# 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_spkb18613 # _entry.id spkb18613 # 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 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" "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" "C9 H11 N O2" 165.189 PHE y PHENYLALANINE c1ccc(cc1)C[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 LYS 2 1 n LEU 3 1 n ILE 4 1 n LEU 5 1 n PHE 6 1 n LEU 7 1 n SER 8 1 n GLY 9 1 n LEU 10 1 n VAL 11 1 n SER 12 1 n LEU 13 1 n VAL 14 1 n LEU 15 1 n CYS 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 @ 2025-07-09 03:18:09)" _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 91.97 _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 85.38 1 1 A LYS 2 2 88.60 1 2 A LEU 3 2 93.51 1 3 A ILE 4 2 94.18 1 4 A LEU 5 2 93.38 1 5 A PHE 6 2 92.60 1 6 A LEU 7 2 93.49 1 7 A SER 8 2 94.23 1 8 A GLY 9 2 96.21 1 9 A LEU 10 2 93.46 1 10 A VAL 11 2 94.91 1 11 A SER 12 2 94.57 1 12 A LEU 13 2 92.73 1 13 A VAL 14 2 93.12 1 14 A LEU 15 2 91.22 1 15 A CYS 16 2 82.84 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 LYS . 2 A 2 A 3 1 n LEU . 3 A 3 A 4 1 n ILE . 4 A 4 A 5 1 n LEU . 5 A 5 A 6 1 n PHE . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n SER . 8 A 8 A 9 1 n GLY . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n VAL . 11 A 11 A 12 1 n SER . 12 A 12 A 13 1 n LEU . 13 A 13 A 14 1 n VAL . 14 A 14 A 15 1 n LEU . 15 A 15 A 16 1 n CYS . 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 ? -2.118 6.958 7.590 1.00 91.77 1 A 1 ATOM 2 C CA . MET A 1 1 ? -1.211 5.933 8.129 1.00 92.36 1 A 1 ATOM 3 C C . MET A 1 1 ? -0.194 5.495 7.076 1.00 92.65 1 A 1 ATOM 4 O O . MET A 1 1 ? -0.547 5.288 5.917 1.00 90.67 1 A 1 ATOM 5 C CB . MET A 1 1 ? -1.999 4.711 8.583 1.00 87.80 1 A 1 ATOM 6 C CG . MET A 1 1 ? -2.873 5.004 9.797 1.00 82.20 1 A 1 ATOM 7 S SD . MET A 1 1 ? -1.910 5.168 11.287 1.00 77.82 1 A 1 ATOM 8 C CE . MET A 1 1 ? -3.205 5.492 12.471 1.00 67.79 1 A 1 ATOM 9 N N . LYS A 1 2 ? 1.064 5.349 7.484 1.00 96.14 2 A 1 ATOM 10 C CA . LYS A 1 2 ? 2.121 4.926 6.568 1.00 95.93 2 A 1 ATOM 11 C C . LYS A 1 2 ? 1.995 3.445 6.232 1.00 96.23 2 A 1 ATOM 12 O O . LYS A 1 2 ? 2.142 3.050 5.078 1.00 95.72 2 A 1 ATOM 13 C CB . LYS A 1 2 ? 3.491 5.189 7.185 1.00 94.45 2 A 1 ATOM 14 C CG . LYS A 1 2 ? 3.943 6.634 7.062 1.00 87.54 2 A 1 ATOM 15 C CD . LYS A 1 2 ? 