# 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_spkb42623 # _entry.id spkb42623 # 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" "C3 H7 N O2 S" 121.158 CYS y CYSTEINE C([C@@H](C(=O)O)N)S ? "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" "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" "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 ILE 2 1 n ARG 3 1 n ARG 4 1 n THR 5 1 n LEU 6 1 n ILE 7 1 n LEU 8 1 n CYS 9 1 n ALA 10 1 n VAL 11 1 n ALA 12 1 n ALA 13 1 n LEU 14 1 n SER 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 @ 2025-07-07 11:28:37)" _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 95.08 _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 90.60 1 1 A ILE 2 2 94.54 1 2 A ARG 3 2 91.37 1 3 A ARG 4 2 90.63 1 4 A THR 5 2 97.39 1 5 A LEU 6 2 97.34 1 6 A ILE 7 2 96.96 1 7 A LEU 8 2 97.19 1 8 A CYS 9 2 98.04 1 9 A ALA 10 2 98.55 1 10 A VAL 11 2 97.89 1 11 A ALA 12 2 98.59 1 12 A ALA 13 2 98.56 1 13 A LEU 14 2 96.26 1 14 A SER 15 2 95.28 1 15 A GLY 16 2 87.64 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 ILE . 2 A 2 A 3 1 n ARG . 3 A 3 A 4 1 n ARG . 4 A 4 A 5 1 n THR . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n ILE . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n CYS . 9 A 9 A 10 1 n ALA . 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 LEU . 14 A 14 A 15 1 n SER . 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 ? -9.282 3.934 10.240 1.00 95.02 1 A 1 ATOM 2 C CA . MET A 1 1 ? -8.737 4.611 9.037 1.00 96.33 1 A 1 ATOM 3 C C . MET A 1 1 ? -7.794 3.682 8.274 1.00 97.04 1 A 1 ATOM 4 O O . MET A 1 1 ? -7.256 2.740 8.830 1.00 95.20 1 A 1 ATOM 5 C CB . MET A 1 1 ? -7.985 5.873 9.459 1.00 93.65 1 A 1 ATOM 6 C CG . MET A 1 1 ? -7.223 5.671 10.749 1.00 87.88 1 A 1 ATOM 7 S SD . MET A 1 1 ? -6.327 7.140 11.235 1.00 85.35 1 A 1 ATOM 8 C CE . MET A 1 1 ? -7.620 8.085 11.982 1.00 74.33 1 A 1 ATOM 9 N N . ILE A 1 2 ? -7.602 3.960 7.006 1.00 97.14 2 A 1 ATOM 10 C CA . ILE A 1 2 ? -6.743 3.125 6.166 1.00 97.40 2 A 1 ATOM 11 C C . ILE A 1 2 ? -6.018 3.961 5.110 1.00 97.91 2 A 1 ATOM 12 O O . ILE A 1 2 ? -5.986 3.613 3.921 1.00 97.11 2 A 1 ATOM 13 C CB . ILE A 1 2 ? -7.586 2.045 5.498 1.00 96.58 