# 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_spkb22042 # _entry.id spkb22042 # 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" "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" "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 LEU 3 1 n ILE 4 1 n ILE 5 1 n LEU 6 1 n VAL 7 1 n ILE 8 1 n SER 9 1 n ILE 10 1 n LEU 11 1 n ILE 12 1 n SER 13 1 n ASN 14 1 n ALA 15 1 n GLY 16 1 n SER 17 # _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 12:49:56)" _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 93.62 _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 88.83 1 1 A ARG 2 2 87.23 1 2 A LEU 3 2 95.04 1 3 A ILE 4 2 96.49 1 4 A ILE 5 2 97.31 1 5 A LEU 6 2 96.10 1 6 A VAL 7 2 97.99 1 7 A ILE 8 2 96.72 1 8 A SER 9 2 95.90 1 9 A ILE 10 2 96.78 1 10 A LEU 11 2 95.69 1 11 A ILE 12 2 96.52 1 12 A SER 13 2 95.12 1 13 A ASN 14 2 94.98 1 14 A ALA 15 2 95.72 1 15 A GLY 16 2 88.76 1 16 A SER 17 2 76.48 1 17 # _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 LEU . 3 A 3 A 4 1 n ILE . 4 A 4 A 5 1 n ILE . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n VAL . 7 A 7 A 8 1 n ILE . 8 A 8 A 9 1 n SER . 9 A 9 A 10 1 n ILE . 10 A 10 A 11 1 n LEU . 11 A 11 A 12 1 n ILE . 12 A 12 A 13 1 n SER . 13 A 13 A 14 1 n ASN . 14 A 14 A 15 1 n ALA . 15 A 15 A 16 1 n GLY . 16 A 16 A 17 1 n SER . 17 A 17 # _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 ? -10.288 -3.457 0.625 1.00 95.50 1 A 1 ATOM 2 C CA . MET A 1 1 ? -9.563 -3.062 -0.597 1.00 96.52 1 A 1 ATOM 3 C C . MET A 1 1 ? -8.051 -3.113 -0.357 1.00 96.82 1 A 1 ATOM 4 O O . MET A 1 1 ? -7.530 -2.385 0.485 1.00 94.48 1 A 1 ATOM 5 C CB . MET A 1 1 ? -9.951 -1.656 -1.018 1.00 92.80 1 A 1 ATOM 6 C CG . MET A 1 1 ? -11.470 -1.443 -1.041 1.00 83.72 1 A 1 ATOM 7 S SD . MET A 1 1 ? -12.325 -2.717 -1.957 1.00 81.02 1 A 1 ATOM 8 C CE . MET A 1 1 ? -14.005 -2.128 -1.850 1.00 69.77 1 A 1 ATOM 9 N N . ARG A 1 2 ? -7.375 -3.969 -1.104 1.00 97.70 2 A 1 ATOM 10 C CA . ARG A 1 2 ? -5.925 -4.107 -0.971 1.00 97.90 2 A 1 ATOM 11 C C . ARG A 1 2 ? -5.187 -2.898 -1.544 1.00 98.21 2 A 1 ATOM 12 O O . ARG A 1 2 ? -4.059 -2.610 -1.151 1.00 97.33 2 A 1 ATOM 13 C CB . ARG A 1 2 ? -5.455 -5.382 -1.669 1.00 96.99 2 A 1 ATOM 14 C CG . ARG A 1 2 ? -5.471 -6.596 -0.763 1.00 89.78 2 A 1 ATOM 15 C CD . ARG A 1 2 ? -6.881 -7.147 -0.595 1.00 87.33 2 A 1 ATOM 16 N NE . ARG A 1 2 ? -7.330 -7.850 -1.799 1.00 79.60 2 A 1 ATOM 17 C CZ . ARG A 1 2 ? -8.497 -8.447 -1.915 1.00 75.93 2 A 1 ATOM 18 N NH1 . ARG A 1 2 ? -9.357 -8.424 -0.917 1.00 68.87 2 A 1 ATOM 19 N NH2 . ARG A 1 2 ? -8.813 -9.069 -3.036 1.00 69.88 2 A 1 ATOM 20 N N . LEU A 1 3 ? -5.836 -2.199 -2.478 1.00 98.13 3 A 1 ATOM 21 C CA . LEU A 1 3 ? -5.228 -1.025 -3.105 1.00 98.45 3 A 1 ATOM 22 C C . LEU A 1 3 ? -4.937 0.062 -2.073 1.00 98.67 3 A 1 ATOM 23 O O . LEU A 1 3 ? -3.875 0.686 -2.098 1.00 98.46 3 A 1 ATOM 24 C CB . LEU A 1 3 ? -6.154 -0.478 -4.193 1.00 98.10 3 A 1 ATOM 25 C CG . LEU A 1 3 ? -5.495 0.558 -5.098 1.00 91.19 3 A 1 ATOM 26 C CD1 . LEU A 1 3 ? -4.425 -0.110 -5.959 1.00 88.98 3 A 1 ATOM 27 C CD2 . LEU A 1 3 ? -6.539 1.217 -5.988 1.00 88.31 3 A 1 ATOM 28 N N . ILE A 1 4 ? -5.889 0.282 -1.166 1.00 98.51 4 A 1 ATOM 29 C CA . ILE A 1 4 ? -5.730 1.295 -0.120 1.00 98.53 4 A 1 ATOM 30 C C . ILE A 1 4 ? -4.587 0.916 0.815 1.00 98.62 4 A 1 ATOM 31 O O . ILE A 1 4 ? -3.798 1.769 1.230 1.00 98.41 4 A 1 ATOM 32 C CB . ILE A 1 4 ? -7.032 1.460 0.681 1.00 98.25 4 A 1 ATOM 33 C CG1 . ILE A 1 4 ? -8.171 1.899 -0.245 1.00 95.47 4 A 1 ATOM 34 C CG2 . ILE A 1 4 ? -6.832 2.482 1.803 1.00 94.89 4 A 1 ATOM 35 C CD1 . ILE A 1 4 ? -9.529 1.844 0.425 1.00 89.27 4 A 1 ATOM 36 N N . ILE A 1 5 ? -4.504 -0.360 1.139 1.00 98.55 5 A 1 ATOM 37 C CA . ILE A 1 5 ? -3.445 -0.861 2.018 1.00 98.55 5 A 1 ATOM 38 C C . ILE A 1 5 ? -2.081 -0.627 1.379 1.00 98.57 5 A 1 ATOM 39 O O . ILE A 1 5 ? -1.111 -0.278 2.058 1.00 98.44 5 A 1 ATOM 40 C CB . ILE A 1 5 ? -3.637 -2.362 2.302 1.00 98.42 5 A 1 ATOM 41 C CG1 . ILE A 1 5 ? -4.983 -2.606 2.984 1.00 97.00 5 A 1 ATOM 42 C CG2 . ILE A 1 5 ? -2.493 -2.884 3.173 1.00 96.78 5 A 1 ATOM 43 C CD1 . ILE A 1 5 ? -5.353 -4.076 3.066 1.00 92.16 5 A 1 ATOM 44 N N . LEU A 1 6 ? -2.022 -0.812 0.074 1.00 98.45 6 A 1 ATOM 45 C CA . LEU A 1 6 ? -0.779 -0.614 -0.667 1.00 98.46 6 A 1 ATOM 46 C C . LEU A 1 6 ? -0.343 0.847 -0.601 1.00 98.59 6 A 1 ATOM 47 O O . LEU A 1 6 ? 0.843 1.143 -0.447 1.00 98.50 6 A 1 ATOM 48 C CB . LEU A 1 6 ? -0.967 -1.035 -2.125 1.00 98.31 6 A 1 ATOM 49 C CG . LEU A 1 6 ? 0.334 -1.153 -2.912 1.00 94.30 6 A 1 ATOM 50 C CD1 . LEU A 1 6 ? 1.129 -2.371 -2.444 1.00 90.74 6 A 1 ATOM 51 C CD2 . LEU A 1 6 ? 