3.197 7.544 8.025 1.00 83.63 2 A 1 ATOM 16 C CE . LYS A 1 2 ? 3.715 8.962 7.952 1.00 77.46 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? 2.995 9.862 8.867 1.00 70.33 2 A 1 ATOM 18 N N . LEU A 1 3 ? 1.730 2.613 7.238 1.00 96.42 3 A 1 ATOM 19 C CA . LEU A 1 3 ? 1.594 1.171 7.044 1.00 96.87 3 A 1 ATOM 20 C C . LEU A 1 3 ? 0.435 0.847 6.108 1.00 97.16 3 A 1 ATOM 21 O O . LEU A 1 3 ? 0.536 -0.036 5.260 1.00 96.32 3 A 1 ATOM 22 C CB . LEU A 1 3 ? 1.384 0.472 8.389 1.00 96.52 3 A 1 ATOM 23 C CG . LEU A 1 3 ? 2.667 0.229 9.178 1.00 91.72 3 A 1 ATOM 24 C CD1 . LEU A 1 3 ? 3.233 1.546 9.699 1.00 86.57 3 A 1 ATOM 25 C CD2 . LEU A 1 3 ? 2.407 -0.723 10.334 1.00 86.48 3 A 1 ATOM 26 N N . ILE A 1 4 ? -0.679 1.562 6.261 1.00 97.22 4 A 1 ATOM 27 C CA . ILE A 1 4 ? -1.867 1.332 5.444 1.00 96.66 4 A 1 ATOM 28 C C . ILE A 1 4 ? -1.565 1.586 3.972 1.00 96.27 4 A 1 ATOM 29 O O . ILE A 1 4 ? -1.863 0.761 3.108 1.00 95.55 4 A 1 ATOM 30 C CB . ILE A 1 4 ? -3.028 2.232 5.900 1.00 96.61 4 A 1 ATOM 31 C CG1 . ILE A 1 4 ? -3.272 2.081 7.406 1.00 93.74 4 A 1 ATOM 32 C CG2 . ILE A 1 4 ? -4.292 1.876 5.113 1.00 91.60 4 A 1 ATOM 33 C CD1 . ILE A 1 4 ? -3.527 0.646 7.824 1.00 85.77 4 A 1 ATOM 34 N N . LEU A 1 5 ? -0.984 2.744 3.681 1.00 97.25 5 A 1 ATOM 35 C CA . LEU A 1 5 ? -0.657 3.111 2.307 1.00 96.88 5 A 1 ATOM 36 C C . LEU A 1 5 ? 0.443 2.221 1.745 1.00 96.78 5 A 1 ATOM 37 O O . LEU A 1 5 ? 0.406 1.825 0.579 1.00 96.33 5 A 1 ATOM 38 C CB . LEU A 1 5 ? -0.225 4.580 2.246 1.00 96.59 5 A 1 ATOM 39 C CG . LEU A 1 5 ? -1.335 5.543 1.835 1.00 90.49 5 A 1 ATOM 40 C CD1 . LEU A 1 5 ? -1.748 5.267 0.397 1.00 86.18 5 A 1 ATOM 41 C CD2 . LEU A 1 5 ? -2.531 5.399 2.757 1.00 86.57 5 A 1 ATOM 42 N N . PHE A 1 6 ? 1.426 1.913 2.583 1.00 96.23 6 A 1 ATOM 43 C CA . PHE A 1 6 ? 2.538 1.062 2.167 1.00 95.65 6 A 1 ATOM 44 C C . PHE A 1 6 ? 2.046 -0.324 1.755 1.00 95.84 6 A 1 ATOM 45 O O . PHE A 1 6 ? 2.377 -0.816 0.679 1.00 95.01 6 A 1 ATOM 46 C CB . PHE A 1 6 ? 3.542 0.936 3.311 1.00 95.53 6 A 1 ATOM 47 C CG . PHE A 1 6 ? 4.696 0.029 2.967 1.00 93.53 6 A 1 ATOM 48 C CD1 . PHE A 1 6 ? 4.701 -1.288 3.391 1.00 89.26 6 A 1 ATOM 49 C CD2 . PHE A 1 6 ? 5.750 0.499 2.208 1.00 89.99 6 A 1 ATOM 50 C CE1 . PHE A 1 6 ? 5.751 -2.134 3.065 1.00 89.11 6 A 1 ATOM 51 C CE2 . PHE A 1 6 ? 