2 A 1 ATOM 14 C CG1 . ILE A 1 2 ? -6.742 1.198 4.569 1.00 92.13 2 A 1 ATOM 15 C CG2 . ILE A 1 2 ? -8.758 2.678 4.751 1.00 91.81 2 A 1 ATOM 16 C CD1 . ILE A 1 2 ? -7.512 0.020 4.011 1.00 86.21 2 A 1 ATOM 17 N N . ARG A 1 3 ? -5.470 5.064 5.519 1.00 98.42 3 A 1 ATOM 18 C CA . ARG A 1 3 ? -4.766 5.944 4.572 1.00 98.52 3 A 1 ATOM 19 C C . ARG A 1 3 ? -3.272 5.631 4.560 1.00 98.64 3 A 1 ATOM 20 O O . ARG A 1 3 ? -2.670 5.440 3.510 1.00 98.25 3 A 1 ATOM 21 C CB . ARG A 1 3 ? -4.989 7.416 4.963 1.00 98.16 3 A 1 ATOM 22 C CG . ARG A 1 3 ? -4.739 8.353 3.810 1.00 94.52 3 A 1 ATOM 23 C CD . ARG A 1 3 ? -6.032 8.809 3.165 1.00 92.39 3 A 1 ATOM 24 N NE . ARG A 1 3 ? -6.966 7.687 3.076 1.00 86.35 3 A 1 ATOM 25 C CZ . ARG A 1 3 ? -7.805 7.378 4.034 1.00 84.48 3 A 1 ATOM 26 N NH1 . ARG A 1 3 ? -7.985 8.151 5.066 1.00 77.26 3 A 1 ATOM 27 N NH2 . ARG A 1 3 ? -8.459 6.251 3.952 1.00 78.11 3 A 1 ATOM 28 N N . ARG A 1 4 ? -2.674 5.587 5.745 1.00 98.32 4 A 1 ATOM 29 C CA . ARG A 1 4 ? -1.235 5.318 5.860 1.00 98.48 4 A 1 ATOM 30 C C . ARG A 1 4 ? -0.901 3.921 5.347 1.00 98.68 4 A 1 ATOM 31 O O . ARG A 1 4 ? 0.097 3.730 4.665 1.00 98.42 4 A 1 ATOM 32 C CB . ARG A 1 4 ? -0.797 5.452 7.313 1.00 98.16 4 A 1 ATOM 33 C CG . ARG A 1 4 ? 0.550 6.113 7.400 1.00 94.39 4 A 1 ATOM 34 C CD . ARG A 1 4 ? 1.118 5.988 8.802 1.00 90.95 4 A 1 ATOM 35 N NE . ARG A 1 4 ? 0.358 6.795 9.760 1.00 85.11 4 A 1 ATOM 36 C CZ . ARG A 1 4 ? 0.595 6.772 11.056 1.00 82.77 4 A 1 ATOM 37 N NH1 . ARG A 1 4 ? 1.534 6.009 11.562 1.00 75.93 4 A 1 ATOM 38 N NH2 . ARG A 1 4 ? -0.132 7.521 11.868 1.00 75.71 4 A 1 ATOM 39 N N . THR A 1 5 ? -1.751 2.963 5.665 1.00 98.61 5 A 1 ATOM 40 C CA . THR A 1 5 ? -1.509 1.584 5.236 1.00 98.63 5 A 1 ATOM 41 C C . THR A 1 5 ? -1.475 1.504 3.709 1.00 98.72 5 A 1 ATOM 42 O O . THR A 1 5 ? -0.695 0.749 3.134 1.00 98.51 5 A 1 ATOM 43 C CB . THR A 1 5 ? -2.598 0.659 5.805 1.00 98.41 5 A 1 ATOM 44 O OG1 . THR A 1 5 ? -2.102 -0.672 5.853 1.00 94.79 5 A 1 ATOM 45 C CG2 . THR A 1 5 ? -3.844 0.693 4.946 1.00 94.04 5 A 1 ATOM 46 N N . LEU A 1 6 ? -2.313 2.303 3.058 1.00 98.60 6 A 1 ATOM 47 C CA . LEU A 1 6 ? -2.359 2.326 1.596 1.00 98.63 6 A 1 ATOM 48 C C . LEU A 1 6 ? -1.065 2.918 1.041 1.00 