# 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_spkb19046 # _entry.id spkb19046 # 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" "C3 H7 N O2 S" 121.158 CYS y CYSTEINE C([C@@H](C(=O)O)N)S ? "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" "C6 H10 N3 O2" 156.162 HIS y HISTIDINE c1c([nH+]c[nH]1)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" "C3 H7 N O3" 105.093 SER y SERINE C([C@@H](C(=O)O)N)O ? "L-PEPTIDE LINKING" "C11 H12 N2 O2" 204.225 TRP y TRYPTOPHAN c1ccc2c(c1)c(c[nH]2)C[C@@H](C(=O)O)N ? "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 LEU 1 1 n VAL 2 1 n LEU 3 1 n LEU 4 1 n LEU 5 1 n SER 6 1 n LEU 7 1 n ALA 8 1 n GLN 9 1 n LEU 10 1 n TRP 11 1 n SER 12 1 n CYS 13 1 n HIS 14 1 n LEU 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 @ 2025-07-05 16:25:33)" _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 95.82 _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 LEU 1 2 95.57 1 1 A VAL 2 2 97.68 1 2 A LEU 3 2 97.19 1 3 A LEU 4 2 96.50 1 4 A LEU 5 2 97.07 1 5 A SER 6 2 97.75 1 6 A LEU 7 2 96.83 1 7 A ALA 8 2 98.48 1 8 A GLN 9 2 95.33 1 9 A LEU 10 2 97.64 1 10 A TRP 11 2 95.25 1 11 A SER 12 2 97.07 1 12 A CYS 13 2 96.27 1 13 A HIS 14 2 90.65 1 14 A LEU 15 2 92.40 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 LEU . 1 A 1 A 2 1 n VAL . 2 A 2 A 3 1 n LEU . 3 A 3 A 4 1 n LEU . 4 A 4 A 5 1 n LEU . 5 A 5 A 6 1 n SER . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n ALA . 8 A 8 A 9 1 n GLN . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n TRP . 11 A 11 A 12 1 n SER . 12 A 12 A 13 1 n CYS . 13 A 13 A 14 1 n HIS . 14 A 14 A 15 1 n LEU . 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 . LEU A 1 1 ? 8.010 2.163 7.380 1.00 96.76 1 A 1 ATOM 2 C CA . LEU A 1 1 ? 7.906 2.694 6.012 1.00 97.46 1 A 1 ATOM 3 C C . LEU A 1 1 ? 7.349 1.636 5.068 1.00 97.88 1 A 1 ATOM 4 O O . LEU A 1 1 ? 6.578 1.952 4.160 1.00 97.40 1 A 1 ATOM 5 C CB . LEU A 1 1 ? 9.289 3.163 5.538 1.00 96.68 1 A 1 ATOM 6 C CG . LEU A 1 1 ? 9.929 4.209 6.464 1.00 93.84 1 A 1 ATOM 7 C CD1 . LEU A 1 1 ? 11.362 4.470 6.042 1.00 92.55 1 A 1 ATOM 8 C CD2 . LEU A 1 1 ? 9.116 5.504 6.413 1.00 91.98 1 A 1 ATOM 9 N N . VAL A 1 2 ? 7.718 0.413 5.313 1.00 98.47 2 A 1 ATOM 10 C CA . VAL A 1 2 ? 7.233 -0.700 4.486 1.00 98.55 2 A 1 ATOM 11 C C . VAL A 1 2 ? 5.748 -0.959 4.746 1.00 98.66 2 A 1 ATOM 12 O O . VAL A 1 2 ? 