# 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_spkb16862 # _entry.id spkb16862 # 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" "C5 H9 N O4" 147.129 GLU y "GLUTAMIC ACID" C(CC(=O)O)[C@@H](C(=O)O)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" "C4 H9 N O3" 119.119 THR y THREONINE C[C@H]([C@@H](C(=O)O)N)O ? "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 THR 3 1 n LEU 4 1 n TRP 5 1 n ILE 6 1 n VAL 7 1 n ALA 8 1 n VAL 9 1 n LEU 10 1 n LEU 11 1 n LEU 12 1 n GLY 13 1 n VAL 14 1 n GLU 15 1 n GLY 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 @ 2025-07-04 21:29:23)" _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 95.07 _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 89.18 1 1 A ARG 2 2 91.57 1 2 A THR 3 2 97.56 1 3 A LEU 4 2 96.88 1 4 A TRP 5 2 95.39 1 5 A ILE 6 2 97.52 1 6 A VAL 7 2 98.16 1 7 A ALA 8 2 98.30 1 8 A VAL 9 2 98.08 1 9 A LEU 10 2 97.36 1 10 A LEU 11 2 97.59 1 11 A LEU 12 2 97.16 1 12 A GLY 13 2 98.03 1 13 A VAL 14 2 96.48 1 14 A GLU 15 2 87.25 1 15 A GLY 16 2 87.85 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 THR . 3 A 3 A 4 1 n LEU . 4 A 4 A 5 1 n TRP . 5 A 5 A 6 1 n ILE . 6 A 6 A 7 1 n VAL . 7 A 7 A 8 1 n ALA . 8 A 8 A 9 1 n VAL . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n LEU . 11 A 11 A 12 1 n LEU . 12 A 12 A 13 1 n GLY . 13 A 13 A 14 1 n VAL . 14 A 14 A 15 1 n GLU . 15 A 15 A 16 1 n GLY . 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 ? -0.668 -2.413 13.056 1.00 95.09 1 A 1 ATOM 2 C CA . MET A 1 1 ? -0.625 -1.220 12.187 1.00 95.77 1 A 1 ATOM 3 C C . MET A 1 1 ? -0.708 -1.631 10.714 1.00 96.63 1 A 1 ATOM 4 O O . MET A 1 1 ? 0.283 -1.596 9.988 1.00 94.72 1 A 1 ATOM 5 C CB . MET A 1 1 ? 0.673 -0.455 12.423 1.00 91.28 1 A 1 ATOM 6 C CG . MET A 1 1 ? 0.798 0.017 13.857 1.00 85.47 1 A 1 ATOM 7 S SD . MET A 1 1 ? 2.385 0.796 14.175 1.00 82.82 1 A 1 ATOM 8 C CE . MET A 1 1 ? 2.224 1.163 15.908 1.00 71.63 1 A 1 ATOM 9 N N . ARG A 1 2 ? -1.898 -2.018 10.288 1.00 97.81 2 A 1 ATOM 10 C CA . ARG A 1 2 ? -2.108 -2.462 8.907 1.00 98.10 2 A 1 ATOM 11 C C . ARG A 1 2 ? -2.400 -1.281 7.982 1.00 98.46 2 A 1 ATOM 12 O O . ARG A 1 2 ? -1.922 -1.233 6.853 1.00 98.01 2 A 1 ATOM 13 C CB . ARG A 1 2 ? -3.280 -3.446 8.864 1.00 97.25 2 A 1 ATOM 14 C CG . ARG A 1 2 ? -2.963 -4.767 9.546 1.00 93.14 2 A 1 ATOM 15 C CD . ARG A 1 2 ? -4.197 -5.645 9.567 1.00 91.74 2 A 1 ATOM 16 N NE . ARG A 1 2 ? -3.898 -6.970 10.110 1.00 87.14 2 A 1 ATOM 17 C CZ . ARG A 1 2 ? -4.828 -7.863 10.397 1.00 86.05 2 A 1 ATOM 18 N NH1 . ARG A 1 2 ? -6.111 -7.585 10.226 1.00 79.48 2 A 1 ATOM 19 N NH2 . ARG A 1 2 ? -4.480 -9.046 10.862 1.00 80.13 2 A 1 ATOM 20 N N . THR A 1 3 ? -3.191 -0.337 8.470 1.00 98.39 3 A 1 ATOM 21 C CA . THR A 1 3 ? -3.561 0.834 7.675 1.00 98.56 3 A 1 ATOM 22 C C . THR A 1 3 ? -2.321 1.588 7.201 1.00 98.65 3 A 1 ATOM 23 O O . THR A 1 3 ? -2.255 2.030 6.053 1.00 98.35 3 A 1 ATOM 24 C CB . THR A 1 3 ? -4.446 1.780 8.495 1.00 98.30 3 A 1 ATOM 25 O OG1 . THR A 1 3 ? -5.470 1.037 9.144 1.00 95.57 3 A 1 ATOM 26 C CG2 . THR A 1 3 ? -5.076 2.834 7.603 1.00 95.12 3 A 1 ATOM 27 N N . LEU A 1 4 ? -1.354 1.735 8.078 1.00 98.62 4 A 1 ATOM 28 C CA . LEU A 1 4 ? -0.114 2.436 7.745 1.00 98.66 4 A 1 ATOM 29 C C . LEU A 1 4 ? 0.589 1.746 6.576 1.00 98.71 4 A 1 ATOM 30 O O . LEU A 1 4 ? 1.116 2.399 5.673 1.00 98.50 4 A 1 ATOM 31 C CB . LEU A 1 4 ? 0.809 2.478 8.971 1.00 98.52 4 A 1 ATOM 32 C CG . LEU A 1 4 ? 1.787 3.651 8.987 1.00 96.45 4 A 1 ATOM 33 C CD1 . LEU A 1 4 ? 2.816 3.531 7.873 1.00 92.74 4 A 1 ATOM 34 C CD2 . LEU A 1 4 ? 1.035 4.969 8.878 1.00 92.86 4 A 1 ATOM 35 N N . TRP A 1 5 ? 0.571 0.406 6.591 1.00 98.28 5 A 1 ATOM 36 C CA . TRP A 1 5 ? 1.213 -0.367 5.528 1.00 98.26 5 A 1 ATOM 37 C C . TRP A 1 5 ? 0.498 -0.138 4.201 1.00 98.39 5 A 1 ATOM 38 O O . TRP A 1 5 ? 1.136 0.052 3.166 1.00 98.11 5 A 1 ATOM 39 C CB . TRP A 1 5 ? 1.193 -1.852 5.889 1.00 97.96 5 A 1 ATOM 40 C CG . TRP A 1 5 ? 2.305 -2.601 5.244 1.00 96.59 5 A 1 ATOM 41 C CD1 . TRP A 1 5 ? 3.591 -2.665 5.674 1.00 93.67 5 A 1 ATOM 42 C CD2 . TRP A 1 5 ? 2.245 -3.386 4.033 1.00 95.47 5 A 1 ATOM 43 N NE1 . TRP A 1 5 ? 4.334 -3.437 4.810 1.00 93.30 5 A 1 ATOM 44 C CE2 . TRP A 1 5 ? 3.536 -3.892 3.798 1.00 95.07 5 A 1 ATOM 45 C CE3 . TRP A 1 5 ? 1.218 -3.700 3.139 1.00 93.22 5 A 1 ATOM 46 C CZ2 . TRP A 1 5 ? 3.822 -4.702 2.689 1.00 92.87 5 A 1 ATOM 47 C CZ3 . TRP A 1 5 ? 1.506 -4.512 2.034 1.00 92.10 5 A 1 ATOM 48 C CH2 . TRP A 1 5 ? 