98.68 6 A 1 ATOM 49 O O . LEU A 1 6 ? -0.531 2.458 0.037 1.00 98.51 6 A 1 ATOM 50 C CB . LEU A 1 6 ? -3.559 3.151 1.127 1.00 98.53 6 A 1 ATOM 51 C CG . LEU A 1 6 ? -4.653 2.297 0.511 1.00 97.11 6 A 1 ATOM 52 C CD1 . LEU A 1 6 ? -4.167 1.641 -0.763 1.00 94.38 6 A 1 ATOM 53 C CD2 . LEU A 1 6 ? -5.116 1.244 1.501 1.00 94.26 6 A 1 ATOM 54 N N . ILE A 1 7 ? -0.579 3.944 1.702 1.00 98.57 7 A 1 ATOM 55 C CA . ILE A 1 7 ? 0.661 4.597 1.274 1.00 98.52 7 A 1 ATOM 56 C C . ILE A 1 7 ? 1.832 3.625 1.382 1.00 98.55 7 A 1 ATOM 57 O O . ILE A 1 7 ? 2.648 3.514 0.466 1.00 98.34 7 A 1 ATOM 58 C CB . ILE A 1 7 ? 0.932 5.830 2.145 1.00 98.39 7 A 1 ATOM 59 C CG1 . ILE A 1 7 ? -0.189 6.850 1.965 1.00 96.62 7 A 1 ATOM 60 C CG2 . ILE A 1 7 ? 2.274 6.456 1.749 1.00 96.67 7 A 1 ATOM 61 C CD1 . ILE A 1 7 ? -0.144 7.940 3.009 1.00 90.02 7 A 1 ATOM 62 N N . LEU A 1 8 ? 1.904 2.928 2.505 1.00 98.65 8 A 1 ATOM 63 C CA . LEU A 1 8 ? 2.985 1.967 2.716 1.00 98.61 8 A 1 ATOM 64 C C . LEU A 1 8 ? 2.874 0.813 1.730 1.00 98.68 8 A 1 ATOM 65 O O . LEU A 1 8 ? 3.874 0.357 1.183 1.00 98.51 8 A 1 ATOM 66 C CB . LEU A 1 8 ? 2.934 1.437 4.146 1.00 98.44 8 A 1 ATOM 67 C CG . LEU A 1 8 ? 3.754 2.289 5.109 1.00 96.66 8 A 1 ATOM 68 C CD1 . LEU A 1 8 ? 2.985 3.540 5.492 1.00 94.08 8 A 1 ATOM 69 C CD2 . LEU A 1 8 ? 4.090 1.478 6.353 1.00 93.86 8 A 1 ATOM 70 N N . CYS A 1 9 ? 1.653 0.359 1.510 1.00 98.66 9 A 1 ATOM 71 C CA . CYS A 1 9 ? 1.418 -0.749 0.588 1.00 98.62 9 A 1 ATOM 72 C C . CYS A 1 9 ? 1.812 -0.353 -0.831 1.00 98.65 9 A 1 ATOM 73 O O . CYS A 1 9 ? 2.425 -1.134 -1.558 1.00 98.36 9 A 1 ATOM 74 C CB . CYS A 1 9 ? -0.057 -1.143 0.629 1.00 98.36 9 A 1 ATOM 75 S SG . CYS A 1 9 ? -0.301 -2.815 0.011 1.00 95.60 9 A 1 ATOM 76 N N . ALA A 1 10 ? 1.447 0.856 -1.220 1.00 98.64 10 A 1 ATOM 77 C CA . ALA A 1 10 ? 1.768 1.348 -2.560 1.00 98.61 10 A 1 ATOM 78 C C . ALA A 1 10 ? 3.280 1.486 -2.734 1.00 98.69 10 A 1 ATOM 79 O O . ALA A 1 10 ? 3.838 1.069 -3.749 1.00 98.43 10 A 1 ATOM 80 C CB . ALA A 1 10 ? 1.095 2.696 -2.791 1.00 98.40 10 A 1 ATOM 81 N N . VAL A 1 11 ? 3.930 2.067 -1.750 1.00 98.65 11 A 1 ATOM 82 C CA . VAL A 1 11 ? 5.383 2.252 -1.811 1.00 98.62 11 A 1 ATOM 83 C C . VAL A 1 11 ? 