# 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_spkb08407 # _entry.id spkb08407 # 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" "C2 H5 N O2" 75.067 GLY y GLYCINE C(C(=O)O)N ? "PEPTIDE LINKING" "C6 H10 N3 O2" 156.162 HIS y HISTIDINE c1c([nH+]c[nH]1)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" "C3 H7 N O3" 105.093 SER y SERINE C([C@@H](C(=O)O)N)O ? "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 GLY 2 1 n HIS 3 1 n SER 4 1 n VAL 5 1 n ALA 6 1 n TRP 7 1 n LEU 8 1 n LEU 9 1 n LEU 10 1 n VAL 11 1 n ALA 12 1 n ALA 13 1 n ALA 14 1 n SER 15 1 n THR 16 1 n LEU 17 1 n ALA 18 # _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 @ 2025-07-08 05:51:06)" _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 93.24 _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 80.27 1 1 A GLY 2 2 92.22 1 2 A HIS 3 2 87.16 1 3 A SER 4 2 94.53 1 4 A VAL 5 2 95.15 1 5 A ALA 6 2 96.91 1 6 A TRP 7 2 94.09 1 7 A LEU 8 2 95.99 1 8 A LEU 9 2 96.13 1 9 A LEU 10 2 95.24 1 10 A VAL 11 2 96.64 1 11 A ALA 12 2 97.46 1 12 A ALA 13 2 97.15 1 13 A ALA 14 2 97.42 1 14 A SER 15 2 95.92 1 15 A THR 16 2 93.37 1 16 A LEU 17 2 91.04 1 17 A ALA 18 2 88.55 1 18 # _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 GLY . 2 A 2 A 3 1 n HIS . 3 A 3 A 4 1 n SER . 4 A 4 A 5 1 n VAL . 5 A 5 A 6 1 n ALA . 6 A 6 A 7 1 n TRP . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n VAL . 11 A 11 A 12 1 n ALA . 12 A 12 A 13 1 n ALA . 13 A 13 A 14 1 n ALA . 14 A 14 A 15 1 n SER . 15 A 15 A 16 1 n THR . 16 A 16 A 17 1 n LEU . 17 A 17 A 18 1 n ALA . 18 A 18 # _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 ? -13.284 3.222 -2.697 1.00 85.59 1 A 1 ATOM 2 C CA . MET A 1 1 ? -11.854 3.483 -2.427 1.00 87.41 1 A 1 ATOM 3 C C . MET A 1 1 ? -11.014 2.238 -2.699 1.00 88.74 1 A 1 ATOM 4 O O . MET A 1 1 ? -10.936 1.343 -1.859 1.00 84.63 1 A 1 ATOM 5 C CB . MET A 1 1 ? -11.648 3.898 -0.971 1.00 82.18 1 A 1 ATOM 6 C CG . MET A 1 1 ? -12.342 5.199 -0.629 1.00 76.39 1 A 1 ATOM 7 S SD . MET A 1 1 ? -12.121 5.640 1.101 1.00 73.16 1 A 1 ATOM 8 C CE . MET A 1 1 ? -12.996 7.182 1.146 1.00 64.04 1 A 1 ATOM 9 N N . GLY A 1 2 ? -10.410 2.187 -3.872 1.00 88.85 2 A 1 ATOM 10 C CA . GLY A 1 2 ? -9.575 1.045 -4.229 1.00 92.41 2 A 1 ATOM 11 C C . GLY A 1 2 ? -8.099 1.371 -4.158 1.00 94.44 2 A 1 ATOM 12 O O . GLY A 1 2 ? -7.331 0.707 -3.462 1.00 93.16 2 A 1 ATOM 13 N N . HIS A 1 3 ? -7.694 2.428 -4.879 1.00 92.91 3 A 1 ATOM 14 C CA . HIS A 1 3 ? -6.291 2.836 -4.912 1.00 94.08 3 A 1 ATOM 15 C C . HIS A 1 3 ? -5.853 3.448 -3.581 1.00 95.56 3 A 1 ATOM 16 O O . HIS A 1 3 ? -4.681 3.389 -3.214 1.00 93.85 3 A 1 ATOM 17 C CB . HIS A 1 3 ? -6.059 3.835 -6.048 1.00 91.32 3 A 1 ATOM 18 C CG . HIS A 1 3 ? -4.626 3.910 -6.466 1.00 87.35 3 A 1 ATOM 19 N ND1 . HIS A 1 3 ? -3.691 4.667 -5.813 1.00 79.67 3 A 1 ATOM 20 C CD2 . HIS A 1 3 ? -3.974 3.294 -7.477 1.00 77.24 3 A 1 ATOM 21 C CE1 . HIS A 1 3 ? -2.520 4.517 -6.409 1.00 79.81 3 A 1 ATOM 22 N NE2 . HIS A 1 3 ? -2.660 3.688 -7.429 1.00 79.81 3 A 1 ATOM 23 N N . SER A 1 4 ? -6.797 4.022 -2.845 1.00 95.09 4 A 1 ATOM 24 C CA . SER A 1 4 ? -6.499 4.640 -1.551 1.00 96.38 4 A 1 ATOM 25 C C . SER A 1 4 ? -5.958 3.612 -0.561 1.00 97.29 4 A 1 ATOM 26 O O . SER A 1 4 ? -5.013 3.879 0.177 1.00 96.28 4 A 1 ATOM 27 C CB . SER A 1 4 ? -7.751 5.295 -0.975 1.00 94.68 4 A 1 ATOM 28 O OG . SER A 1 4 ? -8.227 6.299 -1.848 1.00 87.45 4 A 1 ATOM 29 N N . VAL A 1 5 ? -6.563 2.420 -0.552 1.00 95.90 5 A 1 ATOM 30 C CA . VAL A 1 5 ? -6.130 1.343 0.340 1.00 96.59 5 A 1 ATOM 31 C C . VAL A 1 5 ? -4.724 0.881 -0.030 1.00 97.08 5 A 1 ATOM 32 O O . VAL A 1 5 ? -3.873 0.673 0.840 1.00 96.56 5 A 1 ATOM 33 C CB . VAL A 1 5 ? -7.103 0.154 0.289 1.00 95.69 5 A 1 ATOM 34 C CG1 . VAL A 1 5 ? -6.622 -0.976 1.188 1.00 92.07 5 A 1 ATOM 35 C CG2 . VAL A 1 5 ? -8.498 0.601 0.696 1.00 92.15 5 A 1 ATOM 36 N N . ALA A 1 6 ? -4.484 0.718 -1.327 1.00 96.51 6 A 1 ATOM 37 C CA . ALA A 1 6 ? -3.176 0.289 -1.817 1.00 96.99 6 A 1 ATOM 38 C C . ALA A 1 6 ? -2.101 1.309 -1.458 1.00 97.44 6 A 1 ATOM 39 O O . ALA A 1 6 ? -0.971 0.945 -1.121 1.00 97.06 6 A 1 ATOM 40 C CB . ALA A 1 6 ? -3.226 0.087 -3.326 1.00 96.55 6 A 1 ATOM 41 N N . TRP A 1 7 ? -2.469 2.596 -1.523 1.00 96.30 7 A 1 ATOM 42 C CA . TRP A 1 7 ? -1.543 3.678 -1.186 1.00 96.38 7 A 1 ATOM 43 C C . TRP A 1 7 ? -1.121 3.599 0.277 1.00 97.12 7 A 1 ATOM 44 O O . TRP A 1 7 ? 0.057 3.750 0.602 1.00 96.96 7 A 1 ATOM 45 C CB . TRP A 1 7 ? -2.194 5.033 -1.473 1.00 95.90 7 A 1 ATOM 46 C CG . TRP A 1 7 ? -1.297 6.187 -1.151 1.00 94.59 7 A 1 ATOM 47 C CD1 . TRP A 1 7 ? -1.524 7.161 -0.219 1.00 92.32 7 A 1 ATOM 48 C CD2 . TRP A 1 7 ? -0.021 6.490 -1.739 1.00 93.88 7 A 1 ATOM 49 N NE1 . TRP A 1 7 ? -0.470 8.051 -0.199 1.00 92.03 7 A 1 ATOM 50 C CE2 . TRP A 1 7 ? 0.469 7.662 -1.122 1.00 93.40 7 A 1 ATOM 51 C CE3 . TRP A 1 7 ? 0.753 5.880 -2.733 1.00 92.72 7 A 1 ATOM 52 C CZ2 . TRP A 1 7 ? 