# 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_spkb38148 # _entry.id spkb38148 # 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" "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" "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 ILE 2 1 n ARG 3 1 n ALA 4 1 n PHE 5 1 n LEU 6 1 n VAL 7 1 n VAL 8 1 n ALA 9 1 n LEU 10 1 n ALA 11 1 n SER 12 1 n VAL 13 1 n ALA 14 1 n VAL 15 1 n PHE 16 1 n SER 17 # _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 @ 2025-07-03 21:28:53)" _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 95.93 _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 92.14 1 1 A ILE 2 2 95.53 1 2 A ARG 3 2 91.29 1 3 A ALA 4 2 98.43 1 4 A PHE 5 2 95.95 1 5 A LEU 6 2 96.51 1 6 A VAL 7 2 98.16 1 7 A VAL 8 2 98.16 1 8 A ALA 9 2 98.52 1 9 A LEU 10 2 96.88 1 10 A ALA 11 2 98.44 1 11 A SER 12 2 97.22 1 12 A VAL 13 2 97.85 1 13 A ALA 14 2 98.51 1 14 A VAL 15 2 97.40 1 15 A PHE 16 2 94.86 1 16 A SER 17 2 91.70 1 17 # _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 ILE . 2 A 2 A 3 1 n ARG . 3 A 3 A 4 1 n ALA . 4 A 4 A 5 1 n PHE . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n VAL . 7 A 7 A 8 1 n VAL . 8 A 8 A 9 1 n ALA . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n ALA . 11 A 11 A 12 1 n SER . 12 A 12 A 13 1 n VAL . 13 A 13 A 14 1 n ALA . 14 A 14 A 15 1 n VAL . 15 A 15 A 16 1 n PHE . 16 A 16 A 17 1 n SER . 17 A 17 # _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 ? -9.959 3.626 10.409 1.00 96.38 1 A 1 ATOM 2 C CA . MET A 1 1 ? -8.519 3.356 10.204 1.00 96.79 1 A 1 ATOM 3 C C . MET A 1 1 ? -8.176 3.438 8.716 1.00 97.07 1 A 1 ATOM 4 O O . MET A 1 1 ? -8.713 2.680 7.918 1.00 95.88 1 A 1 ATOM 5 C CB . MET A 1 1 ? -8.175 1.964 10.730 1.00 94.50 1 A 1 ATOM 6 C CG . MET A 1 1 ? -8.369 1.864 12.235 1.00 89.84 1 A 1 ATOM 7 S SD . MET A 1 1 ? -8.337 0.161 12.803 1.00 87.87 1 A 1 ATOM 8 C CE . MET A 1 1 ? -8.750 0.386 14.523 1.00 78.78 1 A 1 ATOM 9 N N . ILE A 1 2 ? -7.307 4.370 8.335 1.00 97.35 2 A 1 ATOM 10 C CA . ILE A 1 2 ? -6.935 4.570 6.929 1.00 97.63 2 A 1 ATOM 11 C C . ILE A 1 2 ? -5.471 4.209 6.681 1.00 98.02 2 A 1 ATOM 12 O O . ILE A 1 2 ? -4.999 4.204 5.546 1.00 97.57 2 A 1 ATOM 13 C CB . ILE A 1 2 ? -7.187 6.029 6.543 1.00 97.12 2 A 1 ATOM 14 C CG1 . ILE A 1 2 ? -8.604 6.457 6.913 1.00 94.13 2 A 1 ATOM 15 C CG2 . ILE A 1 2 ? -6.994 6.214 5.028 1.00 93.40 2 A 1 ATOM 16 C CD1 . ILE A 1 