# 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_spkb18478 # _entry.id spkb18478 # 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" "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" "C9 H11 N O3" 181.189 TYR y TYROSINE c1cc(ccc1C[C@@H](C(=O)O)N)O ? "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 TYR 3 1 n ALA 4 1 n LEU 5 1 n ALA 6 1 n ALA 7 1 n CYS 8 1 n LEU 9 1 n LEU 10 1 n LEU 11 1 n LEU 12 1 n ALA 13 1 n ALA 14 1 n SER 15 1 n SER 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 05:09:06)" _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 94.07 _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 89.66 1 1 A ARG 2 2 86.02 1 2 A TYR 3 2 93.43 1 3 A ALA 4 2 97.49 1 4 A LEU 5 2 94.76 1 5 A ALA 6 2 98.28 1 6 A ALA 7 2 98.27 1 7 A CYS 8 2 96.59 1 8 A LEU 9 2 96.28 1 9 A LEU 10 2 96.66 1 10 A LEU 11 2 96.01 1 11 A LEU 12 2 95.05 1 12 A ALA 13 2 97.71 1 13 A ALA 14 2 96.63 1 14 A SER 15 2 94.11 1 15 A SER 16 2 88.17 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 ARG . 2 A 2 A 3 1 n TYR . 3 A 3 A 4 1 n ALA . 4 A 4 A 5 1 n LEU . 5 A 5 A 6 1 n ALA . 6 A 6 A 7 1 n ALA . 7 A 7 A 8 1 n CYS . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n LEU . 11 A 11 A 12 1 n LEU . 12 A 12 A 13 1 n ALA . 13 A 13 A 14 1 n ALA . 14 A 14 A 15 1 n SER . 15 A 15 A 16 1 n SER . 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 ? -3.049 -12.302 -0.416 1.00 95.02 1 A 1 ATOM 2 C CA . MET A 1 1 ? -3.251 -11.030 -1.128 1.00 95.11 1 A 1 ATOM 3 C C . MET A 1 1 ? -2.517 -9.910 -0.395 1.00 95.43 1 A 1 ATOM 4 O O . MET A 1 1 ? -3.094 -9.221 0.438 1.00 93.60 1 A 1 ATOM 5 C CB . MET A 1 1 ? -4.736 -10.694 -1.206 1.00 93.00 1 A 1 ATOM 6 C CG . MET A 1 1 ? -5.557 -11.797 -1.857 1.00 89.34 1 A 1 ATOM 7 S SD . MET A 1 1 ? -7.316 -11.429 -1.799 1.00 83.66 1 A 1 ATOM 8 C CE . MET A 1 1 ? -7.992 -13.031 -2.179 1.00 72.11 1 A 1 ATOM 9 N N . ARG A 1 2 ? -1.235 -9.760 -0.696 1.00 94.14 2 A 1 ATOM 10 C CA . ARG A 1 2 ? -0.395 -8.763 -0.040 1.00 96.02 2 A 1 ATOM 11 C C . ARG A 1 2 ? -0.342 -7.466 -0.843 1.00 97.00 2 A 1 ATOM 12 O O . ARG A 1 2 ? 0.253 -6.486 -0.409 1.00 96.11 2 A 1 ATOM 13 C CB . ARG A 1 2 ? 1.006 -9.347 0.153 1.00 94.42 2 A 1 ATOM 14 C CG . ARG A 1 2 ? 