1.702 8.229 -1.475 1.00 93.08 7 A 1 ATOM 53 C CZ3 . TRP A 1 7 ? 1.978 6.448 -3.078 1.00 91.25 7 A 1 ATOM 54 C CH2 . TRP A 1 7 ? 2.440 7.607 -2.451 1.00 91.37 7 A 1 ATOM 55 N N . LEU A 1 8 ? -2.083 3.334 1.156 1.00 97.05 8 A 1 ATOM 56 C CA . LEU A 1 8 ? -1.802 3.221 2.585 1.00 97.14 8 A 1 ATOM 57 C C . LEU A 1 8 ? -0.862 2.053 2.863 1.00 97.49 8 A 1 ATOM 58 O O . LEU A 1 8 ? 0.034 2.153 3.705 1.00 97.40 8 A 1 ATOM 59 C CB . LEU A 1 8 ? -3.110 3.025 3.358 1.00 97.06 8 A 1 ATOM 60 C CG . LEU A 1 8 ? -4.014 4.256 3.376 1.00 94.83 8 A 1 ATOM 61 C CD1 . LEU A 1 8 ? -5.378 3.911 3.957 1.00 93.78 8 A 1 ATOM 62 C CD2 . LEU A 1 8 ? -3.372 5.374 4.189 1.00 93.19 8 A 1 ATOM 63 N N . LEU A 1 9 ? -1.065 0.949 2.156 1.00 97.09 9 A 1 ATOM 64 C CA . LEU A 1 9 ? -0.232 -0.237 2.321 1.00 97.03 9 A 1 ATOM 65 C C . LEU A 1 9 ? 1.200 0.036 1.870 1.00 97.27 9 A 1 ATOM 66 O O . LEU A 1 9 ? 2.155 -0.405 2.513 1.00 97.20 9 A 1 ATOM 67 C CB . LEU A 1 9 ? -0.818 -1.404 1.521 1.00 97.00 9 A 1 ATOM 68 C CG . LEU A 1 9 ? -2.151 -1.924 2.058 1.00 95.22 9 A 1 ATOM 69 C CD1 . LEU A 1 9 ? -2.760 -2.929 1.089 1.00 94.19 9 A 1 ATOM 70 C CD2 . LEU A 1 9 ? -1.967 -2.563 3.429 1.00 94.03 9 A 1 ATOM 71 N N . LEU A 1 10 ? 1.350 0.766 0.773 1.00 96.91 10 A 1 ATOM 72 C CA . LEU A 1 10 ? 2.667 1.107 0.244 1.00 96.63 10 A 1 ATOM 73 C C . LEU A 1 10 ? 3.432 1.996 1.219 1.00 97.21 10 A 1 ATOM 74 O O . LEU A 1 10 ? 4.619 1.775 1.480 1.00 97.25 10 A 1 ATOM 75 C CB . LEU A 1 10 ? 2.520 1.818 -1.102 1.00 96.23 10 A 1 ATOM 76 C CG . LEU A 1 10 ? 2.050 0.917 -2.242 1.00 93.19 10 A 1 ATOM 77 C CD1 . LEU A 1 10 ? 1.696 1.751 -3.465 1.00 92.48 10 A 1 ATOM 78 C CD2 . LEU A 1 10 ? 3.125 -0.102 -2.592 1.00 92.01 10 A 1 ATOM 79 N N . VAL A 1 11 ? 2.757 2.991 1.757 1.00 97.29 11 A 1 ATOM 80 C CA . VAL A 1 11 ? 3.373 3.908 2.713 1.00 97.08 11 A 1 ATOM 81 C C . VAL A 1 11 ? 3.755 3.169 3.991 1.00 97.55 11 A 1 ATOM 82 O O . VAL A 1 11 ? 4.834 3.385 4.550 1.00 97.52 11 A 1 ATOM 83 C CB . VAL A 1 11 ? 2.423 5.072 3.050 1.00 96.39 11 A 1 ATOM 84 C CG1 . VAL A 1 11 ? 3.034 5.982 4.114 1.00 95.19 11 A 1 ATOM 85 C CG2 . VAL A 1 11 ? 2.110 5.871 1.797 1.00 95.44 11 A 1 ATOM 86 N N . ALA A 1 12 ? 2.873 2.293 4.452 1.00 97.53 12 A 1 ATOM 87 C CA . ALA A 1 12 ? 3.122 1.519 5.662 1.00 97.44 12 A 1 ATOM 88 C C . ALA A 1 12 ? 4.329 0.603 5.486 1.00 97.84 12 A 1 ATOM 89 O O . ALA A 1 12 ? 5.155 0.472 6.392 1.00 97.46 12 A 1 ATOM 90 C CB . ALA A 1 12 ? 