# 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_spkb24554 # _entry.id spkb24554 # 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" "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" "C4 H9 N O3" 119.119 THR y THREONINE C[C@H]([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" "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 VAL 3 1 n TYR 4 1 n PHE 5 1 n ILE 6 1 n LEU 7 1 n ILE 8 1 n LEU 9 1 n ALA 10 1 n VAL 11 1 n ALA 12 1 n THR 13 1 n VAL 14 1 n SER 15 1 n GLY 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 @ 2025-07-05 05:39:34)" _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 94.24 _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 89.85 1 1 A ARG 2 2 88.78 1 2 A VAL 3 2 96.05 1 3 A TYR 4 2 94.90 1 4 A PHE 5 2 94.28 1 5 A ILE 6 2 96.23 1 6 A LEU 7 2 95.68 1 7 A ILE 8 2 95.79 1 8 A LEU 9 2 95.38 1 9 A ALA 10 2 97.96 1 10 A VAL 11 2 96.93 1 11 A ALA 12 2 97.87 1 12 A THR 13 2 95.49 1 13 A VAL 14 2 95.84 1 14 A SER 15 2 92.83 1 15 A GLY 16 2 85.91 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 VAL . 3 A 3 A 4 1 n TYR . 4 A 4 A 5 1 n PHE . 5 A 5 A 6 1 n ILE . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n ILE . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n ALA . 10 A 10 A 11 1 n VAL . 11 A 11 A 12 1 n ALA . 12 A 12 A 13 1 n THR . 13 A 13 A 14 1 n VAL . 14 A 14 A 15 1 n SER . 15 A 15 A 16 1 n GLY . 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 ? -4.393 8.879 -4.611 1.00 95.40 1 A 1 ATOM 2 C CA . MET A 1 1 ? -3.499 7.821 -4.127 1.00 96.14 1 A 1 ATOM 3 C C . MET A 1 1 ? -3.806 7.474 -2.667 1.00 96.57 1 A 1 ATOM 4 O O . MET A 1 1 ? -3.150 7.955 -1.750 1.00 94.54 1 A 1 ATOM 5 C CB . MET A 1 1 ? -2.043 8.266 -4.249 1.00 93.09 1 A 1 ATOM 6 C CG . MET A 1 1 ? -1.729 9.546 -3.499 1.00 86.53 1 A 1 ATOM 7 S SD . MET A 1 1 ? -0.015 10.072 -3.717 1.00 83.44 1 A 1 ATOM 8 C CE . MET A 1 1 ? -0.146 10.924 -5.270 1.00 73.11 1 A 1 ATOM 9 N N . ARG A 1 2 ? -4.807 6.676 -2.472 1.00 97.06 2 A 1 ATOM 10 C CA . ARG A 1 2 ? -5.206 6.293 -1.123 1.00 97.42 2 A 1 ATOM 11 C C . ARG A 1 2 ? -5.158 4.779 -0.950 1.00 97.86 2 A 1 ATOM 12 O O . ARG A 1 2 ? -4.670 4.271 0.055 1.00 96.91 2 A 1 ATOM 13 C CB . ARG A 1 2 ? -6.621 6.809 -0.846 1.00 96.42 2 A 1 ATOM 14 C CG . ARG A 1 2 ? -6.680 8.312 -0.710 1.00 90.84 2 A 1 ATOM 15 C CD . ARG A 1 2 ? -7.963 8.859 -1.310 1.00 88.16 2 A 1 ATOM 16 N NE . ARG A 1 2 ? -7.855 9.024 -2.762 1.00 82.56 2 A 1 ATOM 17 C CZ . ARG A 1 2 ? -7.275 10.065 -3.350 1.00 80.07 2 A 1 ATOM 18 N NH1 . ARG A 1 2 ? -6.730 11.030 -2.631 1.00 73.87 2 A 1 ATOM 19 N NH2 . ARG A 1 2 ? -7.239 10.121 -4.674 1.00 75.39 2 A 1 ATOM 20 N N . VAL A 1 3 ? -5.659 4.083 -1.938 1.00 97.47 3 A 1 ATOM 21 C CA . VAL A 1 3 ? -5.672 2.625 -1.902 1.00 97.71 3 A 1 ATOM 22 C C . VAL A 1 3 ? -4.252 2.066 -1.896 1.00 98.07 3 A 1 ATOM 23 O O . VAL A 1 3 ? -3.957 1.090 -1.201 1.00 97.49 3 A 1 ATOM 24 C CB . VAL A 1 3 ? -6.443 2.053 -3.101 1.00 96.92 3 A 1 ATOM 25 C CG1 . VAL A 1 3 ? -6.475 0.538 -3.041 1.00 92.30 3 A 1 ATOM 26 C CG2 . VAL A 1 3 ? -7.850 2.616 -3.140 1.00 92.38 3 A 1 ATOM 27 N N . TYR A 1 4 ? -3.405 2.699 -2.667 1.00 98.09 4 A 1 ATOM 28 C CA . TYR A 1 4 ? -2.015 2.258 -2.768 1.00 98.14 4 A 1 ATOM 29 C C . TYR A 1 4 ? -1.299 2.417 -1.433 1.00 98.26 4 A 1 ATOM 30 O O . TYR A 1 4 ? -0.564 1.536 -0.989 1.00 98.05 4 A 1 ATOM 31 C CB . TYR A 1 4 ? -1.285 3.065 -3.843 1.00 97.95 4 A 1 ATOM 32 C CG . TYR A 1 4 ? -1.822 2.802 -5.230 1.00 94.95 4 A 1 ATOM 33 C CD1 . TYR A 1 4 ? -2.919 3.490 -5.711 1.00 92.45 4 A 1 ATOM 34 C CD2 . TYR A 1 4 ? -1.224 1.853 -6.049 1.00 92.83 4 A 1 ATOM 35 C CE1 . TYR A 1 4 ? -3.417 3.241 -6.979 1.00 91.91 4 A 1 ATOM 36 C CE2 . TYR A 1 4 ? -1.712 1.601 -7.322 1.00 92.43 4 A 1 ATOM 37 C CZ . TYR A 1 4 ? -2.809 2.300 -7.779 1.00 92.67 4 A 1 ATOM 38 O OH . TYR A 1 4 ? -3.295 2.056 -9.036 1.00 91.07 4 A 1 ATOM 39 N N . PHE A 1 5 ? -1.529 3.545 -0.803 1.00 97.67 5 A 1 ATOM 40 C CA . PHE A 1 5 ? -0.912 3.819 0.493 1.00 97.79 5 A 1 ATOM 41 C C . PHE A 1 5 ? -1.338 2.777 1.519 1.00 98.03 5 A 1 ATOM 42 O O . PHE A 1 5 ? -0.526 2.265 2.285 1.00 97.57 5 A 1 ATOM 43 C CB . PHE A 1 5 ? -1.306 5.209 0.977 1.00 97.38 5 A 1 ATOM 44 C CG . PHE A 1 5 ? -0.521 5.650 2.181 1.00 95.11 5 A 1 ATOM 45 C CD1 . PHE A 1 5 ? 0.770 6.132 2.044 1.00 91.45 5 A 1 ATOM 46 C CD2 . PHE A 1 5 ? -1.078 5.580 3.447 1.00 91.60 5 A 1 ATOM 47 C CE1 . PHE A 1 5 ? 1.497 6.531 3.152 1.00 90.30 5 A 1 ATOM 48 C CE2 . PHE A 1 5 ? -0.352 5.978 4.562 1.00 90.20 5 A 1 ATOM 49 C CZ . PHE A 1 5 ? 