# 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_spkb23315 # _entry.id spkb23315 # 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" "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" "C5 H9 N O2" 115.130 PRO y PROLINE C1C[C@H](NC1)C(=O)O ? "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 VAL 2 1 n LEU 3 1 n LEU 4 1 n ARG 5 1 n LEU 6 1 n LEU 7 1 n VAL 8 1 n PHE 9 1 n LEU 10 1 n PHE 11 1 n ALA 12 1 n PRO 13 1 n VAL 14 1 n VAL 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 @ 2025-07-03 16:56:27)" _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 92.43 _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 84.01 1 1 A VAL 2 2 94.62 1 2 A LEU 3 2 95.21 1 3 A LEU 4 2 94.84 1 4 A ARG 5 2 88.87 1 5 A LEU 6 2 94.43 1 6 A LEU 7 2 94.09 1 7 A VAL 8 2 96.16 1 8 A PHE 9 2 94.12 1 9 A LEU 10 2 95.66 1 10 A PHE 11 2 93.47 1 11 A ALA 12 2 96.49 1 12 A PRO 13 2 95.63 1 13 A VAL 14 2 92.16 1 14 A VAL 15 2 88.54 1 15 A SER 16 2 81.72 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 VAL . 2 A 2 A 3 1 n LEU . 3 A 3 A 4 1 n LEU . 4 A 4 A 5 1 n ARG . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n VAL . 8 A 8 A 9 1 n PHE . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n PHE . 11 A 11 A 12 1 n ALA . 12 A 12 A 13 1 n PRO . 13 A 13 A 14 1 n VAL . 14 A 14 A 15 1 n VAL . 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 ? -0.276 8.246 7.775 1.00 91.11 1 A 1 ATOM 2 C CA . MET A 1 1 ? 0.846 7.553 8.421 1.00 92.28 1 A 1 ATOM 3 C C . MET A 1 1 ? 0.645 6.044 8.298 1.00 93.29 1 A 1 ATOM 4 O O . MET A 1 1 ? 1.018 5.454 7.288 1.00 90.11 1 A 1 ATOM 5 C CB . MET A 1 1 ? 0.961 7.980 9.876 1.00 85.88 1 A 1 ATOM 6 C CG . MET A 1 1 ? 1.294 9.468 10.038 1.00 78.26 1 A 1 ATOM 7 S SD . MET A 1 1 ? -0.083 10.365 10.744 1.00 74.86 1 A 1 ATOM 8 C CE . MET A 1 1 ? 0.666 11.983 10.997 1.00 66.31 1 A 1 ATOM 9 N N . VAL A 1 2 ? 0.056 5.434 9.326 1.00 96.28 2 A 1 ATOM 10 C CA . VAL A 1 2 ? -0.191 3.992 9.297 1.00 96.83 2 A 1 ATOM 11 C C . VAL A 1 2 ? -1.316 3.651 8.324 1.00 97.67 2 A 1 ATOM 12 O O . VAL A 1 2 ? -1.271 2.635 7.628 1.00 96.88 2 A 1 ATOM 13 C CB . VAL A 1 2 ? -0.550 3.468 10.698 1.00 95.53 2 A 1 ATOM 14 C CG1 . VAL A 1 2 ? -0.720 1.960 10.675 1.00 89.96 2 A 1 ATOM 15 C CG2 . VAL A 1 2 ? 