2 ? -8.648 7.885 7.376 1.00 88.99 2 A 1 ATOM 17 N N . ARG A 1 3 ? -4.749 3.911 7.736 1.00 97.99 3 A 1 ATOM 18 C CA . ARG A 1 3 ? -3.325 3.570 7.615 1.00 98.06 3 A 1 ATOM 19 C C . ARG A 1 3 ? -3.128 2.317 6.771 1.00 98.31 3 A 1 ATOM 20 O O . ARG A 1 3 ? -2.209 2.247 5.960 1.00 97.78 3 A 1 ATOM 21 C CB . ARG A 1 3 ? -2.737 3.365 9.015 1.00 97.05 3 A 1 ATOM 22 C CG . ARG A 1 3 ? -1.828 4.515 9.408 1.00 92.36 3 A 1 ATOM 23 C CD . ARG A 1 3 ? -0.381 4.067 9.319 1.00 90.86 3 A 1 ATOM 24 N NE . ARG A 1 3 ? 0.557 5.180 9.312 1.00 87.19 3 A 1 ATOM 25 C CZ . ARG A 1 3 ? 1.812 5.113 9.760 1.00 85.85 3 A 1 ATOM 26 N NH1 . ARG A 1 3 ? 2.277 4.006 10.309 1.00 79.74 3 A 1 ATOM 27 N NH2 . ARG A 1 3 ? 2.605 6.166 9.657 1.00 79.00 3 A 1 ATOM 28 N N . ALA A 1 4 ? -3.990 1.338 6.953 1.00 98.30 4 A 1 ATOM 29 C CA . ALA A 1 4 ? -3.902 0.088 6.203 1.00 98.51 4 A 1 ATOM 30 C C . ALA A 1 4 ? -4.115 0.324 4.711 1.00 98.67 4 A 1 ATOM 31 O O . ALA A 1 4 ? -3.429 -0.262 3.875 1.00 98.46 4 A 1 ATOM 32 C CB . ALA A 1 4 ? -4.933 -0.897 6.737 1.00 98.22 4 A 1 ATOM 33 N N . PHE A 1 5 ? -5.058 1.202 4.375 1.00 98.20 5 A 1 ATOM 34 C CA . PHE A 1 5 ? -5.358 1.517 2.981 1.00 98.31 5 A 1 ATOM 35 C C . PHE A 1 5 ? -4.170 2.182 2.294 1.00 98.53 5 A 1 ATOM 36 O O . PHE A 1 5 ? -3.848 1.876 1.147 1.00 98.24 5 A 1 ATOM 37 C CB . PHE A 1 5 ? -6.582 2.431 2.917 1.00 98.16 5 A 1 ATOM 38 C CG . PHE A 1 5 ? -6.901 2.840 1.508 1.00 96.41 5 A 1 ATOM 39 C CD1 . PHE A 1 5 ? -7.252 1.887 0.565 1.00 94.05 5 A 1 ATOM 40 C CD2 . PHE A 1 5 ? -6.844 4.171 1.134 1.00 94.15 5 A 1 ATOM 41 C CE1 . PHE A 1 5 ? -7.538 2.257 -0.741 1.00 92.91 5 A 1 ATOM 42 C CE2 . PHE A 1 5 ? -7.130 4.549 -0.172 1.00 92.85 5 A 1 ATOM 43 C CZ . PHE A 1 5 ? -7.478 3.589 -1.109 1.00 93.61 5 A 1 ATOM 44 N N . LEU A 1 6 ? -3.511 3.092 2.984 1.00 98.37 6 A 1 ATOM 45 C CA . LEU A 1 6 ? -2.352 3.790 2.424 1.00 98.43 6 A 1 ATOM 46 C C . LEU A 1 6 ? -1.207 2.818 2.152 1.00 98.61 6 A 1 ATOM 47 O O . LEU A 1 6 ? -0.531 2.908 1.127 1.00 98.52 6 A 1 ATOM 48 C CB . LEU A 1 6 ? -1.896 4.882 3.397 1.00 98.28 6 A 1 ATOM 49 C CG . LEU A 1 6 ? -2.711 6.168 3.285 1.00 94.55 6 A 1 ATOM 50 C CD1 . LEU A 1 6 ? -2.547 7.015 4.541 1.00 92.39 6 A 1 ATOM 51 C CD2 . LEU A 1 6 ? -2.265 6.967 2.063 1.00 92.95 6 A 1 ATOM 52 N N . VAL A 1 7 ? -0.993 1.896 3.050 1.00 98.66 7 A 1 ATOM 53 C CA . VAL A 1 7 ? 