6.806 -0.343 1.875 1.00 89.64 6 A 1 ATOM 52 C CZ . PHE A 1 6 ? 6.808 -1.659 2.305 1.00 88.83 6 A 1 ATOM 53 N N . LEU A 1 7 ? 1.247 -0.952 2.618 1.00 96.82 7 A 1 ATOM 54 C CA . LEU A 1 7 ? 0.721 -2.283 2.338 1.00 96.83 7 A 1 ATOM 55 C C . LEU A 1 7 ? -0.298 -2.244 1.206 1.00 97.07 7 A 1 ATOM 56 O O . LEU A 1 7 ? -0.251 -3.065 0.288 1.00 96.97 7 A 1 ATOM 57 C CB . LEU A 1 7 ? 0.071 -2.857 3.600 1.00 96.60 7 A 1 ATOM 58 C CG . LEU A 1 7 ? 1.035 -3.035 4.773 1.00 89.75 7 A 1 ATOM 59 C CD1 . LEU A 1 7 ? 0.267 -3.461 6.017 1.00 86.18 7 A 1 ATOM 60 C CD2 . LEU A 1 7 ? 2.102 -4.068 4.441 1.00 87.67 7 A 1 ATOM 61 N N . SER A 1 8 ? -1.220 -1.297 1.266 1.00 96.73 8 A 1 ATOM 62 C CA . SER A 1 8 ? -2.262 -1.157 0.254 1.00 96.37 8 A 1 ATOM 63 C C . SER A 1 8 ? -1.664 -0.858 -1.117 1.00 96.58 8 A 1 ATOM 64 O O . SER A 1 8 ? -2.103 -1.398 -2.125 1.00 95.39 8 A 1 ATOM 65 C CB . SER A 1 8 ? -3.230 -0.045 0.645 1.00 95.31 8 A 1 ATOM 66 O OG . SER A 1 8 ? -3.883 -0.352 1.851 1.00 85.00 8 A 1 ATOM 67 N N . GLY A 1 9 ? -0.666 0.010 -1.140 1.00 95.84 9 A 1 ATOM 68 C CA . GLY A 1 9 ? -0.014 0.364 -2.397 1.00 96.14 9 A 1 ATOM 69 C C . GLY A 1 9 ? 0.632 -0.832 -3.066 1.00 96.83 9 A 1 ATOM 70 O O . GLY A 1 9 ? 0.510 -1.022 -4.275 1.00 96.04 9 A 1 ATOM 71 N N . LEU A 1 10 ? 1.318 -1.642 -2.282 1.00 96.42 10 A 1 ATOM 72 C CA . LEU A 1 10 ? 1.993 -2.828 -2.810 1.00 96.50 10 A 1 ATOM 73 C C . LEU A 1 10 ? 0.983 -3.814 -3.381 1.00 96.77 10 A 1 ATOM 74 O O . LEU A 1 10 ? 1.160 -4.327 -4.489 1.00 95.70 10 A 1 ATOM 75 C CB . LEU A 1 10 ? 2.824 -3.481 -1.701 1.00 95.89 10 A 1 ATOM 76 C CG . LEU A 1 10 ? 3.840 -4.494 -2.229 1.00 91.40 10 A 1 ATOM 77 C CD1 . LEU A 1 10 ? 5.041 -4.547 -1.295 1.00 87.04 10 A 1 ATOM 78 C CD2 . LEU A 1 10 ? 3.220 -5.873 -2.330 1.00 87.97 10 A 1 ATOM 79 N N . VAL A 1 11 ? -0.073 -4.096 -2.631 1.00 96.86 11 A 1 ATOM 80 C CA . VAL A 1 11 ? -1.117 -5.023 -3.073 1.00 96.58 11 A 1 ATOM 81 C C . VAL A 1 11 ? -1.855 -4.461 -4.281 1.00 96.66 11 A 1 ATOM 82 O O . VAL A 1 11 ? -2.171 -5.189 -5.224 1.00 95.69 11 A 1 ATOM 83 C CB . VAL A 1 11 ? -2.114 -5.301 -1.941 1.00 95.70 11 A 1 ATOM 84 C CG1 . VAL A 1 11 ? -3.223 -6.225 -2.418 1.00 91.07 11 A 1 ATOM 85 C CG2 . VAL A 1 11 ? -1.397 -5.910 -0.748 1.00 91.78 11 A 1 ATOM 86 N N . SER A 1 12 ? -2.131 -3.170 -4.248 1.00 96.64 12 A 1 ATOM 87 C CA . SER A 1 12 ? -2.841 -2.503 -5.338 1.00 96.79 12 A 1 ATOM 88 C C . SER A 1 12 ? -2.073 -2.626 -6.649 1.00 97.06 12 A 1 ATOM 89 O O . SER A 1 12 ? -2.658 -2.847 -7.704 1.00 95.50 12 A 1 ATOM 90 C CB . SER A 1 12 ? -3.052 -1.032 -5.007 1.00 95.66 12 A 1 ATOM 91 O OG . SER A 1 12 ? -3.825 -0.415 -6.003 1.00 85.78 12 A 1 ATOM 92 N N . LEU A 1 13 ? -0.768 -2.491 -6.574 1.00 96.10 13 A 1 ATOM 93 C CA . LEU A 1 13 ? 0.080 -2.595 -7.761 1.00 96.17 13 A 1 ATOM 94 C C . LEU A 1 13 ? -0.041 -3.972 -8.406 1.00 96.69 13 A 1 ATOM 95 O O . LEU A 1 13 ? -0.006 -4.094 -9.631 1.00 95.15 13 A 1 ATOM 96 C CB . LEU A 1 13 ? 1.537 -2.341 -7.371 1.00 95.38 13 A 1 ATOM 97 C CG . LEU A 1 13 ? 2.501 -2.371 -8.549 1.00 90.46 13 A 1 ATOM 98 C CD1 . LEU A 1 13 ? 2.164 -1.254 -9.531 1.00 85.30 13 A 1 ATOM 99 C CD2 . LEU A 1 13 ? 3.928 -2.209 -8.049 1.00 86.57 13 A 1 ATOM 100 N N . VAL A 1 14 ? -0.171 -5.009 -7.586 1.00 95.47 14 A 1 ATOM 101 C CA . VAL A 1 14 ? -0.286 -6.378 -8.084 1.00 95.46 14 A 1 ATOM 102 C C . VAL A 1 14 ? -1.647 -6.637 -8.712 1.00 95.92 14 A 1 ATOM 103 O O . VAL A 1 14 ? -1.737 -7.223 -9.792 1.00 94.09 14 A 1 ATOM 104 C CB . VAL A 1 14 ? -0.049 -7.391 -6.950 1.00 94.17 14 A 1 ATOM 105 C CG1 . VAL A 1 14 ? -0.171 -8.812 -7.478 1.00 88.51 14 A 1 ATOM 106 C CG2 . VAL A 1 14 ? 1.316 -7.172 -6.331 1.00 88.19 14 A 1 ATOM 107 N N . LEU A 1 15 ? -2.711 -6.238 -8.026 1.00 95.55 15 A 1 ATOM 108 C CA . LEU A 1 15 ? -4.073 -6.469 -8.517 1.00 95.36 15 A 1 ATOM 109 C C . LEU A 1 15 ? -4.436 -5.537 -9.669 1.00 94.96 15 A 1 ATOM 110 O O . LEU A 1 15 ? -5.290 -5.870 -10.494 1.00 92.53 15 A 1 ATOM 111 C CB . LEU A 1 15 ? -5.066 -6.306 -7.359 1.00 94.46 15 A 1 ATOM 112 C CG . LEU A 1 15 ? -5.116 -4.882 -6.791 1.00 90.18 15 A 1 ATOM 113 C CD1 . LEU A 1 15 ? -6.189 -4.057 -7.496 1.00 83.78 15 A 1 ATOM 114 C CD2 . LEU A 1 15 ? -5.402 -4.928 -5.297 1.00 82.95 15 A 1 ATOM 115 N N . CYS A 1 16 ? -3.814 -4.366 -9.731 1.00 92.48 16 A 1 ATOM 116 C CA . CYS A 1 16 ? -4.105 -3.395 -10.788 1.00 88.92 16 A 1 ATOM 117 C C . CYS A 1 16 ? -3.786 -3.968 -12.164 1.00 86.96 16 A 1 ATOM 118 O O . CYS A 1 16 ? -2.624 -4.301 -12.421 1.00 82.47 16 A 1 ATOM 119 C CB . CYS A 1 16 ? -3.317 -2.101 -10.560 1.00 82.80 16 A 1 ATOM 120 S SG . CYS A 1 16 ? -4.137 -0.957 -9.433 1.00 74.82 16 A 1 ATOM 121 O OXT . CYS A 1 16 ? -4.703 -4.100 -13.007 1.00 71.43 16 A 1 #