4.999 -1.340 3.840 1.00 98.39 2 A 1 ATOM 13 C CB . VAL A 1 2 ? 8.064 -1.968 4.758 1.00 98.16 2 A 1 ATOM 14 C CG1 . VAL A 1 2 ? 7.596 -3.123 3.887 1.00 95.79 2 A 1 ATOM 15 C CG2 . VAL A 1 2 ? 9.538 -1.697 4.511 1.00 95.74 2 A 1 ATOM 16 N N . LEU A 1 3 ? 5.330 -0.730 5.971 1.00 98.29 3 A 1 ATOM 17 C CA . LEU A 1 3 ? 3.931 -0.932 6.354 1.00 98.25 3 A 1 ATOM 18 C C . LEU A 1 3 ? 3.019 0.045 5.618 1.00 98.40 3 A 1 ATOM 19 O O . LEU A 1 3 ? 1.891 -0.299 5.252 1.00 98.25 3 A 1 ATOM 20 C CB . LEU A 1 3 ? 3.786 -0.757 7.870 1.00 98.15 3 A 1 ATOM 21 C CG . LEU A 1 3 ? 4.386 -1.903 8.678 1.00 96.27 3 A 1 ATOM 22 C CD1 . LEU A 1 3 ? 4.808 -1.412 10.053 1.00 94.86 3 A 1 ATOM 23 C CD2 . LEU A 1 3 ? 3.375 -3.031 8.817 1.00 95.06 3 A 1 ATOM 24 N N . LEU A 1 4 ? 3.505 1.237 5.395 1.00 98.15 4 A 1 ATOM 25 C CA . LEU A 1 4 ? 2.741 2.259 4.684 1.00 98.11 4 A 1 ATOM 26 C C . LEU A 1 4 ? 2.546 1.869 3.224 1.00 98.23 4 A 1 ATOM 27 O O . LEU A 1 4 ? 1.509 2.171 2.629 1.00 98.19 4 A 1 ATOM 28 C CB . LEU A 1 4 ? 3.469 3.599 4.785 1.00 97.99 4 A 1 ATOM 29 C CG . LEU A 1 4 ? 3.309 4.281 6.140 1.00 94.44 4 A 1 ATOM 30 C CD1 . LEU A 1 4 ? 4.498 5.176 6.430 1.00 93.38 4 A 1 ATOM 31 C CD2 . LEU A 1 4 ? 2.023 5.097 6.165 1.00 93.50 4 A 1 ATOM 32 N N . LEU A 1 5 ? 3.524 1.197 2.667 1.00 98.30 5 A 1 ATOM 33 C CA . LEU A 1 5 ? 3.460 0.753 1.277 1.00 98.20 5 A 1 ATOM 34 C C . LEU A 1 5 ? 2.400 -0.326 1.102 1.00 98.26 5 A 1 ATOM 35 O O . LEU A 1 5 ? 1.713 -0.364 0.077 1.00 98.20 5 A 1 ATOM 36 C CB . LEU A 1 5 ? 4.832 0.235 0.843 1.00 98.15 5 A 1 ATOM 37 C CG . LEU A 1 5 ? 5.800 1.334 0.412 1.00 95.62 5 A 1 ATOM 38 C CD1 . LEU A 1 5 ? 7.239 0.870 0.571 1.00 94.66 5 A 1 ATOM 39 C CD2 . LEU A 1 5 ? 5.536 1.723 -1.035 1.00 95.15 5 A 1 ATOM 40 N N . SER A 1 6 ? 2.262 -1.175 2.095 1.00 98.45 6 A 1 ATOM 41 C CA . SER A 1 6 ? 1.282 -2.254 2.055 1.00 98.39 6 A 1 ATOM 42 C C . SER A 1 6 ? -0.142 -1.700 2.061 1.00 98.49 6 A 1 ATOM 43 O O . SER A 1 6 ? -1.007 -2.182 1.330 1.00 98.24 6 A 1 ATOM 44 C CB . SER A 1 6 ? 1.498 -3.187 3.243 1.00 98.22 6 A 1 ATOM 45 O OG . SER A 1 6 ? 