2.796 -4.997 1.822 1.00 92.11 5 A 1 ATOM 49 N N . ILE A 1 6 ? -0.819 -0.133 4.244 1.00 98.50 6 A 1 ATOM 50 C CA . ILE A 1 6 ? -1.623 0.090 3.041 1.00 98.49 6 A 1 ATOM 51 C C . ILE A 1 6 ? -1.366 1.486 2.479 1.00 98.59 6 A 1 ATOM 52 O O . ILE A 1 6 ? -1.234 1.668 1.267 1.00 98.45 6 A 1 ATOM 53 C CB . ILE A 1 6 ? -3.120 -0.088 3.357 1.00 98.37 6 A 1 ATOM 54 C CG1 . ILE A 1 6 ? -3.403 -1.517 3.824 1.00 97.34 6 A 1 ATOM 55 C CG2 . ILE A 1 6 ? -3.964 0.235 2.123 1.00 97.34 6 A 1 ATOM 56 C CD1 . ILE A 1 6 ? -4.762 -1.665 4.484 1.00 93.04 6 A 1 ATOM 57 N N . VAL A 1 7 ? -1.311 2.458 3.356 1.00 98.51 7 A 1 ATOM 58 C CA . VAL A 1 7 ? -1.062 3.844 2.943 1.00 98.54 7 A 1 ATOM 59 C C . VAL A 1 7 ? 0.301 3.960 2.264 1.00 98.61 7 A 1 ATOM 60 O O . VAL A 1 7 ? 0.447 4.647 1.249 1.00 98.46 7 A 1 ATOM 61 C CB . VAL A 1 7 ? -1.125 4.792 4.152 1.00 98.31 7 A 1 ATOM 62 C CG1 . VAL A 1 7 ? -0.744 6.211 3.748 1.00 97.40 7 A 1 ATOM 63 C CG2 . VAL A 1 7 ? -2.522 4.785 4.754 1.00 97.27 7 A 1 ATOM 64 N N . ALA A 1 8 ? 1.280 3.289 2.822 1.00 98.38 8 A 1 ATOM 65 C CA . ALA A 1 8 ? 2.635 3.319 2.270 1.00 98.36 8 A 1 ATOM 66 C C . ALA A 1 8 ? 2.662 2.726 0.864 1.00 98.44 8 A 1 ATOM 67 O O . ALA A 1 8 ? 3.279 3.287 -0.043 1.00 98.18 8 A 1 ATOM 68 C CB . ALA A 1 8 ? 3.580 2.547 3.183 1.00 98.13 8 A 1 ATOM 69 N N . VAL A 1 9 ? 1.977 1.598 0.682 1.00 98.50 9 A 1 ATOM 70 C CA . VAL A 1 9 ? 1.914 0.936 -0.622 1.00 98.46 9 A 1 ATOM 71 C C . VAL A 1 9 ? 1.182 1.816 -1.628 1.00 98.58 9 A 1 ATOM 72 O O . VAL A 1 9 ? 1.584 1.918 -2.791 1.00 98.35 9 A 1 ATOM 73 C CB . VAL A 1 9 ? 1.209 -0.425 -0.505 1.00 98.12 9 A 1 ATOM 74 C CG1 . VAL A 1 9 ? 1.054 -1.072 -1.871 1.00 97.29 9 A 1 ATOM 75 C CG2 . VAL A 1 9 ? 1.990 -1.341 0.418 1.00 97.25 9 A 1 ATOM 76 N N . LEU A 1 10 ? 0.110 2.447 -1.181 1.00 98.54 10 A 1 ATOM 77 C CA . LEU A 1 10 ? -0.682 3.327 -2.038 1.00 98.52 10 A 1 ATOM 78 C C . LEU A 1 10 ? 0.164 4.500 -2.526 1.00 98.63 10 A 1 ATOM 79 O O . LEU A 1 10 ? 0.135 4.848 -3.706 1.00 98.33 10 A 1 ATOM 80 C CB . LEU A 1 10 ? -1.896 3.843 -1.263 1.00 98.36 10 A 1 ATOM 81 C CG . LEU A 1 10 ? -2.853 4.697 -2.091 1.00 97.01 10 A 1 ATOM 82 C CD1 . LEU A 1 10 ? -3.549 3.848 -3.146 1.00 94.64 10 A 1 ATOM 83 C CD2 . LEU A 1 10 ? -3.886 5.353 -1.192 1.00 94.89 10 A 1 ATOM 84 N N . LEU A 1 11 ? 0.903 5.102 -1.621 1.00 98.63 11 A 1 ATOM 85 C CA . LEU A 1 11 ? 1.764 6.233 -1.967 1.00 98.57 11 A 1 ATOM 86 C C . LEU A 1 11 ? 2.835 5.821 -2.961 1.00 98.57 11 A 1 ATOM 87 O O . LEU A 1 11 ? 3.089 6.526 -3.938 1.00 98.21 11 A 1 ATOM 88 C CB . LEU A 1 11 ? 2.423 6.778 -0.700 1.00 98.37 11 A 1 ATOM 89 C CG . LEU A 1 11 ? 