# 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_spkb16091 # _entry.id spkb16091 # 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" "C4 H8 N2 O3" 132.118 ASN y ASPARAGINE C([C@@H](C(=O)O)N)C(=O)N ? "L-PEPTIDE LINKING" "C3 H7 N O2 S" 121.158 CYS y CYSTEINE C([C@@H](C(=O)O)N)S ? "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" "C11 H12 N2 O2" 204.225 TRP y TRYPTOPHAN c1ccc2c(c1)c(c[nH]2)C[C@@H](C(=O)O)N ? "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 ASN 3 1 n TRP 4 1 n VAL 5 1 n LEU 6 1 n ILE 7 1 n ALA 8 1 n ALA 9 1 n LEU 10 1 n ALA 11 1 n VAL 12 1 n ILE 13 1 n CYS 14 1 n LEU 15 1 n ALA 16 # _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 @ 2025-07-06 22:34:18)" _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 93.90 _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 86.59 1 1 A ARG 2 2 81.08 1 2 A ASN 3 2 94.05 1 3 A TRP 4 2 93.62 1 4 A VAL 5 2 97.01 1 5 A LEU 6 2 95.42 1 6 A ILE 7 2 96.20 1 7 A ALA 8 2 98.11 1 8 A ALA 9 2 98.25 1 9 A LEU 10 2 95.57 1 10 A ALA 11 2 98.14 1 11 A VAL 12 2 97.72 1 12 A ILE 13 2 96.58 1 13 A CYS 14 2 97.91 1 14 A LEU 15 2 94.78 1 15 A ALA 16 2 92.69 1 16 # _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 ASN . 3 A 3 A 4 1 n TRP . 4 A 4 A 5 1 n VAL . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n ILE . 7 A 7 A 8 1 n ALA . 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 VAL . 12 A 12 A 13 1 n ILE . 13 A 13 A 14 1 n CYS . 14 A 14 A 15 1 n LEU . 15 A 15 A 16 1 n ALA . 16 A 16 # _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 ? -9.720 8.479 8.925 1.00 91.79 1 A 1 ATOM 2 C CA . MET A 1 1 ? -8.332 7.974 8.729 1.00 92.17 1 A 1 ATOM 3 C C . MET A 1 1 ? -8.034 7.830 7.234 1.00 93.58 1 A 1 ATOM 4 O O . MET A 1 1 ? -8.863 8.163 6.402 1.00 91.17 1 A 1 ATOM 5 C CB . MET A 1 1 ? -8.208 6.626 9.427 1.00 88.84 1 A 1 ATOM 6 C CG . MET A 1 1 ? -8.281 6.833 10.942 1.00 84.06 1 A 1 ATOM 7 S SD . MET A 1 1 ? -8.326 5.284 11.831 1.00 80.51 1 A 1 ATOM 8 C CE . MET A 1 1 ? -8.486 5.902 13.497 1.00 70.64 1 A 1 ATOM 9 N N . ARG A 1 2 ? -6.851 7.346 6.894 1.00 92.10 2 A 1 ATOM 10 C CA . ARG A 1 2 ? -6.465 7.216 5.476 1.00 93.22 2 A 1 ATOM 11 C C . ARG A 1 2 ? -6.287 5.757 5.056 1.00 94.50 2 A 1 ATOM 12 O O . ARG A 1 2 ? -6.187 5.463 3.872 1.00 92.71 2 A 1 ATOM 13 C CB . ARG A 1 2 ? -5.156 7.983 5.263 1.00 89.97 2 A 1 ATOM 14 C CG . ARG