2.805 -3.725 3.223 1.00 94.74 6 A 1 ATOM 46 N N . LEU A 1 7 ? -0.369 -0.688 2.871 1.00 98.21 7 A 1 ATOM 47 C CA . LEU A 1 7 ? -1.681 -0.058 2.965 1.00 98.10 7 A 1 ATOM 48 C C . LEU A 1 7 ? -2.006 0.736 1.707 1.00 98.15 7 A 1 ATOM 49 O O . LEU A 1 7 ? -3.142 0.706 1.224 1.00 98.03 7 A 1 ATOM 50 C CB . LEU A 1 7 ? -1.718 0.852 4.193 1.00 97.96 7 A 1 ATOM 51 C CG . LEU A 1 7 ? -1.886 0.098 5.508 1.00 95.72 7 A 1 ATOM 52 C CD1 . LEU A 1 7 ? -1.284 0.875 6.658 1.00 94.13 7 A 1 ATOM 53 C CD2 . LEU A 1 7 ? -3.361 -0.169 5.770 1.00 94.36 7 A 1 ATOM 54 N N . ALA A 1 8 ? -1.022 1.438 1.198 1.00 98.55 8 A 1 ATOM 55 C CA . ALA A 1 8 ? -1.201 2.243 -0.006 1.00 98.52 8 A 1 ATOM 56 C C . ALA A 1 8 ? -1.454 1.368 -1.232 1.00 98.55 8 A 1 ATOM 57 O O . ALA A 1 8 ? -2.247 1.722 -2.104 1.00 98.38 8 A 1 ATOM 58 C CB . ALA A 1 8 ? 0.027 3.118 -0.218 1.00 98.42 8 A 1 ATOM 59 N N . GLN A 1 9 ? -0.799 0.237 -1.277 1.00 98.64 9 A 1 ATOM 60 C CA . GLN A 1 9 ? -0.948 -0.692 -2.395 1.00 98.57 9 A 1 ATOM 61 C C . GLN A 1 9 ? -2.340 -1.314 -2.409 1.00 98.62 9 A 1 ATOM 62 O O . GLN A 1 9 ? -2.928 -1.509 -3.476 1.00 98.33 9 A 1 ATOM 63 C CB . GLN A 1 9 ? 0.124 -1.779 -2.311 1.00 98.42 9 A 1 ATOM 64 C CG . GLN A 1 9 ? 1.458 -1.301 -2.860 1.00 95.38 9 A 1 ATOM 65 C CD . GLN A 1 9 ? 2.552 -2.329 -2.674 1.00 92.93 9 A 1 ATOM 66 O OE1 . GLN A 1 9 ? 2.847 -2.741 -1.563 1.00 89.08 9 A 1 ATOM 67 N NE2 . GLN A 1 9 ? 3.172 -2.756 -3.757 1.00 87.99 9 A 1 ATOM 68 N N . LEU A 1 10 ? -2.860 -1.597 -1.232 1.00 98.55 10 A 1 ATOM 69 C CA . LEU A 1 10 ? -4.199 -2.163 -1.108 1.00 98.48 10 A 1 ATOM 70 C C . LEU A 1 10 ? -5.257 -1.164 -1.557 1.00 98.48 10 A 1 ATOM 71 O O . LEU A 1 10 ? -6.268 -1.546 -2.151 1.00 98.22 10 A 1 ATOM 72 C CB . LEU A 1 10 ? -4.445 -2.584 0.342 1.00 98.38 10 A 1 ATOM 73 C CG . LEU A 1 10 ? -4.238 -4.068 0.596 1.00 97.53 10 A 1 ATOM 74 C CD1 . LEU A 1 10 ? -3.999 -4.327 2.067 1.00 95.73 10 A 1 ATOM 75 C CD2 . LEU A 1 10 ? -5.439 -4.862 0.113 1.00 95.76 10 A 1 ATOM 76 N N . TRP A 1 11 ? -5.023 0.102 -1.275 1.00 98.15 11 A 1 ATOM 77 C CA . TRP A 1 11 ? -5.961 1.151 -1.660 1.00 98.00 11 A 1 ATOM 78 C C . TRP A 1 11 ? -6.015 1.299 -3.171 1.00 98.13 11 A 1 ATOM 79 O O . TRP A 1 11 ? -7.087 1.504 -3.736 1.00 97.75 11 A 1 ATOM 80 C CB . TRP A 1 11 ? -5.556 2.470 -0.997 1.00 97.69 11 A 1 ATOM 81 C CG . TRP A 1 11 ? -6.547 2.899 0.035 1.00 96.33 11 A 1 ATOM 82 C CD1 . TRP A 1 11 ? -7.327 4.011 -0.002 1.00 94.07 11 A 1 ATOM 83 C CD2 . TRP A 1 11 ? -6.875 2.219 1.253 1.00 95.21 11 A 1 ATOM 84 N NE1 . TRP A 1 11 ? -8.120 4.067 1.121 1.00 93.52 11 A 1 ATOM 85 C CE2 . TRP A 1 11 ? -7.866 2.979 1.910 1.00 95.09 11 A 1 