# 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_spkb38039 # _entry.id spkb38039 # 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" "C9 H11 N O2" 165.189 PHE y PHENYLALANINE c1ccc(cc1)C[C@@H](C(=O)O)N ? "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 ARG 2 1 n ILE 3 1 n PHE 4 1 n VAL 5 1 n PHE 6 1 n LEU 7 1 n VAL 8 1 n LEU 9 1 n LEU 10 1 n THR 11 1 n VAL 12 1 n ALA 13 1 n ILE 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 @ 2025-07-05 14:48:06)" _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 97.14 _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 93.28 1 1 A ARG 2 2 94.79 1 2 A ILE 3 2 97.68 1 3 A PHE 4 2 97.19 1 4 A VAL 5 2 98.45 1 5 A PHE 6 2 97.80 1 6 A LEU 7 2 97.20 1 7 A VAL 8 2 98.53 1 8 A LEU 9 2 97.78 1 9 A LEU 10 2 97.55 1 10 A THR 11 2 97.80 1 11 A VAL 12 2 98.47 1 12 A ALA 13 2 98.81 1 13 A ILE 14 2 97.54 1 14 A GLY 15 2 95.39 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 ILE . 3 A 3 A 4 1 n PHE . 4 A 4 A 5 1 n VAL . 5 A 5 A 6 1 n PHE . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n VAL . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n THR . 11 A 11 A 12 1 n VAL . 12 A 12 A 13 1 n ALA . 13 A 13 A 14 1 n ILE . 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 ? 0.029 11.012 1.514 1.00 97.55 1 A 1 ATOM 2 C CA . MET A 1 1 ? -0.788 9.803 1.302 1.00 97.71 1 A 1 ATOM 3 C C . MET A 1 1 ? 0.033 8.544 1.581 1.00 97.78 1 A 1 ATOM 4 O O . MET A 1 1 ? 0.753 8.062 0.714 1.00 96.06 1 A 1 ATOM 5 C CB . MET A 1 1 ? -1.293 9.748 -0.137 1.00 96.13 1 A 1 ATOM 6 C CG . MET A 1 1 ? -2.177 10.928 -0.489 1.00 91.71 1 A 1 ATOM 7 S SD . MET A 1 1 ? -2.795 10.823 -2.174 1.00 89.60 1 A 1 ATOM 8 C CE . MET A 1 1 ? -3.589 12.410 -2.326 1.00 79.66 1 A 1 ATOM 9 N N . ARG A 1 2 ? -0.079 8.042 2.789 1.00 98.46 2 A 1 ATOM 10 C CA . ARG A 1 2 ? 0.658 6.840 3.189 1.00 98.57 2 A 1 ATOM 11 C C . ARG A 1 2 ? -0.204 5.586 3.051 1.00 98.66 2 A 1 ATOM 12 O O . ARG A 1 2 ? 0.303 4.499 2.782 1.00 98.20 2 A 1 ATOM 13 C CB . ARG A 1 2 ? 1.127 6.982 4.635 1.00 98.08 2 A 1 ATOM 14 C CG . ARG A 1 2 ? 2.079 8.152 4.843 1.00 95.99 2 A 1 ATOM 15 C CD . ARG A 1 2 ? 3.457 7.841 4.268 1.00 94.91 2 A 1 ATOM 16 N NE . ARG A 1 2 ? 4.365 8.978 4.411 1.00 92.05 2 A 1 ATOM 17 C CZ . ARG A 1 2 ? 