1.743 -8.758 1.331 1.00 87.58 2 A 1 ATOM 15 C CD . ARG A 1 2 ? 3.065 -9.478 1.524 1.00 85.87 2 A 1 ATOM 16 N NE . ARG A 1 2 ? 3.812 -8.935 2.660 1.00 79.56 2 A 1 ATOM 17 C CZ . ARG A 1 2 ? 4.984 -9.406 3.065 1.00 76.57 2 A 1 ATOM 18 N NH1 . ARG A 1 2 ? 5.557 -10.420 2.443 1.00 68.26 2 A 1 ATOM 19 N NH2 . ARG A 1 2 ? 5.588 -8.852 4.098 1.00 70.66 2 A 1 ATOM 20 N N . TYR A 1 3 ? -0.966 -7.480 -2.003 1.00 97.00 3 A 1 ATOM 21 C CA . TYR A 1 3 ? -0.934 -6.337 -2.910 1.00 97.32 3 A 1 ATOM 22 C C . TYR A 1 3 ? -1.898 -5.236 -2.471 1.00 97.81 3 A 1 ATOM 23 O O . TYR A 1 3 ? -1.697 -4.065 -2.798 1.00 97.37 3 A 1 ATOM 24 C CB . TYR A 1 3 ? -1.262 -6.804 -4.330 1.00 96.68 3 A 1 ATOM 25 C CG . TYR A 1 3 ? -0.415 -7.977 -4.771 1.00 93.23 3 A 1 ATOM 26 C CD1 . TYR A 1 3 ? 0.935 -7.805 -5.060 1.00 91.21 3 A 1 ATOM 27 C CD2 . TYR A 1 3 ? -0.966 -9.242 -4.889 1.00 90.64 3 A 1 ATOM 28 C CE1 . TYR A 1 3 ? 1.717 -8.878 -5.460 1.00 90.66 3 A 1 ATOM 29 C CE2 . TYR A 1 3 ? -0.190 -10.324 -5.290 1.00 89.80 3 A 1 ATOM 30 C CZ . TYR A 1 3 ? 1.151 -10.131 -5.574 1.00 90.36 3 A 1 ATOM 31 O OH . TYR A 1 3 ? 1.918 -11.198 -5.968 1.00 89.08 3 A 1 ATOM 32 N N . ALA A 1 4 ? -2.921 -5.608 -1.726 1.00 97.34 4 A 1 ATOM 33 C CA . ALA A 1 4 ? -3.891 -4.638 -1.225 1.00 97.69 4 A 1 ATOM 34 C C . ALA A 1 4 ? -3.226 -3.653 -0.268 1.00 98.07 4 A 1 ATOM 35 O O . ALA A 1 4 ? -3.506 -2.454 -0.302 1.00 97.36 4 A 1 ATOM 36 C CB . ALA A 1 4 ? -5.036 -5.373 -0.541 1.00 97.01 4 A 1 ATOM 37 N N . LEU A 1 5 ? -2.330 -4.165 0.565 1.00 97.70 5 A 1 ATOM 38 C CA . LEU A 1 5 ? -1.584 -3.345 1.511 1.00 97.77 5 A 1 ATOM 39 C C . LEU A 1 5 ? -0.656 -2.397 0.761 1.00 98.09 5 A 1 ATOM 40 O O . LEU A 1 5 ? -0.569 -1.212 1.090 1.00 97.73 5 A 1 ATOM 41 C CB . LEU A 1 5 ? -0.792 -4.253 2.466 1.00 97.35 5 A 1 ATOM 42 C CG . LEU A 1 5 ? -0.227 -3.587 3.717 1.00 92.21 5 A 1 ATOM 43 C CD1 . LEU A 1 5 ? 1.048 -2.831 3.430 1.00 88.51 5 A 1 ATOM 44 C CD2 . LEU A 1 5 ? -1.263 -2.689 4.370 1.00 88.72 5 A 1 ATOM 45 N N . ALA A 1 6 ? 0.025 -2.916 -0.247 1.00 98.40 6 A 1 ATOM 46 C CA . ALA A 1 6 ? 0.931 -2.113 -1.063 1.00 98.36 6 A 1 ATOM 47 C C . ALA A 1 6 ? 0.178 -0.996 -1.784 1.00 98.51 6 A 1 ATOM 48 O O . ALA A 1 6 ? 