# 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_spkb42079 # _entry.id spkb42079 # 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" "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" "C6 H15 N2 O2" 147.195 LYS y LYSINE C(CC[NH3+])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 LYS 2 1 n ARG 3 1 n ILE 4 1 n SER 5 1 n LEU 6 1 n ILE 7 1 n ALA 8 1 n LEU 9 1 n VAL 10 1 n THR 11 1 n ILE 12 1 n MET 13 1 n SER 14 1 n GLY 15 # _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 07:43:33)" _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 94.79 _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 90.94 1 1 A LYS 2 2 91.49 1 2 A ARG 3 2 89.06 1 3 A ILE 4 2 96.11 1 4 A SER 5 2 97.02 1 5 A LEU 6 2 96.57 1 6 A ILE 7 2 97.33 1 7 A ALA 8 2 98.33 1 8 A LEU 9 2 97.11 1 9 A VAL 10 2 97.77 1 10 A THR 11 2 97.38 1 11 A ILE 12 2 97.17 1 12 A MET 13 2 93.57 1 13 A SER 14 2 95.25 1 14 A GLY 15 2 90.45 1 15 # _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 LYS . 2 A 2 A 3 1 n ARG . 3 A 3 A 4 1 n ILE . 4 A 4 A 5 1 n SER . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n ILE . 7 A 7 A 8 1 n ALA . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n VAL . 10 A 10 A 11 1 n THR . 11 A 11 A 12 1 n ILE . 12 A 12 A 13 1 n MET . 13 A 13 A 14 1 n SER . 14 A 14 A 15 1 n GLY . 15 A 15 # _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 ? 7.142 6.282 3.735 1.00 95.57 1 A 1 ATOM 2 C CA . MET A 1 1 ? 6.477 5.395 2.767 1.00 96.91 1 A 1 ATOM 3 C C . MET A 1 1 ? 5.937 4.140 3.446 1.00 97.01 1 A 1 ATOM 4 O O . MET A 1 1 ? 5.755 3.111 2.810 1.00 95.18 1 A 1 ATOM 5 C CB . MET A 1 1 ? 7.469 4.974 1.679 1.00 94.57 1 A 1 ATOM 6 C CG . MET A 1 1 ? 8.020 6.157 0.918 1.00 89.22 1 A 1 ATOM 7 S SD . MET A 1 1 ? 9.187 5.645 -0.351 1.00 84.82 1 A 1 ATOM 8 C CE . MET A 1 1 ? 9.732 7.234 -0.932 1.00 74.22 1 A 1 ATOM 9 N N . LYS A 1 2 ? 5.703 4.233 4.731 1.00 96.57 2 A 1 ATOM 10 C CA . LYS A 1 2 ? 5.217 3.072 5.489 1.00 97.15 2 A 1 ATOM 11 C C . LYS A 1 2 ? 3.730 2.831 5.225 1.00 97.52 2 A 1 ATOM 12 O O . LYS A 1 2 ? 3.309 1.706 4.976 1.00 96.63 2 A 1 ATOM 13 C CB . LYS A 1 2 ? 5.457 3.302 6.988 1.00 96.12 2 A 1 ATOM 14 C CG . LYS A 1 2 ? 