A 1 2 ? -5.368 9.478 5.491 1.00 80.70 2 A 1 ATOM 15 C CD . ARG A 1 2 ? -4.057 10.212 5.403 1.00 79.62 2 A 1 ATOM 16 N NE . ARG A 1 2 ? -4.079 11.344 6.320 1.00 72.19 2 A 1 ATOM 17 C CZ . ARG A 1 2 ? -4.889 12.379 6.177 1.00 69.88 2 A 1 ATOM 18 N NH1 . ARG A 1 2 ? -5.604 12.555 5.100 1.00 64.27 2 A 1 ATOM 19 N NH2 . ARG A 1 2 ? -5.004 13.207 7.161 1.00 62.72 2 A 1 ATOM 20 N N . ASN A 1 3 ? -6.246 4.843 5.987 1.00 96.71 3 A 1 ATOM 21 C CA . ASN A 1 3 ? -6.071 3.412 5.670 1.00 97.25 3 A 1 ATOM 22 C C . ASN A 1 3 ? -4.839 3.197 4.782 1.00 97.85 3 A 1 ATOM 23 O O . ASN A 1 3 ? -4.923 2.620 3.709 1.00 97.56 3 A 1 ATOM 24 C CB . ASN A 1 3 ? -7.326 2.914 4.955 1.00 96.45 3 A 1 ATOM 25 C CG . ASN A 1 3 ? -8.514 2.936 5.900 1.00 93.82 3 A 1 ATOM 26 O OD1 . ASN A 1 3 ? -8.475 2.378 6.977 1.00 87.26 3 A 1 ATOM 27 N ND2 . ASN A 1 3 ? -9.589 3.589 5.505 1.00 85.51 3 A 1 ATOM 28 N N . TRP A 1 4 ? -3.696 3.675 5.237 1.00 97.00 4 A 1 ATOM 29 C CA . TRP A 1 4 ? -2.454 3.534 4.467 1.00 97.27 4 A 1 ATOM 30 C C . TRP A 1 4 ? -2.013 2.076 4.401 1.00 97.74 4 A 1 ATOM 31 O O . TRP A 1 4 ? -1.343 1.675 3.460 1.00 97.34 4 A 1 ATOM 32 C CB . TRP A 1 4 ? -1.361 4.384 5.116 1.00 96.76 4 A 1 ATOM 33 C CG . TRP A 1 4 ? -1.459 5.805 4.675 1.00 95.31 4 A 1 ATOM 34 C CD1 . TRP A 1 4 ? -1.745 6.873 5.453 1.00 91.65 4 A 1 ATOM 35 C CD2 . TRP A 1 4 ? -1.254 6.314 3.344 1.00 93.93 4 A 1 ATOM 36 N NE1 . TRP A 1 4 ? -1.735 8.019 4.688 1.00 91.30 4 A 1 ATOM 37 C CE2 . TRP A 1 4 ? -1.441 7.703 3.387 1.00 93.24 4 A 1 ATOM 38 C CE3 . TRP A 1 4 ? -0.933 5.713 2.119 1.00 90.70 4 A 1 ATOM 39 C CZ2 . TRP A 1 4 ? -1.309 8.494 2.245 1.00 90.92 4 A 1 ATOM 40 C CZ3 . TRP A 1 4 ? -0.803 6.502 0.985 1.00 88.53 4 A 1 ATOM 41 C CH2 . TRP A 1 4 ? -0.992 7.878 1.051 1.00 88.98 4 A 1 ATOM 42 N N . VAL A 1 5 ? -2.379 1.279 5.390 1.00 97.66 5 A 1 ATOM 43 C CA . VAL A 1 5 ? -2.004 -0.142 5.414 1.00 97.77 5 A 1 ATOM 44 C C . VAL A 1 5 ? -2.553 -0.852 4.176 1.00 98.03 5 A 1 ATOM 45 O O . VAL A 1 5 ? -1.851 -1.627 3.528 1.00 97.90 5 A 1 ATOM 46 C CB . VAL A 1 5 ? -2.543 -0.816 6.688 1.00 97.34 5 A 1 ATOM 47 C CG1 . VAL A 1 5 ? -2.147 -2.286 6.714 1.00 95.39 5 A 1 ATOM 48 C CG2 . VAL A 1 5 ? -1.982 -0.111 7.923 1.00 95.01 5 A 1 ATOM 49 N N . LEU A 1 6 ? -3.803 -0.587 3.845 1.00 97.55 6 A 1 ATOM 50 C CA . LEU A 1 6 ? -4.426 -1.220 2.673 1.00 97.70 6 A 1 ATOM 51 C C . LEU A 