# 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_spkb39125 # _entry.id spkb39125 # 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 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 ARG 2 1 n ALA 3 1 n VAL 4 1 n LEU 5 1 n LEU 6 1 n PHE 7 1 n VAL 8 1 n VAL 9 1 n SER 10 1 n LEU 11 1 n ALA 12 1 n ALA 13 1 n LEU 14 # _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 @ 2025-07-05 04:10:59)" _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 94.95 _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 85.13 1 1 A ARG 2 2 88.83 1 2 A ALA 3 2 97.17 1 3 A VAL 4 2 97.60 1 4 A LEU 5 2 96.64 1 5 A LEU 6 2 96.92 1 6 A PHE 7 2 96.37 1 7 A VAL 8 2 97.71 1 8 A VAL 9 2 97.39 1 9 A SER 10 2 97.66 1 10 A LEU 11 2 96.55 1 11 A ALA 12 2 97.87 1 12 A ALA 13 2 97.15 1 13 A LEU 14 2 92.70 1 14 # _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 ALA . 3 A 3 A 4 1 n VAL . 4 A 4 A 5 1 n LEU . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n PHE . 7 A 7 A 8 1 n VAL . 8 A 8 A 9 1 n VAL . 9 A 9 A 10 1 n SER . 10 A 10 A 11 1 n LEU . 11 A 11 A 12 1 n ALA . 12 A 12 A 13 1 n ALA . 13 A 13 A 14 1 n LEU . 14 A 14 # _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 ? 2.703 7.035 -8.809 1.00 89.60 1 A 1 ATOM 2 C CA . MET A 1 1 ? 1.524 6.542 -8.070 1.00 90.36 1 A 1 ATOM 3 C C . MET A 1 1 ? 1.951 5.875 -6.763 1.00 92.66 1 A 1 ATOM 4 O O . MET A 1 1 ? 2.661 4.877 -6.785 1.00 90.11 1 A 1 ATOM 5 C CB . MET A 1 1 ? 0.758 5.532 -8.925 1.00 86.07 1 A 1 ATOM 6 C CG . MET A 1 1 ? 0.047 6.189 -10.098 1.00 81.86 1 A 1 ATOM 7 S SD . MET A 1 1 ? -0.858 4.986 -11.089 1.00 80.40 1 A 1 ATOM 8 C CE . MET A 1 1 ? -1.551 6.050 -12.331 1.00 69.96 1 A 1 ATOM 9 N N . ARG A 1 2 ? 1.537 6.448 -5.653 1.00 94.16 2 A 1 ATOM 10 C CA . ARG A 1 2 ? 1.872 5.911 -4.335 1.00 96.55 2 A 1 ATOM 11 C C . ARG A 1 2 ? 0.720 5.099 -3.758 1.00 97.55 2 A 1 ATOM 12 O O . ARG A 1 2 ? 0.914 4.324 -2.823 1.00 96.68 2 A 1 ATOM 13 C CB . ARG A 1 2 ? 2.222 7.057 -3.393 1.00 94.85 2 A 1 ATOM 14 C CG . ARG A 1 2 ? 3.656 7.517 -3.569 1.00 90.23 2 A 1 ATOM 15 C CD . ARG A 1 2 ? 4.590 6.680 -2.699 1.00 87.90 2 A 1 ATOM 16 N NE . ARG A 1 2 ? 5.966 6.760 -3.166 1.00 84.41 2 A 1 ATOM 17 C CZ . ARG A 1 2 ? 7.007 6.271 -2.498 1.00 83.35 2 A 1 ATOM 18 N NH1 . ARG A 1 2 ? 6.837 5.672 -1.333 1.00 75.86 2 A 1 ATOM 19 N NH2 . ARG A 1 2 ? 8.221 6.381 -3.008 1.00 75.58 2 A 1 ATOM 20 N N . ALA A 1 3 ? -0.455 5.284 -4.318 1.00 96.58 3 A 1 ATOM 21 C CA . ALA A 1 3 ? -1.640 4.568 -3.856 1.00 97.47 3 A 1 ATOM 22 C C . ALA A 1 3 ? -1.470 3.060 -4.013 1.00 98.04 3 A 1 ATOM 23 O O . ALA A 1 3 ? -1.951 2.282 -3.188 1.00 97.29 3 A 1 ATOM 24 C CB . ALA A 1 3 ? -2.864 5.043 -4.625 1.00 96.48 3 A 1 ATOM 25 N N . VAL A 1 4 ? -0.773 2.662 -5.071 1.00 98.21 4 A 1 ATOM 26 C CA . VAL A 1 4 ? -0.530 1.243 -5.337 1.00 98.40 4 A 1 ATOM 27 C C . VAL A 1 4 ? 