0.664 0.135 -1.869 1.00 98.18 6 A 1 ATOM 49 C CB . ALA A 1 6 ? 1.640 -3.011 -2.072 1.00 97.94 6 A 1 ATOM 50 N N . ALA A 1 7 ? -1.004 -1.310 -2.283 1.00 98.29 7 A 1 ATOM 51 C CA . ALA A 1 7 ? -1.838 -0.328 -2.970 1.00 98.33 7 A 1 ATOM 52 C C . ALA A 1 7 ? -2.270 0.777 -2.011 1.00 98.54 7 A 1 ATOM 53 O O . ALA A 1 7 ? -2.270 1.954 -2.369 1.00 98.23 7 A 1 ATOM 54 C CB . ALA A 1 7 ? -3.055 -1.016 -3.574 1.00 97.94 7 A 1 ATOM 55 N N . CYS A 1 8 ? -2.616 0.392 -0.802 1.00 98.14 8 A 1 ATOM 56 C CA . CYS A 1 8 ? -3.018 1.349 0.224 1.00 98.23 8 A 1 ATOM 57 C C . CYS A 1 8 ? -1.860 2.279 0.576 1.00 98.45 8 A 1 ATOM 58 O O . CYS A 1 8 ? -2.051 3.482 0.756 1.00 98.07 8 A 1 ATOM 59 C CB . CYS A 1 8 ? -3.500 0.597 1.465 1.00 97.81 8 A 1 ATOM 60 S SG . CYS A 1 8 ? -4.377 1.676 2.614 1.00 88.82 8 A 1 ATOM 61 N N . LEU A 1 9 ? -0.666 1.715 0.661 1.00 98.01 9 A 1 ATOM 62 C CA . LEU A 1 9 ? 0.542 2.481 0.952 1.00 98.00 9 A 1 ATOM 63 C C . LEU A 1 9 ? 0.828 3.490 -0.153 1.00 98.39 9 A 1 ATOM 64 O O . LEU A 1 9 ? 1.195 4.637 0.123 1.00 98.27 9 A 1 ATOM 65 C CB . LEU A 1 9 ? 1.729 1.530 1.114 1.00 97.75 9 A 1 ATOM 66 C CG . LEU A 1 9 ? 2.868 2.122 1.936 1.00 95.02 9 A 1 ATOM 67 C CD1 . LEU A 1 9 ? 2.662 1.834 3.417 1.00 92.43 9 A 1 ATOM 68 C CD2 . LEU A 1 9 ? 4.199 1.563 1.474 1.00 92.39 9 A 1 ATOM 69 N N . LEU A 1 10 ? 0.643 3.062 -1.393 1.00 98.46 10 A 1 ATOM 70 C CA . LEU A 1 10 ? 0.864 3.928 -2.546 1.00 98.41 10 A 1 ATOM 71 C C . LEU A 1 10 ? -0.121 5.087 -2.547 1.00 98.61 10 A 1 ATOM 72 O O . LEU A 1 10 ? 0.255 6.231 -2.826 1.00 98.39 10 A 1 ATOM 73 C CB . LEU A 1 10 ? 0.730 3.117 -3.836 1.00 98.14 10 A 1 ATOM 74 C CG . LEU A 1 10 ? 1.959 2.279 -4.168 1.00 94.92 10 A 1 ATOM 75 C CD1 . LEU A 1 10 ? 1.613 1.205 -5.186 1.00 93.04 10 A 1 ATOM 76 C CD2 . LEU A 1 10 ? 3.079 3.160 -4.701 1.00 93.30 10 A 1 ATOM 77 N N . LEU A 1 11 ? -1.367 4.792 -2.224 1.00 98.43 11 A 1 ATOM 78 C CA . LEU A 1 11 ? -2.400 5.819 -2.155 1.00 98.31 11 A 1 ATOM 79 C C . LEU A 1 11 ? -2.092 6.810 -1.041 1.00 98.50 11 A 1 ATOM 80 O O . LEU A 1 11 ? -2.286 8.019 -1.204 1.00 98.17 11 A 1 ATOM 81 C CB . LEU A 1 11 ? -3.765 5.169 -1.931 1.00 97.98 11 A 1 ATOM 82 C CG . LEU A 1 11 ? -4.326 4.444 -3.153 1.00 93.78 11 A 1 ATOM 83 C CD1 . LEU A 1 11 ? -5.488 3.545 -2.752 1.00 91.54 11 A 1 ATOM 84 C CD2 . LEU A 1 11 ? -4.786 5.447 -4.205 1.00 91.37 11 A 1 ATOM 85 N N . LEU A 1 12 ? -1.596 6.308 0.072 1.00 98.38 12 A 1 ATOM 86 C CA . LEU A 1 12 ? -1.211 7.150 1.195 1.00 98.09 12 A 1 ATOM 87 C C . LEU A 1 12 ? -0.054 8.058 0.807 1.00 98.21 12 A 1 ATOM 88 O O . LEU A 1 12 ? -0.043 9.243 1.151 1.00 97.70 12 A 1 ATOM 89 C CB . LEU A 1 12 ? -0.819 6.276 2.383 1.00 97.61 12 A 1 ATOM 90 C CG . LEU A 1 12 ? -0.729 7.037 3.700 1.00 92.70 12 A 1 ATOM 91 C CD1 . LEU A 1 12 ? -2.120 7.289 4.271 1.00 89.14 12 A 1 ATOM 92 C CD2 . LEU A 1 12 ? 0.118 6.270 4.692 1.00 88.56 12 A 1 ATOM 93 N N . ALA A 1 13 ? 0.907 7.514 0.085 1.00 98.36 13 A 1 ATOM 94 C CA . ALA A 1 13 ? 2.058 8.278 -0.383 1.00 98.05 13 A 1 ATOM 95 C C . ALA A 1 13 ? 1.630 9.377 -1.350 1.00 98.04 13 A 1 ATOM 96 O O . ALA A 1 13 ? 2.198 10.468 -1.348 1.00 96.72 13 A 1 ATOM 97 C CB . ALA A 1 13 ? 3.063 7.348 -1.057 1.00 97.36 13 A 1 ATOM 98 N N . ALA A 1 14 ? 0.622 9.093 -2.160 1.00 97.99 14 A 1 ATOM 99 C CA . ALA A 1 14 ? 0.091 10.072 -3.106 1.00 97.34 14 A 1 ATOM 100 C C . ALA A 1 14 ? -0.641 11.196 -2.381 1.00 97.13 14 A 1 ATOM 101 O O . ALA A 1 14 ? -0.670 12.332 -2.851 1.00 94.40 14 A 1 ATOM 102 C CB . ALA A 1 14 ? -0.841 9.385 -4.099 1.00 96.28 14 A 1 ATOM 103 N N . SER A 1 15 ? -1.226 10.867 -1.247 1.00 97.19 15 A 1 ATOM 104 C CA . SER A 1 15 ? -1.951 11.842 -0.437 1.00 96.53 15 A 1 ATOM 105 C C . SER A 1 15 ? -1.009 12.662 0.441 1.00 95.64 15 A 1 ATOM 106 O O . SER A 1 15 ? -1.349 13.770 0.862 1.00 92.63 15 A 1 ATOM 107 C CB . SER A 1 15 ? -2.987 11.132 0.433 1.00 95.01 15 A 1 ATOM 108 O OG . SER A 1 15 ? -3.862 12.066 1.029 1.00 87.64 15 A 1 ATOM 109 N N . SER A 1 16 ? 0.151 12.103 0.711 1.00 95.35 16 A 1 ATOM 110 C CA . SER A 1 16 ? 1.153 12.745 1.559 1.00 93.00 16 A 1 ATOM 111 C C . SER A 1 16 ? 2.230 13.406 0.713 1.00 89.81 16 A 1 ATOM 112 O O . SER A 1 16 ? 2.911 14.318 1.216 1.00 84.59 16 A 1 ATOM 113 C CB . SER A 1 16 ? 1.770 11.733 2.522 1.00 88.93 16 A 1 ATOM 114 O OG . SER A 1 16 ? 2.633 12.391 3.431 1.00 82.47 16 A 1 ATOM 115 O OXT . SER A 1 16 ? 2.407 12.977 -0.451 1.00 83.01 16 A 1 #