1 6 ? -3.788 -0.709 1.385 1.00 98.08 6 A 1 ATOM 52 O O . LEU A 1 6 ? -3.503 -1.476 0.472 1.00 98.14 6 A 1 ATOM 53 C CB . LEU A 1 6 ? -5.928 -0.906 2.681 1.00 97.59 6 A 1 ATOM 54 C CG . LEU A 1 6 ? -6.694 -1.892 3.567 1.00 93.09 6 A 1 ATOM 55 C CD1 . LEU A 1 6 ? -8.048 -1.312 3.955 1.00 90.15 6 A 1 ATOM 56 C CD2 . LEU A 1 6 ? -6.898 -3.204 2.806 1.00 91.03 6 A 1 ATOM 57 N N . ILE A 1 7 ? -3.560 0.571 1.312 1.00 98.08 7 A 1 ATOM 58 C CA . ILE A 1 7 ? -2.948 1.168 0.121 1.00 98.04 7 A 1 ATOM 59 C C . ILE A 1 7 ? -1.525 0.642 -0.056 1.00 98.29 7 A 1 ATOM 60 O O . ILE A 1 7 ? -1.110 0.308 -1.166 1.00 98.32 7 A 1 ATOM 61 C CB . ILE A 1 7 ? -2.934 2.696 0.262 1.00 97.69 7 A 1 ATOM 62 C CG1 . ILE A 1 7 ? -4.380 3.216 0.301 1.00 95.55 7 A 1 ATOM 63 C CG2 . ILE A 1 7 ? -2.195 3.312 -0.932 1.00 95.28 7 A 1 ATOM 64 C CD1 . ILE A 1 7 ? -4.444 4.647 0.805 1.00 88.34 7 A 1 ATOM 65 N N . ALA A 1 8 ? -0.771 0.568 1.033 1.00 98.14 8 A 1 ATOM 66 C CA . ALA A 1 8 ? 0.610 0.079 0.975 1.00 98.12 8 A 1 ATOM 67 C C . ALA A 1 8 ? 0.637 -1.386 0.543 1.00 98.34 8 A 1 ATOM 68 O O . ALA A 1 8 ? 1.460 -1.784 -0.276 1.00 98.20 8 A 1 ATOM 69 C CB . ALA A 1 8 ? 1.261 0.233 2.345 1.00 97.74 8 A 1 ATOM 70 N N . ALA A 1 9 ? -0.257 -2.180 1.088 1.00 98.28 9 A 1 ATOM 71 C CA . ALA A 1 9 ? -0.317 -3.606 0.747 1.00 98.29 9 A 1 ATOM 72 C C . ALA A 1 9 ? -0.637 -3.786 -0.736 1.00 98.48 9 A 1 ATOM 73 O O . ALA A 1 9 ? -0.041 -4.623 -1.410 1.00 98.27 9 A 1 ATOM 74 C CB . ALA A 1 9 ? -1.381 -4.281 1.603 1.00 97.95 9 A 1 ATOM 75 N N . LEU A 1 10 ? -1.563 -3.004 -1.237 1.00 98.13 10 A 1 ATOM 76 C CA . LEU A 1 10 ? -1.942 -3.092 -2.653 1.00 98.01 10 A 1 ATOM 77 C C . LEU A 1 10 ? -0.763 -2.724 -3.546 1.00 98.29 10 A 1 ATOM 78 O O . LEU A 1 10 ? -0.537 -3.349 -4.582 1.00 98.13 10 A 1 ATOM 79 C CB . LEU A 1 10 ? -3.117 -2.151 -2.914 1.00 97.56 10 A 1 ATOM 80 C CG . LEU A 1 10 ? -3.928 -2.631 -4.113 1.00 93.74 10 A 1 ATOM 81 C CD1 . LEU A 1 10 ? -5.419 -2.580 -3.794 1.00 89.82 10 A 1 ATOM 82 C CD2 . LEU A 1 10 ? -3.634 -1.764 -5.324 1.00 90.91 10 A 1 ATOM 83 N N . ALA A 1 11 ? -0.002 -1.718 -3.155 1.00 98.27 11 A 1 ATOM 84 C CA . ALA A 1 11 ? 1.167 -1.286 -3.932 1.00 98.23 11 A 1 ATOM 85 C C . ALA A 1 11 ? 2.208 -2.402 -3.994 1.00 98.42 11 A 1 ATOM 86 O O . ALA A 1 11 ? 2.787 -2.659 -5.045 1.00 98.04 11 A 1 ATOM 87 C CB . ALA A 1 11 ? 