0.069 0.900 2.898 1.00 98.67 7 A 1 ATOM 54 C C . VAL A 1 7 ? -0.213 -0.009 1.708 1.00 98.74 7 A 1 ATOM 55 O O . VAL A 1 7 ? 0.691 -0.348 0.943 1.00 98.61 7 A 1 ATOM 56 C CB . VAL A 1 7 ? 0.211 0.063 4.178 1.00 98.43 7 A 1 ATOM 57 C CG1 . VAL A 1 7 ? 1.263 -1.026 3.994 1.00 96.96 7 A 1 ATOM 58 C CG2 . VAL A 1 7 ? 0.585 0.961 5.349 1.00 97.08 7 A 1 ATOM 59 N N . VAL A 1 8 ? -1.460 -0.394 1.549 1.00 98.73 8 A 1 ATOM 60 C CA . VAL A 1 8 ? -1.857 -1.270 0.445 1.00 98.70 8 A 1 ATOM 61 C C . VAL A 1 8 ? -1.656 -0.570 -0.894 1.00 98.74 8 A 1 ATOM 62 O O . VAL A 1 8 ? -1.225 -1.185 -1.873 1.00 98.57 8 A 1 ATOM 63 C CB . VAL A 1 8 ? -3.329 -1.697 0.597 1.00 98.45 8 A 1 ATOM 64 C CG1 . VAL A 1 8 ? -3.785 -2.496 -0.615 1.00 96.89 8 A 1 ATOM 65 C CG2 . VAL A 1 8 ? -3.505 -2.523 1.860 1.00 97.02 8 A 1 ATOM 66 N N . ALA A 1 9 ? -1.965 0.713 -0.947 1.00 98.65 9 A 1 ATOM 67 C CA . ALA A 1 9 ? -1.812 1.492 -2.176 1.00 98.58 9 A 1 ATOM 68 C C . ALA A 1 9 ? -0.348 1.552 -2.612 1.00 98.65 9 A 1 ATOM 69 O O . ALA A 1 9 ? -0.029 1.345 -3.781 1.00 98.39 9 A 1 ATOM 70 C CB . ALA A 1 9 ? -2.356 2.899 -1.955 1.00 98.33 9 A 1 ATOM 71 N N . LEU A 1 10 ? 0.539 1.824 -1.676 1.00 98.64 10 A 1 ATOM 72 C CA . LEU A 1 10 ? 1.970 1.889 -1.973 1.00 98.56 10 A 1 ATOM 73 C C . LEU A 1 10 ? 2.516 0.520 -2.352 1.00 98.64 10 A 1 ATOM 74 O O . LEU A 1 10 ? 3.349 0.401 -3.255 1.00 98.41 10 A 1 ATOM 75 C CB . LEU A 1 10 ? 2.715 2.435 -0.752 1.00 98.29 10 A 1 ATOM 76 C CG . LEU A 1 10 ? 2.781 3.959 -0.742 1.00 95.28 10 A 1 ATOM 77 C CD1 . LEU A 1 10 ? 2.980 4.480 0.673 1.00 93.43 10 A 1 ATOM 78 C CD2 . LEU A 1 10 ? 3.911 4.440 -1.641 1.00 93.76 10 A 1 ATOM 79 N N . ALA A 1 11 ? 2.052 -0.501 -1.671 1.00 98.63 11 A 1 ATOM 80 C CA . ALA A 1 11 ? 2.491 -1.867 -1.948 1.00 98.56 11 A 1 ATOM 81 C C . ALA A 1 11 ? 2.091 -2.293 -3.356 1.00 98.61 11 A 1 ATOM 82 O O . ALA A 1 11 ? 2.857 -2.959 -4.053 1.00 98.10 11 A 1 ATOM 83 C CB . ALA A 1 11 ? 1.889 -2.814 -0.919 1.00 98.31 11 A 1 ATOM 84 N N . SER A 1 12 ? 0.905 -1.894 -3.783 1.00 98.63 12 A 1 ATOM 85 C CA . SER A 1 12 ? 0.404 -2.234 -5.113 1.00 98.58 12 A 1 ATOM 86 C C . SER A 1 12 ? 1.291 -1.635 -6.199 1.00 98.63 12 A 1 ATOM 87 O O . SER A 1 12 ? 1.624 -2.298 -7.182 1.00 98.20 12 A 1 ATOM 88 C CB . SER A 1 12 ? -1.025 -1.727 -5.274 1.00 98.18 12 A 1 ATOM 89 O OG . SER A 1 12 ? -1.560 -2.178 -6.490 1.00 91.08 12 A 1 ATOM 90 N N . VAL A 1 13 ? 1.685 -0.380 -6.035 1.00 98.67 13 A 1 ATOM 91 C CA . VAL A 1 13 ? 