU A 1 12 ? -6.231 -0.151 -4.233 1.00 95.31 12 A 1 ATOM 92 C CD1 . LEU A 1 12 ? -5.537 -1.502 -4.303 1.00 92.33 12 A 1 ATOM 93 C CD2 . LEU A 1 12 ? -6.494 0.379 -5.636 1.00 91.80 12 A 1 ATOM 94 N N . ALA A 1 13 ? -9.654 0.660 -1.278 1.00 97.40 13 A 1 ATOM 95 C CA . ALA A 1 13 ? -10.901 0.419 -0.558 1.00 97.23 13 A 1 ATOM 96 C C . ALA A 1 13 ? -11.772 1.670 -0.496 1.00 97.56 13 A 1 ATOM 97 O O . ALA A 1 13 ? -12.994 1.587 -0.604 1.00 96.80 13 A 1 ATOM 98 C CB . ALA A 1 13 ? -10.594 -0.076 0.851 1.00 96.55 13 A 1 ATOM 99 N N . LEU A 1 14 ? -11.168 2.849 -0.337 1.00 97.04 14 A 1 ATOM 100 C CA . LEU A 1 14 ? -11.901 4.116 -0.250 1.00 96.66 14 A 1 ATOM 101 C C . LEU A 1 14 ? -12.756 4.338 -1.487 1.00 96.91 14 A 1 ATOM 102 O O . LEU A 1 14 ? -13.910 4.744 -1.380 1.00 95.34 14 A 1 ATOM 103 C CB . LEU A 1 14 ? -10.908 5.267 -0.086 1.00 95.55 14 A 1 ATOM 104 C CG . LEU A 1 14 ? -10.130 5.190 1.229 1.00 93.85 14 A 1 ATOM 105 C CD1 . LEU A 1 14 ? -9.071 6.279 1.257 1.00 90.02 14 A 1 ATOM 106 C CD2 . LEU A 1 14 ? -11.083 5.346 2.406 1.00 88.24 14 A 1 ATOM 107 N N . GLY A 1 15 ? -12.220 4.079 -2.658 1.00 94.64 15 A 1 ATOM 108 C CA . GLY A 1 15 ? -12.968 4.243 -3.913 1.00 92.23 15 A 1 ATOM 109 C C . GLY A 1 15 ? -13.901 5.449 -3.894 1.00 90.29 15 A 1 ATOM 110 O O . GLY A 1 15 ? -15.077 5.298 -4.257 1.00 85.98 15 A 1 ATOM 111 O OXT . GLY A 1 15 ? -13.466 6.542 -3.523 1.00 88.61 15 A 1 #