0.937 6.455 4.412 1.00 89.96 5 A 1 ATOM 50 N N . ILE A 1 6 ? -2.623 2.486 1.522 1.00 98.19 6 A 1 ATOM 51 C CA . ILE A 1 6 ? -3.170 1.503 2.449 1.00 98.12 6 A 1 ATOM 52 C C . ILE A 1 6 ? -2.614 0.120 2.143 1.00 98.25 6 A 1 ATOM 53 O O . ILE A 1 6 ? -2.304 -0.657 3.048 1.00 97.88 6 A 1 ATOM 54 C CB . ILE A 1 6 ? -4.705 1.474 2.369 1.00 97.80 6 A 1 ATOM 55 C CG1 . ILE A 1 6 ? -5.282 2.843 2.727 1.00 95.67 6 A 1 ATOM 56 C CG2 . ILE A 1 6 ? -5.267 0.418 3.319 1.00 95.32 6 A 1 ATOM 57 C CD1 . ILE A 1 6 ? -6.751 2.960 2.387 1.00 88.59 6 A 1 ATOM 58 N N . LEU A 1 7 ? -2.510 -0.168 0.876 1.00 98.11 7 A 1 ATOM 59 C CA . LEU A 1 7 ? -1.993 -1.459 0.436 1.00 98.09 7 A 1 ATOM 60 C C . LEU A 1 7 ? -0.559 -1.658 0.908 1.00 98.20 7 A 1 ATOM 61 O O . LEU A 1 7 ? -0.221 -2.692 1.488 1.00 98.04 7 A 1 ATOM 62 C CB . LEU A 1 7 ? -2.047 -1.552 -1.090 1.00 97.87 7 A 1 ATOM 63 C CG . LEU A 1 7 ? -1.975 -2.979 -1.622 1.00 92.83 7 A 1 ATOM 64 C CD1 . LEU A 1 7 ? -3.311 -3.677 -1.438 1.00 90.98 7 A 1 ATOM 65 C CD2 . LEU A 1 7 ? -1.573 -2.990 -3.084 1.00 91.35 7 A 1 ATOM 66 N N . ILE A 1 8 ? 0.256 -0.666 0.655 1.00 97.87 8 A 1 ATOM 67 C CA . ILE A 1 8 ? 1.655 -0.721 1.052 1.00 97.71 8 A 1 ATOM 68 C C . ILE A 1 8 ? 1.777 -0.796 2.563 1.00 97.85 8 A 1 ATOM 69 O O . ILE A 1 8 ? 2.590 -1.552 3.106 1.00 97.51 8 A 1 ATOM 70 C CB . ILE A 1 8 ? 2.416 0.510 0.534 1.00 97.35 8 A 1 ATOM 71 C CG1 . ILE A 1 8 ? 2.328 0.584 -0.995 1.00 94.94 8 A 1 ATOM 72 C CG2 . ILE A 1 8 ? 3.872 0.446 0.982 1.00 94.59 8 A 1 ATOM 73 C CD1 . ILE A 1 8 ? 2.962 -0.607 -1.685 1.00 88.50 8 A 1 ATOM 74 N N . LEU A 1 9 ? 0.975 -0.005 3.230 1.00 97.92 9 A 1 ATOM 75 C CA . LEU A 1 9 ? 0.986 0.024 4.686 1.00 97.65 9 A 1 ATOM 76 C C . LEU A 1 9 ? 0.564 -1.325 5.247 1.00 97.80 9 A 1 ATOM 77 O O . LEU A 1 9 ? 1.160 -1.835 6.193 1.00 97.45 9 A 1 ATOM 78 C CB . LEU A 1 9 ? 0.041 1.111 5.193 1.00 97.18 9 A 1 ATOM 79 C CG . LEU A 1 9 ? 0.394 1.625 6.584 1.00 93.21 9 A 1 ATOM 80 C CD1 . LEU A 1 9 ? 1.605 2.545 6.511 1.00 90.90 9 A 1 ATOM 81 C CD2 . LEU A 1 9 ? -0.788 2.362 7.194 1.00 90.95 9 A 1 ATOM 82 N N . ALA A 1 10 ? -0.474 -1.888 4.664 1.00 98.16 10 A 1 ATOM 83 C CA . ALA A 1 10 ? -0.982 -3.180 5.102 1.00 98.10 10 A 1 ATOM 84 C C . ALA A 1 10 ? 0.067 -4.265 4.909 1.00 98.17 10 A 1 ATOM 85 O O . ALA A 1 10 ? 0.315 -5.064 5.810 1.00 97.58 10 A 1 ATOM 86 C CB . ALA A 1 10 ? -2.244 -3.535 4.333 1.00 97.79 10 A 1 ATOM 87 N N . VAL A 1 11 ? 0.678 -4.282 3.751 1.00 98.19 11 A 1 ATOM 88 C CA . VAL A 1 11 ? 