5.628 8.977 4.008 1.00 91.34 2 A 1 ATOM 18 N NH1 . ARG A 1 2 ? 6.148 7.905 3.440 1.00 87.92 2 A 1 ATOM 19 N NH2 . ARG A 1 2 ? 6.369 10.053 4.175 1.00 88.46 2 A 1 ATOM 20 N N . ILE A 1 3 ? -1.496 5.741 3.235 1.00 98.71 3 A 1 ATOM 21 C CA . ILE A 1 3 ? -2.440 4.624 3.150 1.00 98.75 3 A 1 ATOM 22 C C . ILE A 1 3 ? -2.431 4.004 1.758 1.00 98.83 3 A 1 ATOM 23 O O . ILE A 1 3 ? -2.481 2.782 1.606 1.00 98.69 3 A 1 ATOM 24 C CB . ILE A 1 3 ? -3.860 5.091 3.503 1.00 98.58 3 A 1 ATOM 25 C CG1 . ILE A 1 3 ? -3.902 5.658 4.927 1.00 97.05 3 A 1 ATOM 26 C CG2 . ILE A 1 3 ? -4.853 3.939 3.353 1.00 96.76 3 A 1 ATOM 27 C CD1 . ILE A 1 3 ? -3.650 4.612 5.993 1.00 94.06 3 A 1 ATOM 28 N N . PHE A 1 4 ? -2.368 4.846 0.752 1.00 98.86 4 A 1 ATOM 29 C CA . PHE A 1 4 ? -2.373 4.384 -0.634 1.00 98.88 4 A 1 ATOM 30 C C . PHE A 1 4 ? -1.190 3.463 -0.906 1.00 98.90 4 A 1 ATOM 31 O O . PHE A 1 4 ? -1.340 2.396 -1.502 1.00 98.80 4 A 1 ATOM 32 C CB . PHE A 1 4 ? -2.330 5.587 -1.574 1.00 98.79 4 A 1 ATOM 33 C CG . PHE A 1 4 ? -2.922 5.284 -2.921 1.00 97.60 4 A 1 ATOM 34 C CD1 . PHE A 1 4 ? -4.298 5.296 -3.102 1.00 95.64 4 A 1 ATOM 35 C CD2 . PHE A 1 4 ? -2.106 4.989 -4.002 1.00 95.90 4 A 1 ATOM 36 C CE1 . PHE A 1 4 ? -4.850 5.017 -4.343 1.00 95.02 4 A 1 ATOM 37 C CE2 . PHE A 1 4 ? -2.652 4.706 -5.247 1.00 95.26 4 A 1 ATOM 38 C CZ . PHE A 1 4 ? -4.029 4.721 -5.418 1.00 95.42 4 A 1 ATOM 39 N N . VAL A 1 5 ? -0.027 3.858 -0.465 1.00 98.85 5 A 1 ATOM 40 C CA . VAL A 1 5 ? 1.188 3.062 -0.646 1.00 98.86 5 A 1 ATOM 41 C C . VAL A 1 5 ? 1.074 1.736 0.098 1.00 98.88 5 A 1 ATOM 42 O O . VAL A 1 5 ? 1.498 0.689 -0.396 1.00 98.78 5 A 1 ATOM 43 C CB . VAL A 1 5 ? 2.424 3.827 -0.146 1.00 98.73 5 A 1 ATOM 44 C CG1 . VAL A 1 5 ? 3.684 2.994 -0.310 1.00 97.60 5 A 1 ATOM 45 C CG2 . VAL A 1 5 ? 2.563 5.145 -0.893 1.00 97.48 5 A 1 ATOM 46 N N . PHE A 1 6 ? 0.517 1.803 1.276 1.00 98.88 6 A 1 ATOM 47 C CA . PHE A 1 6 ? 0.340 0.612 2.101 1.00 98.89 6 A 1 ATOM 48 C C . PHE A 1 6 ? -0.581 -0.390 1.416 1.00 98.89 6 A 1 ATOM 49 O O . PHE A 1 6 ? -0.332 -1.596 1.442 1.00 98.79 6 A 1 ATOM 50 C CB . PHE A 1 6 ? -0.237 1.016 3.457 1.00 98.81 6 A 1 ATOM 51 C CG . PHE A 1 6 ? 0.194 0.095 4.569 1.00 98.36 6 A 1 ATOM 52 C CD1 . PHE A 1 6 ? 