1.768 -0.043 -3.289 1.00 97.75 11 A 1 ATOM 88 N N . VAL A 1 12 ? 2.448 -3.063 -2.875 1.00 98.51 12 A 1 ATOM 89 C CA . VAL A 1 12 ? 3.432 -4.153 -2.820 1.00 98.46 12 A 1 ATOM 90 C C . VAL A 1 12 ? 2.977 -5.320 -3.694 1.00 98.58 12 A 1 ATOM 91 O O . VAL A 1 12 ? 3.778 -5.920 -4.409 1.00 98.29 12 A 1 ATOM 92 C CB . VAL A 1 12 ? 3.616 -4.625 -1.374 1.00 97.96 12 A 1 ATOM 93 C CG1 . VAL A 1 12 ? 4.547 -5.830 -1.326 1.00 96.14 12 A 1 ATOM 94 C CG2 . VAL A 1 12 ? 4.195 -3.492 -0.539 1.00 96.11 12 A 1 ATOM 95 N N . ILE A 1 13 ? 1.708 -5.648 -3.633 1.00 98.36 13 A 1 ATOM 96 C CA . ILE A 1 13 ? 1.164 -6.757 -4.428 1.00 98.22 13 A 1 ATOM 97 C C . ILE A 1 13 ? 1.307 -6.458 -5.922 1.00 98.33 13 A 1 ATOM 98 O O . ILE A 1 13 ? 1.640 -7.340 -6.712 1.00 97.87 13 A 1 ATOM 99 C CB . ILE A 1 13 ? -0.316 -6.974 -4.071 1.00 97.78 13 A 1 ATOM 100 C CG1 . ILE A 1 13 ? -0.432 -7.496 -2.636 1.00 95.84 13 A 1 ATOM 101 C CG2 . ILE A 1 13 ? -0.940 -7.996 -5.034 1.00 95.32 13 A 1 ATOM 102 C CD1 . ILE A 1 13 ? -1.839 -7.299 -2.084 1.00 90.90 13 A 1 ATOM 103 N N . CYS A 1 14 ? 1.055 -5.240 -6.307 1.00 98.53 14 A 1 ATOM 104 C CA . CYS A 1 14 ? 1.166 -4.850 -7.718 1.00 98.52 14 A 1 ATOM 105 C C . CYS A 1 14 ? 2.614 -4.971 -8.198 1.00 98.61 14 A 1 ATOM 106 O O . CYS A 1 14 ? 2.866 -5.333 -9.341 1.00 98.19 14 A 1 ATOM 107 C CB . CYS A 1 14 ? 0.683 -3.405 -7.880 1.00 98.17 14 A 1 ATOM 108 S SG . CYS A 1 14 ? -1.116 -3.313 -7.776 1.00 95.43 14 A 1 ATOM 109 N N . LEU A 1 15 ? 3.557 -4.648 -7.329 1.00 97.81 15 A 1 ATOM 110 C CA . LEU A 1 15 ? 4.982 -4.722 -7.681 1.00 97.62 15 A 1 ATOM 111 C C . LEU A 1 15 ? 5.455 -6.171 -7.736 1.00 97.86 15 A 1 ATOM 112 O O . LEU A 1 15 ? 6.246 -6.539 -8.607 1.00 97.04 15 A 1 ATOM 113 C CB . LEU A 1 15 ? 5.793 -3.945 -6.642 1.00 97.00 15 A 1 ATOM 114 C CG . LEU A 1 15 ? 7.289 -3.971 -6.946 1.00 93.80 15 A 1 ATOM 115 C CD1 . LEU A 1 15 ? 7.570 -3.207 -8.241 1.00 88.95 15 A 1 ATOM 116 C CD2 . LEU A 1 15 ? 8.068 -3.335 -5.802 1.00 88.19 15 A 1 ATOM 117 N N . ALA A 1 16 ? 4.999 -6.992 -6.809 1.00 96.74 16 A 1 ATOM 118 C CA . ALA A 1 16 ? 5.407 -8.394 -6.746 1.00 95.35 16 A 1 ATOM 119 C C . ALA A 1 16 ? 4.823 -9.192 -7.913 1.00 94.50 16 A 1 ATOM 120 O O . ALA A 1 16 ? 3.712 -8.874 -8.369 1.00 91.43 16 A 1 ATOM 121 C CB . ALA A 1 16 ? 4.988 -8.997 -5.409 1.00 92.93 16 A 1 ATOM 122 O OXT . ALA A 1 16 ? 5.451 -10.148 -8.363 1.00 85.18 16 A 1 #