ATOM 86 C CE3 . TRP A 1 11 ? -6.432 1.045 1.853 1.00 93.79 11 A 1 ATOM 87 C CZ2 . TRP A 1 11 ? -8.406 2.587 3.139 1.00 93.41 11 A 1 ATOM 88 C CZ3 . TRP A 1 11 ? -6.971 0.658 3.077 1.00 90.96 11 A 1 ATOM 89 C CH2 . TRP A 1 11 ? -7.948 1.429 3.705 1.00 91.38 11 A 1 ATOM 90 N N . SER A 1 12 ? -4.888 1.187 -3.815 1.00 98.48 12 A 1 ATOM 91 C CA . SER A 1 12 ? -4.812 1.303 -5.269 1.00 98.39 12 A 1 ATOM 92 C C . SER A 1 12 ? -5.497 0.128 -5.954 1.00 98.32 12 A 1 ATOM 93 O O . SER A 1 12 ? -6.140 0.295 -6.991 1.00 97.58 12 A 1 ATOM 94 C CB . SER A 1 12 ? -3.357 1.385 -5.712 1.00 97.80 12 A 1 ATOM 95 O OG . SER A 1 12 ? -2.764 2.586 -5.279 1.00 91.85 12 A 1 ATOM 96 N N . CYS A 1 13 ? -5.381 -1.043 -5.364 1.00 97.53 13 A 1 ATOM 97 C CA . CYS A 1 13 ? -5.976 -2.256 -5.915 1.00 97.35 13 A 1 ATOM 98 C C . CYS A 1 13 ? -7.473 -2.335 -5.606 1.00 97.60 13 A 1 ATOM 99 O O . CYS A 1 13 ? -8.258 -2.816 -6.421 1.00 96.36 13 A 1 ATOM 100 C CB . CYS A 1 13 ? -5.257 -3.483 -5.356 1.00 96.09 13 A 1 ATOM 101 S SG . CYS A 1 13 ? -5.027 -4.771 -6.583 1.00 92.68 13 A 1 ATOM 102 N N . HIS A 1 14 ? -7.841 -1.872 -4.430 1.00 96.12 14 A 1 ATOM 103 C CA . HIS A 1 14 ? -9.236 -1.890 -4.006 1.00 96.00 14 A 1 ATOM 104 C C . HIS A 1 14 ? -10.073 -0.879 -4.776 1.00 96.35 14 A 1 ATOM 105 O O . HIS A 1 14 ? -11.287 -1.040 -4.900 1.00 95.17 14 A 1 ATOM 106 C CB . HIS A 1 14 ? -9.326 -1.609 -2.503 1.00 94.62 14 A 1 ATOM 107 C CG . HIS A 1 14 ? -9.280 -2.854 -1.680 1.00 91.19 14 A 1 ATOM 108 N ND1 . HIS A 1 14 ? -10.327 -3.281 -0.914 1.00 84.82 14 A 1 ATOM 109 C CD2 . HIS A 1 14 ? -8.296 -3.763 -1.521 1.00 82.55 14 A 1 ATOM 110 C CE1 . HIS A 1 14 ? -9.970 -4.412 -0.314 1.00 84.69 14 A 1 ATOM 111 N NE2 . HIS A 1 14 ? -8.747 -4.730 -0.664 1.00 84.98 14 A 1 ATOM 112 N N . LEU A 1 15 ? -9.436 0.131 -5.277 1.00 95.98 15 A 1 ATOM 113 C CA . LEU A 1 15 ? -10.111 1.178 -6.023 1.00 95.32 15 A 1 ATOM 114 C C . LEU A 1 15 ? -10.525 0.687 -7.415 1.00 94.62 15 A 1 ATOM 115 O O . LEU A 1 15 ? -11.697 0.872 -7.791 1.00 92.95 15 A 1 ATOM 116 C CB . LEU A 1 15 ? -9.188 2.399 -6.121 1.00 94.04 15 A 1 ATOM 117 C CG . LEU A 1 15 ? -9.899 3.690 -6.522 1.00 92.63 15 A 1 ATOM 118 C CD1 . LEU A 1 15 ? -10.869 4.116 -5.428 1.00 90.58 15 A 1 ATOM 119 C CD2 . LEU A 1 15 ? -8.891 4.790 -6.773 1.00 88.05 15 A 1 ATOM 120 O OXT . LEU A 1 15 ? -9.706 0.152 -8.135 1.00 87.40 15 A 1 #