1.456 0.221 5.131 1.00 97.01 6 A 1 ATOM 53 C CD2 . PHE A 1 6 ? -0.662 -0.882 5.044 1.00 97.18 6 A 1 ATOM 54 C CE1 . PHE A 1 6 ? 1.862 -0.624 6.152 1.00 96.31 6 A 1 ATOM 55 C CE2 . PHE A 1 6 ? -0.261 -1.733 6.067 1.00 96.34 6 A 1 ATOM 56 C CZ . PHE A 1 6 ? 1.003 -1.604 6.622 1.00 96.38 6 A 1 ATOM 57 N N . LEU A 1 7 ? -1.641 0.116 0.809 1.00 98.87 7 A 1 ATOM 58 C CA . LEU A 1 7 ? -2.606 -0.725 0.102 1.00 98.86 7 A 1 ATOM 59 C C . LEU A 1 7 ? -1.947 -1.441 -1.072 1.00 98.89 7 A 1 ATOM 60 O O . LEU A 1 7 ? -2.136 -2.641 -1.269 1.00 98.83 7 A 1 ATOM 61 C CB . LEU A 1 7 ? -3.780 0.128 -0.398 1.00 98.74 7 A 1 ATOM 62 C CG . LEU A 1 7 ? -5.093 -0.085 0.347 1.00 94.74 7 A 1 ATOM 63 C CD1 . LEU A 1 7 ? -5.590 -1.503 0.153 1.00 93.77 7 A 1 ATOM 64 C CD2 . LEU A 1 7 ? -4.934 0.230 1.820 1.00 94.89 7 A 1 ATOM 65 N N . VAL A 1 8 ? -1.175 -0.709 -1.832 1.00 98.86 8 A 1 ATOM 66 C CA . VAL A 1 8 ? -0.479 -1.269 -2.989 1.00 98.84 8 A 1 ATOM 67 C C . VAL A 1 8 ? 0.513 -2.338 -2.554 1.00 98.87 8 A 1 ATOM 68 O O . VAL A 1 8 ? 0.616 -3.399 -3.170 1.00 98.78 8 A 1 ATOM 69 C CB . VAL A 1 8 ? 0.255 -0.168 -3.768 1.00 98.72 8 A 1 ATOM 70 C CG1 . VAL A 1 8 ? 1.060 -0.761 -4.913 1.00 97.80 8 A 1 ATOM 71 C CG2 . VAL A 1 8 ? -0.740 0.849 -4.305 1.00 97.83 8 A 1 ATOM 72 N N . LEU A 1 9 ? 1.235 -2.049 -1.496 1.00 98.88 9 A 1 ATOM 73 C CA . LEU A 1 9 ? 2.223 -2.987 -0.972 1.00 98.85 9 A 1 ATOM 74 C C . LEU A 1 9 ? 1.563 -4.298 -0.555 1.00 98.86 9 A 1 ATOM 75 O O . LEU A 1 9 ? 2.088 -5.381 -0.816 1.00 98.76 9 A 1 ATOM 76 C CB . LEU A 1 9 ? 2.934 -2.368 0.234 1.00 98.74 9 A 1 ATOM 77 C CG . LEU A 1 9 ? 4.242 -3.080 0.595 1.00 97.08 9 A 1 ATOM 78 C CD1 . LEU A 1 9 ? 5.397 -2.507 -0.221 1.00 95.51 9 A 1 ATOM 79 C CD2 . LEU A 1 9 ? 4.539 -2.942 2.078 1.00 95.55 9 A 1 ATOM 80 N N . LEU A 1 10 ? 0.428 -4.191 0.095 1.00 98.89 10 A 1 ATOM 81 C CA . LEU A 1 10 ? -0.313 -5.358 0.565 1.00 98.85 10 A 1 ATOM 82 C C . LEU A 1 10 ? -0.801 -6.195 -0.608 1.00 98.88 10 A 1 ATOM 83 O O . LEU A 1 10 ? -0.738 -7.425 -0.577 1.00 98.76 10 A 1 ATOM 84 C CB . LEU A 1 10 ? -1.493 -4.898 1.424 1.00 98.72 10 A 1 ATOM 85 C CG . LEU A 1 10 ? -1.834 -5.862 2.557 1.00 96.36 10 A 1 ATOM 86 C CD1 . LEU A 1 10 ? -2.308 -5.092 3.779 1.00 94.77 