6.937 3.397 7.332 1.00 90.98 2 A 1 ATOM 15 C CD . LYS A 1 2 ? 7.138 3.695 8.806 1.00 89.32 2 A 1 ATOM 16 C CE . LYS A 1 2 ? 8.614 3.820 9.139 1.00 82.15 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? 8.815 4.190 10.572 1.00 76.96 2 A 1 ATOM 18 N N . ARG A 1 3 ? 2.938 3.891 5.284 1.00 96.72 3 A 1 ATOM 19 C CA . ARG A 1 3 ? 1.492 3.777 5.072 1.00 97.81 3 A 1 ATOM 20 C C . ARG A 1 3 ? 1.172 3.576 3.594 1.00 98.17 3 A 1 ATOM 21 O O . ARG A 1 3 ? 0.297 2.795 3.242 1.00 97.42 3 A 1 ATOM 22 C CB . ARG A 1 3 ? 0.795 5.040 5.579 1.00 97.22 3 A 1 ATOM 23 C CG . ARG A 1 3 ? 1.086 5.320 7.050 1.00 92.65 3 A 1 ATOM 24 C CD . ARG A 1 3 ? 0.489 4.239 7.937 1.00 90.05 3 A 1 ATOM 25 N NE . ARG A 1 3 ? 0.658 4.552 9.357 1.00 83.48 3 A 1 ATOM 26 C CZ . ARG A 1 3 ? 0.307 3.741 10.335 1.00 79.50 3 A 1 ATOM 27 N NH1 . ARG A 1 3 ? -0.211 2.562 10.072 1.00 74.38 3 A 1 ATOM 28 N NH2 . ARG A 1 3 ? 0.481 4.105 11.588 1.00 72.22 3 A 1 ATOM 29 N N . ILE A 1 4 ? 1.874 4.271 2.741 1.00 97.52 4 A 1 ATOM 30 C CA . ILE A 1 4 ? 1.641 4.188 1.299 1.00 97.65 4 A 1 ATOM 31 C C . ILE A 1 4 ? 1.972 2.792 0.777 1.00 97.78 4 A 1 ATOM 32 O O . ILE A 1 4 ? 1.300 2.277 -0.117 1.00 97.23 4 A 1 ATOM 33 C CB . ILE A 1 4 ? 2.480 5.242 0.559 1.00 97.61 4 A 1 ATOM 34 C CG1 . ILE A 1 4 ? 2.125 6.646 1.057 1.00 95.28 4 A 1 ATOM 35 C CG2 . ILE A 1 4 ? 2.225 5.142 -0.947 1.00 94.52 4 A 1 ATOM 36 C CD1 . ILE A 1 4 ? 3.100 7.705 0.561 1.00 91.26 4 A 1 ATOM 37 N N . SER A 1 5 ? 2.995 2.182 1.341 1.00 98.35 5 A 1 ATOM 38 C CA . SER A 1 5 ? 3.415 0.851 0.900 1.00 98.35 5 A 1 ATOM 39 C C . SER A 1 5 ? 2.301 -0.171 1.112 1.00 98.40 5 A 1 ATOM 40 O O . SER A 1 5 ? 2.090 -1.053 0.280 1.00 98.17 5 A 1 ATOM 41 C CB . SER A 1 5 ? 4.659 0.419 1.679 1.00 98.08 5 A 1 ATOM 42 O OG . SER A 1 5 ? 4.360 0.261 3.043 1.00 90.79 5 A 1 ATOM 43 N N . LEU A 1 6 ? 1.589 -0.050 2.205 1.00 98.17 6 A 1 ATOM 44 C CA . LEU A 1 6 ? 