0.046 -1.271 -4.401 1.00 91.45 6 A 1 ATOM 52 N N . VAL A 1 7 ? -1.310 1.752 -0.719 1.00 98.46 7 A 1 ATOM 53 C CA . VAL A 1 7 ? -1.028 3.189 -0.665 1.00 98.51 7 A 1 ATOM 54 C C . VAL A 1 7 ? -0.433 3.565 0.688 1.00 98.59 7 A 1 ATOM 55 O O . VAL A 1 7 ? 0.512 4.354 0.768 1.00 98.47 7 A 1 ATOM 56 C CB . VAL A 1 7 ? -2.309 4.007 -0.914 1.00 98.24 7 A 1 ATOM 57 C CG1 . VAL A 1 7 ? -2.039 5.498 -0.766 1.00 96.92 7 A 1 ATOM 58 C CG2 . VAL A 1 7 ? -2.858 3.713 -2.299 1.00 96.76 7 A 1 ATOM 59 N N . ILE A 1 8 ? -0.992 2.996 1.742 1.00 98.30 8 A 1 ATOM 60 C CA . ILE A 1 8 ? -0.509 3.266 3.095 1.00 98.24 8 A 1 ATOM 61 C C . ILE A 1 8 ? 0.936 2.800 3.239 1.00 98.33 8 A 1 ATOM 62 O O . ILE A 1 8 ? 1.765 3.485 3.846 1.00 98.29 8 A 1 ATOM 63 C CB . ILE A 1 8 ? -1.396 2.562 4.135 1.00 98.08 8 A 1 ATOM 64 C CG1 . ILE A 1 8 ? -2.825 3.106 4.075 1.00 96.50 8 A 1 ATOM 65 C CG2 . ILE A 1 8 ? -0.820 2.760 5.541 1.00 96.22 8 A 1 ATOM 66 C CD1 . ILE A 1 8 ? -3.825 2.239 4.822 1.00 89.81 8 A 1 ATOM 67 N N . SER A 1 9 ? 1.231 1.647 2.670 1.00 97.89 9 A 1 ATOM 68 C CA . SER A 1 9 ? 2.579 1.088 2.724 1.00 97.81 9 A 1 ATOM 69 C C . SER A 1 9 ? 3.574 2.008 2.021 1.00 98.04 9 A 1 ATOM 70 O O . SER A 1 9 ? 4.692 2.209 2.494 1.00 97.84 9 A 1 ATOM 71 C CB . SER A 1 9 ? 2.606 -0.296 2.075 1.00 97.31 9 A 1 ATOM 72 O OG . SER A 1 9 ? 3.866 -0.896 2.242 1.00 86.49 9 A 1 ATOM 73 N N . ILE A 1 10 ? 3.148 2.571 0.894 1.00 98.42 10 A 1 ATOM 74 C CA . ILE A 1 10 ? 3.995 3.481 0.125 1.00 98.27 10 A 1 ATOM 75 C C . ILE A 1 10 ? 4.259 4.757 0.918 1.00 98.35 10 A 1 ATOM 76 O O . ILE A 1 10 ? 5.374 5.286 0.913 1.00 98.17 10 A 1 ATOM 77 C CB . ILE A 1 10 ? 3.337 3.826 -1.222 1.00 98.02 10 A 1 ATOM 78 C CG1 . ILE A 1 10 ? 3.207 2.568 -2.082 1.00 96.42 10 A 1 ATOM 79 C CG2 . ILE A 1 10 ? 4.158 4.887 -1.962 1.00 96.02 10 A 1 ATOM 80 C CD1 . ILE A 1 10 ? 2.243 2.727 -3.239 1.00 90.58 10 A 1 ATOM 81 N N . LEU A 1 11 ? 3.224 5.248 1.593 1.00 98.48 11 A 1 ATOM 82 C CA . LEU A 1 11 ? 3.350 6.463 2.394 1.00 98.40 11 A 1 ATOM 83 C C . LEU A 1 11 ? 4.365 6.273 3.513 1.00 98.46 11 A 1 ATOM 84 O O . LEU A 1 11 ? 5.165 7.166 3.794 1.00 98.20 11 A 1 ATOM 85 C CB . LEU A 1 11 ? 1.987 6.830 2.986 1.00 98.10 11 A 1 ATOM 86 C CG . LEU A 1 11 ? 1.046 7.483 1.983 1.00 93.22 11 A 1 ATOM 87 C CD1 . LEU A 1 11 ? -0.395 7.395 2.468 1.00 90.15 11 A 1 ATOM 88 C CD2 . LEU A 1 11 ? 1.434 8.939 1.775 1.00 90.51 11 A 1 ATOM 89 N N . ILE A 1 12 ? 4.331 5.111 4.148 1.00 98.42 12 A 1 ATOM 90 C CA . ILE A 1 12 ? 