10 A 1 ATOM 87 C CD2 . LEU A 1 10 ? -2.903 -6.849 2.117 1.00 95.18 10 A 1 ATOM 88 N N . THR A 1 11 ? -1.279 -5.531 -1.638 1.00 98.85 11 A 1 ATOM 89 C CA . THR A 1 11 ? -1.781 -6.207 -2.832 1.00 98.82 11 A 1 ATOM 90 C C . THR A 1 11 ? -0.661 -6.953 -3.548 1.00 98.85 11 A 1 ATOM 91 O O . THR A 1 11 ? -0.845 -8.087 -3.987 1.00 98.59 11 A 1 ATOM 92 C CB . THR A 1 11 ? -2.414 -5.202 -3.795 1.00 98.60 11 A 1 ATOM 93 O OG1 . THR A 1 11 ? -3.400 -4.440 -3.111 1.00 95.44 11 A 1 ATOM 94 C CG2 . THR A 1 11 ? -3.076 -5.919 -4.958 1.00 95.45 11 A 1 ATOM 95 N N . VAL A 1 12 ? 0.485 -6.329 -3.660 1.00 98.91 12 A 1 ATOM 96 C CA . VAL A 1 12 ? 1.636 -6.933 -4.324 1.00 98.86 12 A 1 ATOM 97 C C . VAL A 1 12 ? 2.125 -8.152 -3.555 1.00 98.88 12 A 1 ATOM 98 O O . VAL A 1 12 ? 2.518 -9.160 -4.148 1.00 98.68 12 A 1 ATOM 99 C CB . VAL A 1 12 ? 2.779 -5.917 -4.466 1.00 98.67 12 A 1 ATOM 100 C CG1 . VAL A 1 12 ? 4.034 -6.582 -5.015 1.00 97.57 12 A 1 ATOM 101 C CG2 . VAL A 1 12 ? 2.361 -4.780 -5.380 1.00 97.69 12 A 1 ATOM 102 N N . ALA A 1 13 ? 2.112 -8.056 -2.244 1.00 98.91 13 A 1 ATOM 103 C CA . ALA A 1 13 ? 2.568 -9.148 -1.390 1.00 98.88 13 A 1 ATOM 104 C C . ALA A 1 13 ? 1.684 -10.380 -1.544 1.00 98.89 13 A 1 ATOM 105 O O . ALA A 1 13 ? 2.169 -11.512 -1.505 1.00 98.67 13 A 1 ATOM 106 C CB . ALA A 1 13 ? 2.585 -8.703 0.068 1.00 98.72 13 A 1 ATOM 107 N N . ILE A 1 14 ? 0.395 -10.160 -1.695 1.00 98.82 14 A 1 ATOM 108 C CA . ILE A 1 14 ? -0.562 -11.251 -1.843 1.00 98.76 14 A 1 ATOM 109 C C . ILE A 1 14 ? -0.596 -11.769 -3.274 1.00 98.78 14 A 1 ATOM 110 O O . ILE A 1 14 ? -0.474 -12.978 -3.509 1.00 98.46 14 A 1 ATOM 111 C CB . ILE A 1 14 ? -1.974 -10.804 -1.419 1.00 98.44 14 A 1 ATOM 112 C CG1 . ILE A 1 14 ? -1.993 -10.452 0.066 1.00 96.71 14 A 1 ATOM 113 C CG2 . ILE A 1 14 ? -2.986 -11.915 -1.706 1.00 96.32 14 A 1 ATOM 114 C CD1 . ILE A 1 14 ? -3.266 -9.743 0.494 1.00 94.02 14 A 1 ATOM 115 N N . GLY A 1 15 ? -0.798 -10.878 -4.199 1.00 97.90 15 A 1 ATOM 116 C CA . GLY A 1 15 ? -0.891 -11.241 -5.610 1.00 96.79 15 A 1 ATOM 117 C C . GLY A 1 15 ? 0.442 -11.457 -6.252 1.00 95.66 15 A 1 ATOM 118 O O . GLY A 1 15 ? 1.065 -12.508 -5.987 1.00 91.63 15 A 1 ATOM 119 O OXT . GLY A 1 15 ? 0.831 -10.574 -7.026 1.00 94.99 15 A 1 #