# 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_spkb16968 # _entry.id spkb16968 # 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" "C4 H8 N2 O3" 132.118 ASN y ASPARAGINE C([C@@H](C(=O)O)N)C(=O)N ? "L-PEPTIDE LINKING" "C5 H10 N2 O3" 146.144 GLN y GLUTAMINE C(CC(=O)N)[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" "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" # _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 GLN 2 1 n ASN 3 1 n ILE 4 1 n PHE 5 1 n LEU 6 1 n ALA 7 1 n ALA 8 1 n THR 9 1 n LEU 10 1 n LEU 11 1 n GLY 12 1 n ALA 13 1 n ALA 14 1 n PHE 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 @ 2025-07-03 02:17:36)" _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 94.78 _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 88.50 1 1 A GLN 2 2 91.04 1 2 A ASN 3 2 94.84 1 3 A ILE 4 2 95.88 1 4 A PHE 5 2 94.61 1 5 A LEU 6 2 95.55 1 6 A ALA 7 2 97.95 1 7 A ALA 8 2 98.11 1 8 A THR 9 2 96.50 1 9 A LEU 10 2 97.38 1 10 A LEU 11 2 96.60 1 11 A GLY 12 2 97.95 1 12 A ALA 13 2 97.91 1 13 A ALA 14 2 97.83 1 14 A PHE 15 2 92.39 1 15 A ALA 16 2 90.34 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 GLN . 2 A 2 A 3 1 n ASN . 3 A 3 A 4 1 n ILE . 4 A 4 A 5 1 n PHE . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n ALA . 7 A 7 A 8 1 n ALA . 8 A 8 A 9 1 n THR . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n LEU . 11 A 11 A 12 1 n GLY . 12 A 12 A 13 1 n ALA . 13 A 13 A 14 1 n ALA . 14 A 14 A 15 1 n PHE . 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 ? -4.242 13.040 5.674 1.00 92.01 1 A 1 ATOM 2 C CA . MET A 1 1 ? -3.748 12.265 4.523 1.00 93.38 1 A 1 ATOM 3 C C . MET A 1 1 ? -3.426 10.825 4.928 1.00 93.90 1 A 1 ATOM 4 O O . MET A 1 1 ? -2.369 10.286 4.588 1.00 92.88 1 A 1 ATOM 5 C CB . MET A 1 1 ? -2.489 12.907 3.944 1.00 89.61 1 A 1 ATOM 6 C CG . MET A 1 1 ? -2.681 14.351 3.555 1.00 86.26 1 A 1 ATOM 7 S SD . MET A 1 1 ? -1.202 15.022 2.788 1.00 85.08 1 A 1 ATOM 8 C CE . MET A 1 1 ? -1.500 16.755 2.997 1.00 74.88 1 A 1 ATOM 9 N N . GLN A 1 2 ? -4.356 10.205 5.641 1.00 94.64 2 A 1 ATOM 10 C CA . GLN A 1 2 ? -4.163 8.840 6.120 1.00 95.60 2 A 1 ATOM 11 C C . GLN A 1 2 ? -4.273 7.839 4.974 1.00 96.67 2 A 1 ATOM 12 O O . GLN A 1 2 ? -3.651 6.780 