0.496 -0.970 2.515 1.00 98.33 6 A 1 ATOM 45 C C . LEU A 1 6 ? -0.647 -0.805 1.519 1.00 98.41 6 A 1 ATOM 46 O O . LEU A 1 6 ? -1.233 -1.787 1.062 1.00 98.23 6 A 1 ATOM 47 C CB . LEU A 1 6 ? -0.006 -0.708 3.933 1.00 98.21 6 A 1 ATOM 48 C CG . LEU A 1 6 ? -1.071 -1.701 4.380 1.00 95.81 6 A 1 ATOM 49 C CD1 . LEU A 1 6 ? -0.470 -3.096 4.520 1.00 92.08 6 A 1 ATOM 50 C CD2 . LEU A 1 6 ? -1.666 -1.266 5.716 1.00 93.30 6 A 1 ATOM 51 N N . ILE A 1 7 ? -0.963 0.426 1.194 1.00 98.39 7 A 1 ATOM 52 C CA . ILE A 1 7 ? -2.045 0.720 0.252 1.00 98.25 7 A 1 ATOM 53 C C . ILE A 1 7 ? -1.690 0.199 -1.136 1.00 98.27 7 A 1 ATOM 54 O O . ILE A 1 7 ? -2.538 -0.352 -1.839 1.00 98.01 7 A 1 ATOM 55 C CB . ILE A 1 7 ? -2.310 2.231 0.196 1.00 98.09 7 A 1 ATOM 56 C CG1 . ILE A 1 7 ? -2.741 2.743 1.574 1.00 96.77 7 A 1 ATOM 57 C CG2 . ILE A 1 7 ? -3.399 2.528 -0.841 1.00 96.58 7 A 1 ATOM 58 C CD1 . ILE A 1 7 ? -2.729 4.263 1.662 1.00 94.31 7 A 1 ATOM 59 N N . ALA A 1 8 ? -0.453 0.369 -1.516 1.00 98.39 8 A 1 ATOM 60 C CA . ALA A 1 8 ? 0.001 -0.087 -2.829 1.00 98.41 8 A 1 ATOM 61 C C . ALA A 1 8 ? -0.067 -1.608 -2.935 1.00 98.46 8 A 1 ATOM 62 O O . ALA A 1 8 ? -0.441 -2.151 -3.971 1.00 98.12 8 A 1 ATOM 63 C CB . ALA A 1 8 ? 1.427 0.391 -3.060 1.00 98.28 8 A 1 ATOM 64 N N . LEU A 1 9 ? 0.291 -2.282 -1.863 1.00 98.29 9 A 1 ATOM 65 C CA . LEU A 1 9 ? 0.282 -3.745 -1.846 1.00 98.13 9 A 1 ATOM 66 C C . LEU A 1 9 ? -1.135 -4.285 -1.989 1.00 98.22 9 A 1 ATOM 67 O O . LEU A 1 9 ? -1.384 -5.185 -2.789 1.00 97.95 9 A 1 ATOM 68 C CB . LEU A 1 9 ? 0.894 -4.241 -0.540 1.00 97.90 9 A 1 ATOM 69 C CG . LEU A 1 9 ? 1.031 -5.760 -0.477 1.00 96.83 9 A 1 ATOM 70 C CD1 . LEU A 1 9 ? 2.072 -6.240 -1.485 1.00 94.49 9 A 1 ATOM 71 C CD2 . LEU A 1 9 ? 1.442 -6.188 0.928 1.00 95.07 9 A 1 ATOM 72 N N . VAL A 1 10 ? -2.047 -3.751 -1.211 1.00 98.51 10 A 1 ATOM 73 C CA . VAL A 1 10 ? -3.438 -4.209 -1.254 1.00 98.47 10 A 1 ATOM 74 C C . VAL A 1 10 ? -4.086 -3.842 -2.582 1.00 98.53 10 A 1 ATOM 75 O O . VAL A 1 10 ? -4.955 -4.564 -3.075 1.00 98.25 10 A 1 ATOM 76 C CB . VAL A 1 10 ? -4.233 -3.604 -0.081 1.00 98.19 10 A 1 ATOM 77 C CG1 . VAL A 1 10 ? -4.358 -2.094 -0.220 1.00 96.22 10 A 1 ATOM 78 C CG2 . VAL A 1 10 ? -5.612 -4.242 -0.004 1.00 96.22 10 A 1 ATOM 79 N N . THR A 1 11 ? -3.677 -2.752 -3.168 1.00 98.55 11 A 1 ATOM 80 C CA . THR A 1 11 ? -4.234 -2.308 -4.447 1.00 98.50 11 A 1 ATOM 81 