0.514 3.864 11.708 1.00 89.17 2 A 1 ATOM 16 N N . LEU A 1 3 ? -2.310 4.497 8.270 1.00 97.42 3 A 1 ATOM 17 C CA . LEU A 1 3 ? -3.451 4.294 7.375 1.00 97.66 3 A 1 ATOM 18 C C . LEU A 1 3 ? -3.009 4.359 5.919 1.00 97.90 3 A 1 ATOM 19 O O . LEU A 1 3 ? -3.479 3.590 5.079 1.00 97.34 3 A 1 ATOM 20 C CB . LEU A 1 3 ? -4.517 5.356 7.645 1.00 97.44 3 A 1 ATOM 21 C CG . LEU A 1 3 ? -5.863 5.051 7.001 1.00 93.25 3 A 1 ATOM 22 C CD1 . LEU A 1 3 ? -6.616 4.012 7.827 1.00 90.49 3 A 1 ATOM 23 C CD2 . LEU A 1 3 ? -6.691 6.315 6.874 1.00 90.16 3 A 1 ATOM 24 N N . LEU A 1 4 ? -2.102 5.260 5.618 1.00 97.59 4 A 1 ATOM 25 C CA . LEU A 1 4 ? -1.580 5.421 4.267 1.00 97.45 4 A 1 ATOM 26 C C . LEU A 1 4 ? -0.755 4.209 3.860 1.00 97.45 4 A 1 ATOM 27 O O . LEU A 1 4 ? -0.763 3.801 2.702 1.00 96.75 4 A 1 ATOM 28 C CB . LEU A 1 4 ? -0.725 6.690 4.193 1.00 97.12 4 A 1 ATOM 29 C CG . LEU A 1 4 ? -0.816 7.404 2.851 1.00 92.72 4 A 1 ATOM 30 C CD1 . LEU A 1 4 ? -2.096 8.223 2.772 1.00 90.04 4 A 1 ATOM 31 C CD2 . LEU A 1 4 ? 0.393 8.290 2.641 1.00 89.63 4 A 1 ATOM 32 N N . ARG A 1 5 ? -0.053 3.641 4.823 1.00 97.24 5 A 1 ATOM 33 C CA . ARG A 1 5 ? 0.794 2.472 4.574 1.00 97.20 5 A 1 ATOM 34 C C . ARG A 1 5 ? -0.066 1.265 4.201 1.00 97.39 5 A 1 ATOM 35 O O . ARG A 1 5 ? 0.276 0.510 3.294 1.00 95.91 5 A 1 ATOM 36 C CB . ARG A 1 5 ? 1.606 2.158 5.837 1.00 96.52 5 A 1 ATOM 37 C CG . ARG A 1 5 ? 2.871 1.378 5.533 1.00 90.43 5 A 1 ATOM 38 C CD . ARG A 1 5 ? 3.979 2.330 5.105 1.00 88.42 5 A 1 ATOM 39 N NE . ARG A 1 5 ? 4.965 1.660 4.267 1.00 84.53 5 A 1 ATOM 40 C CZ . ARG A 1 5 ? 5.925 0.886 4.747 1.00 80.47 5 A 1 ATOM 41 N NH1 . ARG A 1 5 ? 6.047 0.675 6.048 1.00 74.69 5 A 1 ATOM 42 N NH2 . ARG A 1 5 ? 6.774 0.299 3.919 1.00 74.73 5 A 1 ATOM 43 N N . LEU A 1 6 ? -1.168 1.098 4.904 1.00 97.36 6 A 1 ATOM 44 C CA . LEU A 1 6 ? -2.073 -0.018 4.647 1.00 97.28 6 A 1 ATOM 45 C C . LEU A 1 6 ? -2.766 0.143 3.297 1.00 97.52 6 A 1 ATOM 46 O O . LEU A 1 6 ? -2.994 -0.836 2.587 1.00 96.98 6 A 1 ATOM 47 C CB . LEU A 1 6 ? -3.116 -0.097 5.765 1.00 97.04 6 A 1 ATOM 48 C CG . LEU A 