5.003 1.00 95.76 2 A 1 ATOM 13 C CB . GLN A 1 2 ? -5.204 8.511 7.193 1.00 94.27 2 A 1 ATOM 14 C CG . GLN A 1 2 ? -5.349 9.562 8.271 1.00 90.77 2 A 1 ATOM 15 C CD . GLN A 1 2 ? -4.160 9.605 9.217 1.00 88.55 2 A 1 ATOM 16 O OE1 . GLN A 1 2 ? -3.097 10.100 8.877 1.00 82.80 2 A 1 ATOM 17 N NE2 . GLN A 1 2 ? -4.335 9.074 10.410 1.00 80.34 2 A 1 ATOM 18 N N . ASN A 1 3 ? -5.061 8.184 3.963 1.00 96.35 3 A 1 ATOM 19 C CA . ASN A 1 3 ? -5.301 7.314 2.813 1.00 97.24 3 A 1 ATOM 20 C C . ASN A 1 3 ? -4.015 7.062 2.027 1.00 97.85 3 A 1 ATOM 21 O O . ASN A 1 3 ? -3.727 5.938 1.623 1.00 97.56 3 A 1 ATOM 22 C CB . ASN A 1 3 ? -6.363 7.932 1.900 1.00 96.34 3 A 1 ATOM 23 C CG . ASN A 1 3 ? -7.146 6.878 1.157 1.00 94.28 3 A 1 ATOM 24 O OD1 . ASN A 1 3 ? -6.601 5.892 0.691 1.00 91.03 3 A 1 ATOM 25 N ND2 . ASN A 1 3 ? -8.446 7.085 1.034 1.00 88.08 3 A 1 ATOM 26 N N . ILE A 1 4 ? -3.242 8.118 1.832 1.00 97.14 4 A 1 ATOM 27 C CA . ILE A 1 4 ? -1.983 8.022 1.093 1.00 97.57 4 A 1 ATOM 28 C C . ILE A 1 4 ? -0.986 7.154 1.851 1.00 97.94 4 A 1 ATOM 29 O O . ILE A 1 4 ? -0.263 6.350 1.259 1.00 97.72 4 A 1 ATOM 30 C CB . ILE A 1 4 ? -1.388 9.420 0.836 1.00 97.31 4 A 1 ATOM 31 C CG1 . ILE A 1 4 ? -2.354 10.262 -0.009 1.00 95.07 4 A 1 ATOM 32 C CG2 . ILE A 1 4 ? -0.036 9.306 0.132 1.00 93.83 4 A 1 ATOM 33 C CD1 . ILE A 1 4 ? -1.958 11.718 -0.098 1.00 90.44 4 A 1 ATOM 34 N N . PHE A 1 5 ? -0.962 7.316 3.170 1.00 96.76 5 A 1 ATOM 35 C CA . PHE A 1 5 ? -0.054 6.550 4.018 1.00 96.96 5 A 1 ATOM 36 C C . PHE A 1 5 ? -0.395 5.066 3.968 1.00 97.60 5 A 1 ATOM 37 O O . PHE A 1 5 ? 0.496 4.219 3.866 1.00 97.59 5 A 1 ATOM 38 C CB . PHE A 1 5 ? -0.132 7.071 5.454 1.00 96.66 5 A 1 ATOM 39 C CG . PHE A 1 5 ? 1.069 6.708 6.280 1.00 94.89 5 A 1 ATOM 40 C CD1 . PHE A 1 5 ? 2.240 7.445 6.175 1.00 92.33 5 A 1 ATOM 41 C CD2 . PHE A 1 5 ? 1.022 5.639 7.156 1.00 92.92 5 A 1 ATOM 42 C CE1 . PHE A 1 5 ? 3.355 7.117 6.933 1.00 92.05 5 A 1 ATOM 43 C CE2 . PHE A 1 5 ? 2.138 5.300 7.918 1.00 91.52 5 A 1 ATOM 44 C CZ . PHE A 1 5 ? 