2.546 0.296 -7.006 1.00 98.56 13 A 1 ATOM 92 C C . VAL A 1 13 ? 3.925 -0.349 -7.051 1.00 98.60 13 A 1 ATOM 93 O O . VAL A 1 13 ? 4.518 -0.499 -8.120 1.00 98.20 13 A 1 ATOM 94 C CB . VAL A 1 13 ? 2.683 1.787 -6.656 1.00 98.12 13 A 1 ATOM 95 C CG1 . VAL A 1 13 ? 3.617 2.481 -7.639 1.00 96.17 13 A 1 ATOM 96 C CG2 . VAL A 1 13 ? 1.323 2.454 -6.663 1.00 96.60 13 A 1 ATOM 97 N N . ALA A 1 14 ? 4.442 -0.718 -5.903 1.00 98.70 14 A 1 ATOM 98 C CA . ALA A 1 14 ? 5.760 -1.346 -5.817 1.00 98.62 14 A 1 ATOM 99 C C . ALA A 1 14 ? 5.778 -2.709 -6.499 1.00 98.66 14 A 1 ATOM 100 O O . ALA A 1 14 ? 6.749 -3.069 -7.161 1.00 98.21 14 A 1 ATOM 101 C CB . ALA A 1 14 ? 6.166 -1.489 -4.356 1.00 98.34 14 A 1 ATOM 102 N N . VAL A 1 15 ? 4.710 -3.466 -6.337 1.00 98.53 15 A 1 ATOM 103 C CA . VAL A 1 15 ? 4.612 -4.800 -6.939 1.00 98.43 15 A 1 ATOM 104 C C . VAL A 1 15 ? 4.459 -4.706 -8.453 1.00 98.46 15 A 1 ATOM 105 O O . VAL A 1 15 ? 5.031 -5.503 -9.200 1.00 97.86 15 A 1 ATOM 106 C CB . VAL A 1 15 ? 3.429 -5.575 -6.340 1.00 97.90 15 A 1 ATOM 107 C CG1 . VAL A 1 15 ? 3.243 -6.904 -7.055 1.00 95.20 15 A 1 ATOM 108 C CG2 . VAL A 1 15 ? 3.654 -5.809 -4.854 1.00 95.43 15 A 1 ATOM 109 N N . PHE A 1 16 ? 3.680 -3.737 -8.904 1.00 98.14 16 A 1 ATOM 110 C CA . PHE A 1 16 ? 3.451 -3.557 -10.336 1.00 97.96 16 A 1 ATOM 111 C C . PHE A 1 16 ? 4.630 -2.880 -11.021 1.00 98.07 16 A 1 ATOM 112 O O . PHE A 1 16 ? 4.777 -2.957 -12.241 1.00 97.22 16 A 1 ATOM 113 C CB . PHE A 1 16 ? 2.189 -2.717 -10.550 1.00 97.36 16 A 1 ATOM 114 C CG . PHE A 1 16 ? 1.754 -2.702 -11.986 1.00 95.05 16 A 1 ATOM 115 C CD1 . PHE A 1 16 ? 1.242 -3.845 -12.579 1.00 92.68 16 A 1 ATOM 116 C CD2 . PHE A 1 16 ? 1.865 -1.547 -12.745 1.00 92.81 16 A 1 ATOM 117 C CE1 . PHE A 1 16 ? 0.846 -3.836 -13.908 1.00 91.81 16 A 1 ATOM 118 C CE2 . PHE A 1 16 ? 1.470 -1.530 -14.080 1.00 91.08 16 A 1 ATOM 119 C CZ . PHE A 1 16 ? 0.957 -2.680 -14.658 1.00 91.32 16 A 1 ATOM 120 N N . SER A 1 17 ? 5.456 -2.209 -10.263 1.00 96.91 17 A 1 ATOM 121 C CA . SER A 1 17 ? 6.616 -1.499 -10.811 1.00 95.67 17 A 1 ATOM 122 C C . SER A 1 17 ? 7.675 -2.488 -11.292 1.00 93.22 17 A 1 ATOM 123 O O . SER A 1 17 ? 8.591 -2.076 -12.023 1.00 87.93 17 A 1 ATOM 124 C CB . SER A 1 17 ? 7.202 -0.552 -9.766 1.00 93.18 17 A 1 ATOM 125 O OG . SER A 1 17 ? 8.238 0.216 -10.347 1.00 87.26 17 A 1 ATOM 126 O OXT . SER A 1 17 ? 7.608 -3.669 -10.922 1.00 87.70 17 A 1 #