1 6 ? -2.932 -1.285 6.695 1.00 91.57 6 A 1 ATOM 49 C CD1 . LEU A 1 6 ? -3.490 -0.981 8.076 1.00 88.42 6 A 1 ATOM 50 C CD2 . LEU A 1 6 ? -3.616 -2.511 6.113 1.00 89.25 6 A 1 ATOM 51 N N . LEU A 1 7 ? -3.083 1.372 2.947 1.00 96.89 7 A 1 ATOM 52 C CA . LEU A 1 7 ? -3.741 1.666 1.678 1.00 96.75 7 A 1 ATOM 53 C C . LEU A 1 7 ? -2.838 1.315 0.506 1.00 96.94 7 A 1 ATOM 54 O O . LEU A 1 7 ? -3.281 0.724 -0.478 1.00 96.40 7 A 1 ATOM 55 C CB . LEU A 1 7 ? -4.117 3.148 1.631 1.00 96.49 7 A 1 ATOM 56 C CG . LEU A 1 7 ? -5.610 3.393 1.469 1.00 91.83 7 A 1 ATOM 57 C CD1 . LEU A 1 7 ? -6.058 4.578 2.312 1.00 88.31 7 A 1 ATOM 58 C CD2 . LEU A 1 7 ? -5.946 3.632 0.012 1.00 89.07 7 A 1 ATOM 59 N N . VAL A 1 8 ? -1.577 1.667 0.620 1.00 97.33 8 A 1 ATOM 60 C CA . VAL A 1 8 ? -0.599 1.381 -0.426 1.00 97.13 8 A 1 ATOM 61 C C . VAL A 1 8 ? -0.348 -0.120 -0.528 1.00 97.13 8 A 1 ATOM 62 O O . VAL A 1 8 ? -0.134 -0.654 -1.615 1.00 96.45 8 A 1 ATOM 63 C CB . VAL A 1 8 ? 0.723 2.113 -0.145 1.00 96.54 8 A 1 ATOM 64 C CG1 . VAL A 1 8 ? 1.745 1.803 -1.224 1.00 94.38 8 A 1 ATOM 65 C CG2 . VAL A 1 8 ? 0.490 3.611 -0.063 1.00 94.17 8 A 1 ATOM 66 N N . PHE A 1 9 ? -0.383 -0.788 0.609 1.00 97.41 9 A 1 ATOM 67 C CA . PHE A 1 9 ? -0.159 -2.232 0.657 1.00 97.20 9 A 1 ATOM 68 C C . PHE A 1 9 ? -1.269 -2.980 -0.072 1.00 97.35 9 A 1 ATOM 69 O O . PHE A 1 9 ? -1.036 -4.039 -0.647 1.00 96.29 9 A 1 ATOM 70 C CB . PHE A 1 9 ? -0.096 -2.693 2.113 1.00 96.75 9 A 1 ATOM 71 C CG . PHE A 1 9 ? 1.256 -3.253 2.488 1.00 94.80 9 A 1 ATOM 72 C CD1 . PHE A 1 9 ? 2.392 -2.469 2.396 1.00 91.35 9 A 1 ATOM 73 C CD2 . PHE A 1 9 ? 1.374 -4.557 2.933 1.00 91.69 9 A 1 ATOM 74 C CE1 . PHE A 1 9 ? 3.635 -2.974 2.735 1.00 90.94 9 A 1 ATOM 75 C CE2 . PHE A 1 9 ? 2.618 -5.071 3.279 1.00 90.84 9 A 1 ATOM 76 C CZ . PHE A 1 9 ? 3.748 -4.279 3.180 1.00 90.73 9 A 1 ATOM 77 N N . LEU A 1 10 ? -2.460 -2.421 -0.045 1.00 97.51 10 A 1 ATOM 78 C CA . LEU A 1 10 ? -3.604 -3.036 -0.709 1.00 97.43 10 A 1 ATOM 79 C C . LEU A 1 10 ? -3.677 -2.644 -2.180 1.00 97.56 10 A 1 ATOM 80 O O . LEU A 1 10 ? -4.257 -3.367 -2.992 1.00 96.59 10 A 1 ATOM 81 C CB . LEU A 1 10 ? -4.891 -2.622 0.004 1.00 97.16 10 A 