3.305 6.041 7.806 1.00 91.42 5 A 1 ATOM 45 N N . LEU A 1 6 ? -1.691 4.766 4.034 1.00 97.24 6 A 1 ATOM 46 C CA . LEU A 1 6 ? -2.165 3.386 3.985 1.00 97.34 6 A 1 ATOM 47 C C . LEU A 1 6 ? -1.851 2.762 2.629 1.00 97.83 6 A 1 ATOM 48 O O . LEU A 1 6 ? -1.403 1.623 2.543 1.00 98.01 6 A 1 ATOM 49 C CB . LEU A 1 6 ? -3.674 3.335 4.256 1.00 97.17 6 A 1 ATOM 50 C CG . LEU A 1 6 ? -4.132 2.202 5.172 1.00 93.06 6 A 1 ATOM 51 C CD1 . LEU A 1 6 ? -3.690 0.845 4.662 1.00 91.80 6 A 1 ATOM 52 C CD2 . LEU A 1 6 ? -3.635 2.440 6.589 1.00 91.94 6 A 1 ATOM 53 N N . ALA A 1 7 ? -2.084 3.529 1.572 1.00 97.88 7 A 1 ATOM 54 C CA . ALA A 1 7 ? -1.812 3.062 0.217 1.00 97.95 7 A 1 ATOM 55 C C . ALA A 1 7 ? -0.332 2.736 0.038 1.00 98.21 7 A 1 ATOM 56 O O . ALA A 1 7 ? 0.020 1.754 -0.616 1.00 98.04 7 A 1 ATOM 57 C CB . ALA A 1 7 ? -2.239 4.123 -0.791 1.00 97.68 7 A 1 ATOM 58 N N . ALA A 1 8 ? 0.527 3.545 0.631 1.00 98.06 8 A 1 ATOM 59 C CA . ALA A 1 8 ? 1.966 3.329 0.561 1.00 98.17 8 A 1 ATOM 60 C C . ALA A 1 8 ? 2.357 2.036 1.265 1.00 98.36 8 A 1 ATOM 61 O O . ALA A 1 8 ? 3.248 1.320 0.807 1.00 98.05 8 A 1 ATOM 62 C CB . ALA A 1 8 ? 2.703 4.509 1.185 1.00 97.91 8 A 1 ATOM 63 N N . THR A 1 9 ? 1.681 1.736 2.369 1.00 97.66 9 A 1 ATOM 64 C CA . THR A 1 9 ? 1.941 0.517 3.132 1.00 97.57 9 A 1 ATOM 65 C C . THR A 1 9 ? 1.542 -0.715 2.331 1.00 97.97 9 A 1 ATOM 66 O O . THR A 1 9 ? 2.287 -1.696 2.285 1.00 97.53 9 A 1 ATOM 67 C CB . THR A 1 9 ? 1.180 0.535 4.459 1.00 96.98 9 A 1 ATOM 68 O OG1 . THR A 1 9 ? 1.538 1.701 5.189 1.00 94.27 9 A 1 ATOM 69 C CG2 . THR A 1 9 ? 1.505 -0.685 5.301 1.00 93.51 9 A 1 ATOM 70 N N . LEU A 1 10 ? 0.381 -0.649 1.697 1.00 98.05 10 A 1 ATOM 71 C CA . LEU A 1 10 ? -0.113 -1.759 0.888 1.00 98.01 10 A 1 ATOM 72 C C . LEU A 1 10 ? 0.794 -2.005 -0.310 1.00 98.15 10 A 1 ATOM 73 O O . LEU A 1 10 ? 1.099 -3.149 -0.648 1.00 97.90 10 A 1 ATOM 74 C CB . LEU A 1 10 ? -1.538 -1.467 0.417 1.00 97.90 10 A 1 ATOM 75 C CG . LEU A 1 10 ? -2.578 -1.458 1.537 1.00 97.13 10 A 1 ATOM 76 C CD1 . LEU A 1 10 ? -3.867 -0.818 1.056 1.00 96.04 10 A 1 ATOM 77 C CD2 . LEU A 1 10 ? -2.843 -2.873 2.030 1.00 95.89 10 A 1 ATOM 78 N N . LEU A 1 11 ? 1.217 -0.929 -0.938 1.00 97.98 11 A 1 ATOM 79 C CA . LEU A 1 11 ? 2.101 -1.018 -2.093 1.00 97.80 11 A 1 ATOM 80 C C . LEU A 1 11 ? 3.466 -1.559 -1.685 1.00 97.87 11 A 1 ATOM 81 O O . LEU A 1 11 ? 4.043 -2.400 -2.373 1.00 97.54 11 A 1 ATOM 82 C CB . LEU A 1 11 ? 2.246 0.361 -2.741 1.00 97.44 11 A 1 ATOM 83 C CG . LEU A 1 11 ? 