5.263 4.799 5.225 1.00 98.18 12 A 1 ATOM 91 C C . ILE A 1 12 ? 6.685 4.706 4.686 1.00 98.16 12 A 1 ATOM 92 O O . ILE A 1 12 ? 7.637 5.149 5.335 1.00 97.93 12 A 1 ATOM 93 C CB . ILE A 1 12 ? 4.877 3.479 5.909 1.00 97.80 12 A 1 ATOM 94 C CG1 . ILE A 1 12 ? 3.494 3.592 6.550 1.00 95.80 12 A 1 ATOM 95 C CG2 . ILE A 1 12 ? 5.915 3.107 6.969 1.00 95.61 12 A 1 ATOM 96 C CD1 . ILE A 1 12 ? 2.897 2.245 6.916 1.00 90.24 12 A 1 ATOM 97 N N . SER A 1 13 ? 6.817 4.144 3.493 1.00 98.43 13 A 1 ATOM 98 C CA . SER A 1 13 ? 8.125 3.990 2.863 1.00 98.19 13 A 1 ATOM 99 C C . SER A 1 13 ? 8.741 5.343 2.530 1.00 98.13 13 A 1 ATOM 100 O O . SER A 1 13 ? 9.924 5.573 2.780 1.00 96.70 13 A 1 ATOM 101 C CB . SER A 1 13 ? 8.001 3.152 1.594 1.00 97.23 13 A 1 ATOM 102 O OG . SER A 1 13 ? 7.569 1.845 1.907 1.00 82.03 13 A 1 ATOM 103 N N . ASN A 1 14 ? 7.929 6.247 1.959 1.00 98.41 14 A 1 ATOM 104 C CA . ASN A 1 14 ? 8.416 7.573 1.587 1.00 98.24 14 A 1 ATOM 105 C C . ASN A 1 14 ? 8.602 8.461 2.812 1.00 98.21 14 A 1 ATOM 106 O O . ASN A 1 14 ? 9.378 9.421 2.772 1.00 96.99 14 A 1 ATOM 107 C CB . ASN A 1 14 ? 7.452 8.229 0.595 1.00 97.64 14 A 1 ATOM 108 C CG . ASN A 1 14 ? 6.126 8.586 1.234 1.00 93.95 14 A 1 ATOM 109 O OD1 . ASN A 1 14 ? 6.064 9.339 2.187 1.00 88.99 14 A 1 ATOM 110 N ND2 . ASN A 1 14 ? 5.047 8.064 0.682 1.00 87.44 14 A 1 ATOM 111 N N . ALA A 1 15 ? 7.896 8.147 3.884 1.00 97.70 15 A 1 ATOM 112 C CA . ALA A 1 15 ? 7.992 8.920 5.123 1.00 97.00 15 A 1 ATOM 113 C C . ALA A 1 15 ? 9.406 8.857 5.686 1.00 96.35 15 A 1 ATOM 114 O O . ALA A 1 15 ? 9.902 9.824 6.268 1.00 91.94 15 A 1 ATOM 115 C CB . ALA A 1 15 ? 6.993 8.402 6.151 1.00 95.59 15 A 1 ATOM 116 N N . GLY A 1 16 ? 10.065 7.726 5.495 1.00 94.88 16 A 1 ATOM 117 C CA . GLY A 1 16 ? 11.423 7.548 5.983 1.00 90.56 16 A 1 ATOM 118 C C . GLY A 1 16 ? 11.450 7.246 7.468 1.00 87.42 16 A 1 ATOM 119 O O . GLY A 1 16 ? 10.731 7.859 8.253 1.00 82.17 16 A 1 ATOM 120 N N . SER A 1 17 ? 12.307 6.302 7.842 1.00 89.69 17 A 1 ATOM 121 C CA . SER A 1 17 ? 12.414 5.915 9.241 1.00 84.30 17 A 1 ATOM 122 C C . SER A 1 17 ? 13.727 5.179 9.496 1.00 77.40 17 A 1 ATOM 123 O O . SER A 1 17 ? 14.438 4.856 8.530 1.00 70.01 17 A 1 ATOM 124 C CB . SER A 1 17 ? 11.232 5.040 9.661 1.00 76.88 17 A 1 ATOM 125 O OG . SER A 1 17 ? 11.251 4.825 11.066 1.00 68.25 17 A 1 ATOM 126 O OXT . SER A 1 17 ? 14.053 4.897 10.651 1.00 68.81 17 A 1 #