0.284 0.627 -4.208 1.00 98.50 4 A 1 ATOM 28 O O . VAL A 1 4 ? 0.001 -0.484 -3.749 1.00 98.14 4 A 1 ATOM 29 C CB . VAL A 1 4 ? 0.201 1.051 -6.678 1.00 98.14 4 A 1 ATOM 30 C CG1 . VAL A 1 4 ? 0.456 -0.424 -6.945 1.00 96.27 4 A 1 ATOM 31 C CG2 . VAL A 1 4 ? -0.613 1.655 -7.816 1.00 95.57 4 A 1 ATOM 32 N N . LEU A 1 5 ? 1.299 1.359 -3.761 1.00 97.76 5 A 1 ATOM 33 C CA . LEU A 1 5 ? 2.147 0.883 -2.677 1.00 97.90 5 A 1 ATOM 34 C C . LEU A 1 5 ? 1.339 0.766 -1.391 1.00 98.09 5 A 1 ATOM 35 O O . LEU A 1 5 ? 1.539 -0.155 -0.603 1.00 97.83 5 A 1 ATOM 36 C CB . LEU A 1 5 ? 3.320 1.845 -2.475 1.00 97.87 5 A 1 ATOM 37 C CG . LEU A 1 5 ? 4.391 1.738 -3.559 1.00 95.65 5 A 1 ATOM 38 C CD1 . LEU A 1 5 ? 5.247 2.991 -3.587 1.00 94.08 5 A 1 ATOM 39 C CD2 . LEU A 1 5 ? 5.269 0.516 -3.308 1.00 93.97 5 A 1 ATOM 40 N N . LEU A 1 6 ? 0.442 1.704 -1.194 1.00 98.16 6 A 1 ATOM 41 C CA . LEU A 1 6 ? -0.416 1.704 -0.018 1.00 98.13 6 A 1 ATOM 42 C C . LEU A 1 6 ? -1.294 0.459 -0.002 1.00 98.25 6 A 1 ATOM 43 O O . LEU A 1 6 ? -1.596 -0.091 1.056 1.00 98.05 6 A 1 ATOM 44 C CB . LEU A 1 6 ? -1.288 2.963 -0.005 1.00 97.98 6 A 1 ATOM 45 C CG . LEU A 1 6 ? -0.897 3.991 1.047 1.00 96.13 6 A 1 ATOM 46 C CD1 . LEU A 1 6 ? -1.150 3.438 2.444 1.00 94.32 6 A 1 ATOM 47 C CD2 . LEU A 1 6 ? 0.560 4.387 0.904 1.00 94.30 6 A 1 ATOM 48 N N . PHE A 1 7 ? -1.696 0.035 -1.192 1.00 97.99 7 A 1 ATOM 49 C CA . PHE A 1 7 ? -2.523 -1.159 -1.327 1.00 98.01 7 A 1 ATOM 50 C C . PHE A 1 7 ? -1.759 -2.396 -0.869 1.00 98.32 7 A 1 ATOM 51 O O . PHE A 1 7 ? -2.284 -3.230 -0.127 1.00 98.02 7 A 1 ATOM 52 C CB . PHE A 1 7 ? -2.953 -1.327 -2.784 1.00 97.82 7 A 1 ATOM 53 C CG . PHE A 1 7 ? -4.408 -0.997 -2.998 1.00 96.82 7 A 1 ATOM 54 C CD1 . PHE A 1 7 ? -5.383 -1.954 -2.757 1.00 95.32 7 A 1 ATOM 55 C CD2 . PHE A 1 7 ? -4.787 0.262 -3.433 1.00 95.35 7 A 1 ATOM 56 C CE1 . PHE A 1 7 ? -6.725 -1.655 -2.948 1.00 94.12 7 A 1 ATOM 57 C CE2 . PHE A 1 7 ? -6.128 0.567 -3.625 1.00 93.93 7 A 1 ATOM 58 C CZ . PHE A 1 7 ? -7.100 -0.390 -3.381 1.00 94.41 7 A 1 ATOM 59 N N . VAL A 1 8 ? -0.519 -2.501 -1.328 1.00 98.20 8 A 1 ATOM 60 C CA . VAL A 1 8 ? 0.324 -3.639 -0.972 1.00 98.23 8 A 1 ATOM 61 C C . VAL A 1 8 ? 0.670 -3.608 0.509 1.00 98.38 8 A 1 ATOM 62 O O . VAL A 1 8 ? 0.668 -4.642 1.183 1.00 98.08 8 A 1 ATOM 63 C CB . VAL A 1 8 ? 1.615 -3.650 -1.811 1.00 97.94 8 A 1 ATOM 64 C CG1 . VAL A 1 8 ? 2.486 -4.840 -1.447 1.00 96.60 8 A 1 ATOM 65 C CG2 . VAL A 1 8 ? 