2.747 0.331 -4.180 1.00 95.70 11 A 1 ATOM 84 C CD1 . LEU A 1 11 ? 1.685 -0.254 -5.105 1.00 94.15 11 A 1 ATOM 85 C CD2 . LEU A 1 11 ? 3.117 1.732 -4.630 1.00 94.30 11 A 1 ATOM 86 N N . GLY A 1 12 ? 3.971 -1.087 -0.557 1.00 97.90 12 A 1 ATOM 87 C CA . GLY A 1 12 ? 5.256 -1.549 -0.048 1.00 97.73 12 A 1 ATOM 88 C C . GLY A 1 12 ? 5.218 -2.997 0.387 1.00 98.16 12 A 1 ATOM 89 O O . GLY A 1 12 ? 6.195 -3.727 0.217 1.00 98.01 12 A 1 ATOM 90 N N . ALA A 1 13 ? 4.082 -3.433 0.931 1.00 98.08 13 A 1 ATOM 91 C CA . ALA A 1 13 ? 3.905 -4.810 1.386 1.00 98.05 13 A 1 ATOM 92 C C . ALA A 1 13 ? 4.033 -5.793 0.229 1.00 98.34 13 A 1 ATOM 93 O O . ALA A 1 13 ? 4.488 -6.920 0.419 1.00 97.66 13 A 1 ATOM 94 C CB . ALA A 1 13 ? 2.544 -4.969 2.062 1.00 97.40 13 A 1 ATOM 95 N N . ALA A 1 14 ? 3.651 -5.371 -0.972 1.00 97.97 14 A 1 ATOM 96 C CA . ALA A 1 14 ? 3.750 -6.214 -2.161 1.00 97.99 14 A 1 ATOM 97 C C . ALA A 1 14 ? 5.208 -6.491 -2.529 1.00 98.15 14 A 1 ATOM 98 O O . ALA A 1 14 ? 5.518 -7.511 -3.143 1.00 97.52 14 A 1 ATOM 99 C CB . ALA A 1 14 ? 3.025 -5.554 -3.329 1.00 97.52 14 A 1 ATOM 100 N N . PHE A 1 15 ? 6.083 -5.580 -2.154 1.00 96.81 15 A 1 ATOM 101 C CA . PHE A 1 15 ? 7.510 -5.717 -2.436 1.00 96.18 15 A 1 ATOM 102 C C . PHE A 1 15 ? 8.259 -6.366 -1.275 1.00 96.71 15 A 1 ATOM 103 O O . PHE A 1 15 ? 9.421 -6.752 -1.425 1.00 95.52 15 A 1 ATOM 104 C CB . PHE A 1 15 ? 8.120 -4.348 -2.726 1.00 94.47 15 A 1 ATOM 105 C CG . PHE A 1 15 ? 7.624 -3.732 -4.003 1.00 92.20 15 A 1 ATOM 106 C CD1 . PHE A 1 15 ? 6.452 -3.005 -4.025 1.00 89.41 15 A 1 ATOM 107 C CD2 . PHE A 1 15 ? 8.342 -3.883 -5.177 1.00 89.82 15 A 1 ATOM 108 C CE1 . PHE A 1 15 ? 5.992 -2.437 -5.199 1.00 89.18 15 A 1 ATOM 109 C CE2 . PHE A 1 15 ? 7.892 -3.317 -6.356 1.00 87.69 15 A 1 ATOM 110 C CZ . PHE A 1 15 ? 6.714 -2.594 -6.367 1.00 88.27 15 A 1 ATOM 111 N N . ALA A 1 16 ? 7.589 -6.462 -0.138 1.00 94.85 16 A 1 ATOM 112 C CA . ALA A 1 16 ? 8.197 -7.014 1.071 1.00 93.56 16 A 1 ATOM 113 C C . ALA A 1 16 ? 7.285 -8.057 1.702 1.00 92.43 16 A 1 ATOM 114 O O . ALA A 1 16 ? 7.655 -8.625 2.744 1.00 88.83 16 A 1 ATOM 115 C CB . ALA A 1 16 ? 8.498 -5.893 2.062 1.00 89.92 16 A 1 ATOM 116 O OXT . ALA A 1 16 ? 6.187 -8.315 1.151 1.00 82.45 16 A 1 #