1.602 7.864 -0.016 1.00 97.39 11 A 1 ATOM 90 C CD1 . LEU A 1 11 ? 2.001 7.990 1.442 1.00 95.52 11 A 1 ATOM 91 C CD2 . LEU A 1 11 ? 1.798 9.192 -0.726 1.00 95.47 11 A 1 ATOM 92 N N . LEU A 1 12 ? 3.447 4.682 -2.722 1.00 98.59 12 A 1 ATOM 93 C CA . LEU A 1 12 ? 4.497 4.176 -3.598 1.00 98.49 12 A 1 ATOM 94 C C . LEU A 1 12 ? 3.949 3.846 -4.980 1.00 98.52 12 A 1 ATOM 95 O O . LEU A 1 12 ? 4.567 4.178 -5.991 1.00 97.92 12 A 1 ATOM 96 C CB . LEU A 1 12 ? 5.126 2.933 -2.976 1.00 98.23 12 A 1 ATOM 97 C CG . LEU A 1 12 ? 6.389 2.466 -3.683 1.00 96.81 12 A 1 ATOM 98 C CD1 . LEU A 1 12 ? 7.536 3.431 -3.413 1.00 94.53 12 A 1 ATOM 99 C CD2 . LEU A 1 12 ? 6.763 1.068 -3.216 1.00 94.15 12 A 1 ATOM 100 N N . GLY A 1 13 ? 2.786 3.208 -5.022 1.00 98.27 13 A 1 ATOM 101 C CA . GLY A 1 13 ? 2.166 2.830 -6.286 1.00 98.14 13 A 1 ATOM 102 C C . GLY A 1 13 ? 1.665 4.016 -7.078 1.00 98.25 13 A 1 ATOM 103 O O . GLY A 1 13 ? 1.852 4.083 -8.294 1.00 97.45 13 A 1 ATOM 104 N N . VAL A 1 14 ? 1.018 4.959 -6.410 1.00 98.08 14 A 1 ATOM 105 C CA . VAL A 1 14 ? 0.467 6.147 -7.065 1.00 97.92 14 A 1 ATOM 106 C C . VAL A 1 14 ? 1.561 7.151 -7.413 1.00 98.03 14 A 1 ATOM 107 O O . VAL A 1 14 ? 1.572 7.712 -8.510 1.00 96.98 14 A 1 ATOM 108 C CB . VAL A 1 14 ? -0.588 6.821 -6.170 1.00 97.09 14 A 1 ATOM 109 C CG1 . VAL A 1 14 ? -1.088 8.109 -6.813 1.00 93.62 14 A 1 ATOM 110 C CG2 . VAL A 1 14 ? -1.756 5.882 -5.930 1.00 93.63 14 A 1 ATOM 111 N N . GLU A 1 15 ? 2.459 7.380 -6.474 1.00 96.48 15 A 1 ATOM 112 C CA . GLU A 1 15 ? 3.544 8.341 -6.685 1.00 95.66 15 A 1 ATOM 113 C C . GLU A 1 15 ? 4.570 7.824 -7.679 1.00 94.36 15 A 1 ATOM 114 O O . GLU A 1 15 ? 5.303 8.604 -8.284 1.00 88.70 15 A 1 ATOM 115 C CB . GLU A 1 15 ? 4.219 8.661 -5.353 1.00 93.44 15 A 1 ATOM 116 C CG . GLU A 1 15 ? 3.351 9.552 -4.478 1.00 84.72 15 A 1 ATOM 117 C CD . GLU A 1 15 ? 3.228 10.946 -5.063 1.00 81.37 15 A 1 ATOM 118 O OE1 . GLU A 1 15 ? 4.261 11.526 -5.410 1.00 74.34 15 A 1 ATOM 119 O OE2 . GLU A 1 15 ? 2.099 11.443 -5.174 1.00 76.14 15 A 1 ATOM 120 N N . GLY A 1 16 ? 4.617 6.535 -7.861 1.00 93.90 16 A 1 ATOM 121 C CA . GLY A 1 16 ? 5.547 5.906 -8.797 1.00 90.72 16 A 1 ATOM 122 C C . GLY A 1 16 ? 6.361 4.832 -8.110 1.00 87.48 16 A 1 ATOM 123 O O . GLY A 1 16 ? 7.287 5.175 -7.371 1.00 80.88 16 A 1 ATOM 124 O OXT . GLY A 1 16 ? 6.034 3.638 -8.306 1.00 86.28 16 A 1 #