6.088 0.906 -1.804 1.00 98.68 11 A 1 ATOM 84 O O . VAL A 1 11 ? 7.065 0.702 -2.528 1.00 98.39 11 A 1 ATOM 85 C CB . VAL A 1 11 ? 5.869 3.088 -0.620 1.00 98.28 11 A 1 ATOM 86 C CG1 . VAL A 1 11 ? 7.386 3.197 -0.631 1.00 96.02 11 A 1 ATOM 87 C CG2 . VAL A 1 11 ? 5.247 4.472 -0.679 1.00 96.61 11 A 1 ATOM 88 N N . ALA A 1 12 ? 5.599 -0.005 -0.988 1.00 98.75 12 A 1 ATOM 89 C CA . ALA A 1 12 ? 6.197 -1.337 -0.897 1.00 98.68 12 A 1 ATOM 90 C C . ALA A 1 12 ? 6.077 -2.070 -2.228 1.00 98.73 12 A 1 ATOM 91 O O . ALA A 1 12 ? 7.020 -2.721 -2.671 1.00 98.43 12 A 1 ATOM 92 C CB . ALA A 1 12 ? 5.509 -2.134 0.203 1.00 98.38 12 A 1 ATOM 93 N N . ALA A 1 13 ? 4.923 -1.966 -2.859 1.00 98.74 13 A 1 ATOM 94 C CA . ALA A 1 13 ? 4.691 -2.617 -4.148 1.00 98.68 13 A 1 ATOM 95 C C . ALA A 1 13 ? 5.616 -2.041 -5.214 1.00 98.71 13 A 1 ATOM 96 O O . ALA A 1 13 ? 6.180 -2.775 -6.022 1.00 98.29 13 A 1 ATOM 97 C CB . ALA A 1 13 ? 3.237 -2.431 -4.567 1.00 98.38 13 A 1 ATOM 98 N N . LEU A 1 14 ? 5.754 -0.730 -5.224 1.00 98.49 14 A 1 ATOM 99 C CA . LEU A 1 14 ? 6.617 -0.062 -6.196 1.00 98.36 14 A 1 ATOM 100 C C . LEU A 1 14 ? 8.082 -0.303 -5.871 1.00 98.40 14 A 1 ATOM 101 O O . LEU A 1 14 ? 8.928 -0.358 -6.763 1.00 97.33 14 A 1 ATOM 102 C CB . LEU A 1 14 ? 6.324 1.443 -6.193 1.00 97.94 14 A 1 ATOM 103 C CG . LEU A 1 14 ? 5.305 1.853 -7.249 1.00 96.35 14 A 1 ATOM 104 C CD1 . LEU A 1 14 ? 5.911 1.679 -8.633 1.00 92.13 14 A 1 ATOM 105 C CD2 . LEU A 1 14 ? 4.049 1.016 -7.124 1.00 91.09 14 A 1 ATOM 106 N N . SER A 1 15 ? 8.379 -0.442 -4.595 1.00 98.00 15 A 1 ATOM 107 C CA . SER A 1 15 ? 9.753 -0.685 -4.145 1.00 97.76 15 A 1 ATOM 108 C C . SER A 1 15 ? 10.288 -1.976 -4.750 1.00 97.59 15 A 1 ATOM 109 O O . SER A 1 15 ? 11.464 -2.068 -5.104 1.00 94.32 15 A 1 ATOM 110 C CB . SER A 1 15 ? 9.800 -0.763 -2.621 1.00 96.33 15 A 1 ATOM 111 O OG . SER A 1 15 ? 11.134 -0.795 -2.173 1.00 87.68 15 A 1 ATOM 112 N N . GLY A 1 16 ? 9.413 -2.954 -4.885 1.00 94.30 16 A 1 ATOM 113 C CA . GLY A 1 16 ? 9.802 -4.234 -5.459 1.00 90.84 16 A 1 ATOM 114 C C . GLY A 1 16 ? 10.145 -5.243 -4.380 1.00 88.38 16 A 1 ATOM 115 O O . GLY A 1 16 ? 10.863 -4.900 -3.439 1.00 79.05 16 A 1 ATOM 116 O OXT . GLY A 1 16 ? 9.672 -6.404 -4.474 1.00 85.65 16 A 1 #