1.278 -3.685 -3.298 1.00 96.53 8 A 1 ATOM 66 N N . VAL A 1 9 ? 0.974 -2.424 1.001 1.00 98.18 9 A 1 ATOM 67 C CA . VAL A 1 9 ? 1.332 -2.255 2.406 1.00 98.07 9 A 1 ATOM 68 C C . VAL A 1 9 ? 0.174 -2.669 3.304 1.00 98.23 9 A 1 ATOM 69 O O . VAL A 1 9 ? 0.374 -3.293 4.348 1.00 97.93 9 A 1 ATOM 70 C CB . VAL A 1 9 ? 1.735 -0.799 2.699 1.00 97.67 9 A 1 ATOM 71 C CG1 . VAL A 1 9 ? 1.955 -0.589 4.189 1.00 95.71 9 A 1 ATOM 72 C CG2 . VAL A 1 9 ? 3.002 -0.442 1.938 1.00 95.96 9 A 1 ATOM 73 N N . SER A 1 10 ? -1.018 -2.323 2.887 1.00 98.50 10 A 1 ATOM 74 C CA . SER A 1 10 ? -2.210 -2.656 3.659 1.00 98.48 10 A 1 ATOM 75 C C . SER A 1 10 ? -2.373 -4.167 3.785 1.00 98.58 10 A 1 ATOM 76 O O . SER A 1 10 ? -2.761 -4.678 4.833 1.00 98.37 10 A 1 ATOM 77 C CB . SER A 1 10 ? -3.446 -2.051 3.001 1.00 98.11 10 A 1 ATOM 78 O OG . SER A 1 10 ? -3.390 -0.639 3.049 1.00 93.92 10 A 1 ATOM 79 N N . LEU A 1 11 ? -2.065 -4.872 2.709 1.00 98.23 11 A 1 ATOM 80 C CA . LEU A 1 11 ? -2.163 -6.327 2.702 1.00 98.15 11 A 1 ATOM 81 C C . LEU A 1 11 ? -1.090 -6.946 3.584 1.00 98.35 11 A 1 ATOM 82 O O . LEU A 1 11 ? -1.346 -7.916 4.302 1.00 98.07 11 A 1 ATOM 83 C CB . LEU A 1 11 ? -2.015 -6.843 1.273 1.00 97.75 11 A 1 ATOM 84 C CG . LEU A 1 11 ? -3.286 -6.701 0.447 1.00 94.85 11 A 1 ATOM 85 C CD1 . LEU A 1 11 ? -2.965 -6.711 -1.037 1.00 93.48 11 A 1 ATOM 86 C CD2 . LEU A 1 11 ? -4.251 -7.830 0.787 1.00 93.54 11 A 1 ATOM 87 N N . ALA A 1 12 ? 0.111 -6.392 3.504 1.00 98.10 12 A 1 ATOM 88 C CA . ALA A 1 12 ? 1.230 -6.887 4.295 1.00 98.02 12 A 1 ATOM 89 C C . ALA A 1 12 ? 1.040 -6.580 5.775 1.00 98.17 12 A 1 ATOM 90 O O . ALA A 1 12 ? 1.593 -7.267 6.635 1.00 97.59 12 A 1 ATOM 91 C CB . ALA A 1 12 ? 2.530 -6.270 3.798 1.00 97.46 12 A 1 ATOM 92 N N . ALA A 1 13 ? 0.279 -5.555 6.059 1.00 97.80 13 A 1 ATOM 93 C CA . ALA A 1 13 ? 0.033 -5.134 7.435 1.00 97.43 13 A 1 ATOM 94 C C . ALA A 1 13 ? -0.941 -6.071 8.138 1.00 97.72 13 A 1 ATOM 95 O O . ALA A 1 13 ? -1.076 -6.034 9.363 1.00 96.54 13 A 1 ATOM 96 C CB . ALA A 1 13 ? -0.499 -3.707 7.460 1.00 96.25 13 A 1 ATOM 97 N N . LEU A 1 14 ? -1.611 -6.914 7.373 1.00 96.43 14 A 1 ATOM 98 C CA . LEU A 1 14 ? -2.588 -7.845 7.920 1.00 95.88 14 A 1 ATOM 99 C C . LEU A 1 14 ? -1.961 -8.755 8.968 1.00 95.61 14 A 1 ATOM 100 O O . LEU A 1 14 ? -0.893 -9.333 8.704 1.00 92.82 14 A 1 ATOM 101 C CB . LEU A 1 14 ? -3.207 -8.681 6.800 1.00 93.51 14 A 1 ATOM 102 C CG . LEU A 1 14 ? -4.385 -8.012 6.084 1.00 92.49 14 A 1 ATOM 103 C CD1 . LEU A 1 14 ? -4.631 -8.672 4.739 1.00 91.45 14 A 1 ATOM 104 C CD2 . LEU A 1 14 ? -5.633 -8.109 6.951 1.00 88.98 14 A 1 ATOM 105 O OXT . LEU A 1 14 ? -2.553 -8.914 10.048 1.00 87.13 14 A 1 #