1.889 0.692 6.018 1.00 97.02 12 A 1 ATOM 91 N N . ALA A 1 13 ? 4.436 -0.028 4.319 1.00 97.51 13 A 1 ATOM 92 C CA . ALA A 1 13 ? 5.550 -0.926 4.029 1.00 97.19 13 A 1 ATOM 93 C C . ALA A 1 13 ? 6.871 -0.167 4.025 1.00 97.60 13 A 1 ATOM 94 O O . ALA A 1 13 ? 7.868 -0.636 4.581 1.00 97.00 13 A 1 ATOM 95 C CB . ALA A 1 13 ? 5.333 -1.609 2.683 1.00 96.43 13 A 1 ATOM 96 N N . ALA A 1 14 ? 6.881 1.001 3.404 1.00 97.77 14 A 1 ATOM 97 C CA . ALA A 1 14 ? 8.085 1.828 3.336 1.00 97.55 14 A 1 ATOM 98 C C . ALA A 1 14 ? 8.493 2.316 4.721 1.00 97.85 14 A 1 ATOM 99 O O . ALA A 1 14 ? 9.680 2.356 5.051 1.00 97.18 14 A 1 ATOM 100 C CB . ALA A 1 14 ? 7.845 3.018 2.414 1.00 96.77 14 A 1 ATOM 101 N N . SER A 1 15 ? 7.512 2.679 5.532 1.00 97.91 15 A 1 ATOM 102 C CA . SER A 1 15 ? 7.761 3.161 6.889 1.00 97.74 15 A 1 ATOM 103 C C . SER A 1 15 ? 8.289 2.047 7.785 1.00 97.88 15 A 1 ATOM 104 O O . SER A 1 15 ? 9.135 2.281 8.650 1.00 96.62 15 A 1 ATOM 105 C CB . SER A 1 15 ? 6.481 3.736 7.495 1.00 96.74 15 A 1 ATOM 106 O OG . SER A 1 15 ? 6.732 4.254 8.781 1.00 88.65 15 A 1 ATOM 107 N N . THR A 1 16 ? 7.786 0.839 7.574 1.00 96.65 16 A 1 ATOM 108 C CA . THR A 1 16 ? 8.206 -0.316 8.371 1.00 96.06 16 A 1 ATOM 109 C C . THR A 1 16 ? 9.677 -0.645 8.133 1.00 96.21 16 A 1 ATOM 110 O O . THR A 1 16 ? 10.419 -0.944 9.073 1.00 94.05 16 A 1 ATOM 111 C CB . THR A 1 16 ? 7.359 -1.551 8.035 1.00 94.22 16 A 1 ATOM 112 O OG1 . THR A 1 16 ? 5.984 -1.273 8.296 1.00 88.84 16 A 1 ATOM 113 C CG2 . THR A 1 16 ? 7.783 -2.741 8.879 1.00 87.53 16 A 1 ATOM 114 N N . LEU A 1 17 ? 10.091 -0.596 6.874 1.00 95.83 17 A 1 ATOM 115 C CA . LEU A 1 17 ? 11.471 -0.887 6.504 1.00 95.13 17 A 1 ATOM 116 C C . LEU A 1 17 ? 12.408 0.236 6.918 1.00 95.62 17 A 1 ATOM 117 O O . LEU A 1 17 ? 13.550 -0.010 7.325 1.00 93.83 17 A 1 ATOM 118 C CB . LEU A 1 17 ? 11.571 -1.121 4.998 1.00 93.10 17 A 1 ATOM 119 C CG . LEU A 1 17 ? 10.846 -2.371 4.506 1.00 88.57 17 A 1 ATOM 120 C CD1 . LEU A 1 17 ? 10.811 -2.403 2.986 1.00 84.76 17 A 1 ATOM 121 C CD2 . LEU A 1 17 ? 11.527 -3.623 5.043 1.00 81.50 17 A 1 ATOM 122 N N . ALA A 1 18 ? 11.929 1.468 6.804 1.00 93.76 18 A 1 ATOM 123 C CA . ALA A 1 18 ? 12.724 2.648 7.131 1.00 92.07 18 A 1 ATOM 124 C C . ALA A 1 18 ? 12.701 2.914 8.632 1.00 90.67 18 A 1 ATOM 125 O O . ALA A 1 18 ? 11.640 3.269 9.161 1.00 86.85 18 A 1 ATOM 126 C CB . ALA A 1 18 ? 12.220 3.851 6.361 1.00 87.45 18 A 1 ATOM 127 O OXT . ALA A 1 18 ? 13.753 2.764 9.278 1.00 80.48 18 A 1 #