C C . THR A 1 11 ? -3.848 -3.276 -5.562 1.00 98.53 11 A 1 ATOM 82 O O . THR A 1 11 ? -4.667 -3.617 -6.411 1.00 98.14 11 A 1 ATOM 83 C CB . THR A 1 11 ? -3.724 -0.906 -4.787 1.00 98.22 11 A 1 ATOM 84 O OG1 . THR A 1 11 ? -4.108 0.005 -3.765 1.00 95.32 11 A 1 ATOM 85 C CG2 . THR A 1 11 ? -4.324 -0.428 -6.105 1.00 94.38 11 A 1 ATOM 86 N N . ILE A 1 12 ? -2.615 -3.712 -5.566 1.00 98.47 12 A 1 ATOM 87 C CA . ILE A 1 12 ? -2.130 -4.634 -6.591 1.00 98.34 12 A 1 ATOM 88 C C . ILE A 1 12 ? -2.842 -5.979 -6.478 1.00 98.31 12 A 1 ATOM 89 O O . ILE A 1 12 ? -3.220 -6.583 -7.479 1.00 97.74 12 A 1 ATOM 90 C CB . ILE A 1 12 ? -0.611 -4.827 -6.450 1.00 98.01 12 A 1 ATOM 91 C CG1 . ILE A 1 12 ? 0.108 -3.505 -6.729 1.00 96.35 12 A 1 ATOM 92 C CG2 . ILE A 1 12 ? -0.128 -5.902 -7.424 1.00 96.05 12 A 1 ATOM 93 C CD1 . ILE A 1 12 ? 1.550 -3.513 -6.258 1.00 94.10 12 A 1 ATOM 94 N N . MET A 1 13 ? -3.004 -6.451 -5.259 1.00 98.37 13 A 1 ATOM 95 C CA . MET A 1 13 ? -3.670 -7.735 -5.026 1.00 98.29 13 A 1 ATOM 96 C C . MET A 1 13 ? -5.153 -7.659 -5.375 1.00 98.23 13 A 1 ATOM 97 O O . MET A 1 13 ? -5.730 -8.632 -5.852 1.00 97.37 13 A 1 ATOM 98 C CB . MET A 1 13 ? -3.518 -8.135 -3.557 1.00 97.90 13 A 1 ATOM 99 C CG . MET A 1 13 ? -2.096 -8.530 -3.220 1.00 94.79 13 A 1 ATOM 100 S SD . MET A 1 13 ? -1.947 -9.110 -1.527 1.00 86.61 13 A 1 ATOM 101 C CE . MET A 1 13 ? -0.241 -9.658 -1.546 1.00 76.98 13 A 1 ATOM 102 N N . SER A 1 14 ? -5.745 -6.528 -5.134 1.00 98.11 14 A 1 ATOM 103 C CA . SER A 1 14 ? -7.169 -6.323 -5.409 1.00 97.77 14 A 1 ATOM 104 C C . SER A 1 14 ? -7.437 -6.115 -6.897 1.00 97.57 14 A 1 ATOM 105 O O . SER A 1 14 ? -8.542 -6.378 -7.375 1.00 94.69 14 A 1 ATOM 106 C CB . SER A 1 14 ? -7.668 -5.114 -4.621 1.00 96.36 14 A 1 ATOM 107 O OG . SER A 1 14 ? -9.044 -4.931 -4.831 1.00 87.00 14 A 1 ATOM 108 N N . GLY A 1 15 ? -6.456 -5.643 -7.619 1.00 95.30 15 A 1 ATOM 109 C CA . GLY A 1 15 ? -6.610 -5.376 -9.045 1.00 93.10 15 A 1 ATOM 110 C C . GLY A 1 15 ? -6.830 -6.641 -9.857 1.00 90.52 15 A 1 ATOM 111 O O . GLY A 1 15 ? -6.323 -7.695 -9.478 1.00 83.61 15 A 1 ATOM 112 O OXT . GLY A 1 15 ? -7.508 -6.570 -10.900 1.00 89.71 15 A 1 #