1.707 -5.266 3.447 1.00 98.02 11 A 1 ATOM 89 C C . VAL A 1 11 ? 2.897 -5.093 4.372 1.00 98.02 11 A 1 ATOM 90 O O . VAL A 1 11 ? 3.471 -6.070 4.859 1.00 97.12 11 A 1 ATOM 91 C CB . VAL A 1 11 ? 2.170 -5.147 1.991 1.00 97.43 11 A 1 ATOM 92 C CG1 . VAL A 1 11 ? 3.286 -6.134 1.708 1.00 94.41 11 A 1 ATOM 93 C CG2 . VAL A 1 11 ? 1.004 -5.385 1.056 1.00 95.34 11 A 1 ATOM 94 N N . ALA A 1 12 ? 3.258 -3.856 4.603 1.00 98.23 12 A 1 ATOM 95 C CA . ALA A 1 12 ? 4.380 -3.548 5.478 1.00 98.11 12 A 1 ATOM 96 C C . ALA A 1 12 ? 4.087 -3.990 6.900 1.00 98.17 12 A 1 ATOM 97 O O . ALA A 1 12 ? 4.967 -4.473 7.608 1.00 97.29 12 A 1 ATOM 98 C CB . ALA A 1 12 ? 4.670 -2.055 5.458 1.00 97.56 12 A 1 ATOM 99 N N . THR A 1 13 ? 2.851 -3.814 7.313 1.00 98.06 13 A 1 ATOM 100 C CA . THR A 1 13 ? 2.436 -4.200 8.655 1.00 97.81 13 A 1 ATOM 101 C C . THR A 1 13 ? 2.446 -5.713 8.806 1.00 97.71 13 A 1 ATOM 102 O O . THR A 1 13 ? 2.891 -6.245 9.824 1.00 96.07 13 A 1 ATOM 103 C CB . THR A 1 13 ? 1.032 -3.675 8.962 1.00 96.89 13 A 1 ATOM 104 O OG1 . THR A 1 13 ? 0.991 -2.266 8.738 1.00 91.37 13 A 1 ATOM 105 C CG2 . THR A 1 13 ? 0.659 -3.955 10.403 1.00 90.52 13 A 1 ATOM 106 N N . VAL A 1 14 ? 1.931 -6.396 7.799 1.00 97.99 14 A 1 ATOM 107 C CA . VAL A 1 14 ? 1.898 -7.852 7.812 1.00 97.63 14 A 1 ATOM 108 C C . VAL A 1 14 ? 3.310 -8.416 7.802 1.00 97.52 14 A 1 ATOM 109 O O . VAL A 1 14 ? 3.612 -9.388 8.505 1.00 95.63 14 A 1 ATOM 110 C CB . VAL A 1 14 ? 1.118 -8.397 6.609 1.00 96.57 14 A 1 ATOM 111 C CG1 . VAL A 1 14 ? 1.169 -9.913 6.591 1.00 92.06 14 A 1 ATOM 112 C CG2 . VAL A 1 14 ? -0.316 -7.924 6.653 1.00 93.47 14 A 1 ATOM 113 N N . SER A 1 15 ? 4.157 -7.800 7.019 1.00 96.76 15 A 1 ATOM 114 C CA . SER A 1 15 ? 5.548 -8.214 6.919 1.00 96.16 15 A 1 ATOM 115 C C . SER A 1 15 ? 6.348 -7.677 8.096 1.00 95.62 15 A 1 ATOM 116 O O . SER A 1 15 ? 5.960 -6.697 8.722 1.00 90.41 15 A 1 ATOM 117 C CB . SER A 1 15 ? 6.154 -7.721 5.612 1.00 93.89 15 A 1 ATOM 118 O OG . SER A 1 15 ? 5.417 -8.232 4.519 1.00 84.14 15 A 1 ATOM 119 N N . GLY A 1 16 ? 7.440 -8.326 8.391 1.00 92.67 16 A 1 ATOM 120 C CA . GLY A 1 16 ? 8.272 -7.868 9.501 1.00 88.69 16 A 1 ATOM 121 C C . GLY A 1 16 ? 9.129 -6.697 9.091 1.00 85.97 16 A 1 ATOM 122 O O . GLY A 1 16 ? 9.330 -5.797 9.926 1.00 78.77 16 A 1 ATOM 123 O OXT . GLY A 1 16 ? 9.588 -6.650 7.963 1.00 83.47 16 A 1 #