1 ATOM 82 C CG . LEU A 1 10 ? -5.204 -3.453 1.244 1.00 95.26 10 A 1 ATOM 83 C CD1 . LEU A 1 10 ? -6.103 -2.679 2.192 1.00 91.77 10 A 1 ATOM 84 C CD2 . LEU A 1 10 ? -5.875 -4.755 0.834 1.00 91.96 10 A 1 ATOM 85 N N . PHE A 1 11 ? -3.106 -1.504 -2.522 1.00 97.02 11 A 1 ATOM 86 C CA . PHE A 1 11 ? -3.111 -1.026 -3.895 1.00 96.93 11 A 1 ATOM 87 C C . PHE A 1 11 ? -1.972 -1.622 -4.706 1.00 97.25 11 A 1 ATOM 88 O O . PHE A 1 11 ? -2.083 -1.764 -5.924 1.00 96.03 11 A 1 ATOM 89 C CB . PHE A 1 11 ? -3.009 0.502 -3.914 1.00 96.15 11 A 1 ATOM 90 C CG . PHE A 1 11 ? -4.353 1.167 -4.081 1.00 94.46 11 A 1 ATOM 91 C CD1 . PHE A 1 11 ? -4.949 1.237 -5.327 1.00 90.41 11 A 1 ATOM 92 C CD2 . PHE A 1 11 ? -5.010 1.712 -2.995 1.00 90.86 11 A 1 ATOM 93 C CE1 . PHE A 1 11 ? -6.183 1.844 -5.489 1.00 89.88 11 A 1 ATOM 94 C CE2 . PHE A 1 11 ? -6.250 2.320 -3.153 1.00 89.44 11 A 1 ATOM 95 C CZ . PHE A 1 11 ? -6.835 2.386 -4.400 1.00 89.69 11 A 1 ATOM 96 N N . ALA A 1 12 ? -0.883 -1.962 -4.033 1.00 97.04 12 A 1 ATOM 97 C CA . ALA A 1 12 ? 0.279 -2.540 -4.705 1.00 96.83 12 A 1 ATOM 98 C C . ALA A 1 12 ? -0.042 -3.889 -5.357 1.00 97.17 12 A 1 ATOM 99 O O . ALA A 1 12 ? 0.237 -4.086 -6.541 1.00 95.70 12 A 1 ATOM 100 C CB . ALA A 1 12 ? 1.434 -2.671 -3.719 1.00 95.70 12 A 1 ATOM 101 N N . PRO A 1 13 ? -0.625 -4.829 -4.601 1.00 96.70 13 A 1 ATOM 102 C CA . PRO A 1 13 ? -0.955 -6.150 -5.145 1.00 96.47 13 A 1 ATOM 103 C C . PRO A 1 13 ? -2.151 -6.136 -6.091 1.00 96.83 13 A 1 ATOM 104 O O . PRO A 1 13 ? -2.179 -6.881 -7.068 1.00 94.50 13 A 1 ATOM 105 C CB . PRO A 1 13 ? -1.267 -6.982 -3.896 1.00 94.99 13 A 1 ATOM 106 C CG . PRO A 1 13 ? -1.719 -5.990 -2.887 1.00 93.70 13 A 1 ATOM 107 C CD . PRO A 1 13 ? -0.935 -4.732 -3.169 1.00 96.20 13 A 1 ATOM 108 N N . VAL A 1 14 ? -3.137 -5.310 -5.811 1.00 95.63 14 A 1 ATOM 109 C CA . VAL A 1 14 ? -4.339 -5.242 -6.643 1.00 95.29 14 A 1 ATOM 110 C C . VAL A 1 14 ? -4.054 -4.615 -8.003 1.00 95.07 14 A 1 ATOM 111 O O . VAL A 1 14 ? -4.711 -4.936 -8.992 1.00 91.44 14 A 1 ATOM 112 C CB . VAL A 1 14 ? -5.447 -4.439 -5.939 1.00 93.28 14 A 1 ATOM 113 C CG1 . VAL A 1 14 ? -5.846 -5.117 -4.641 1.00 87.15 14 A 1 ATOM 114 C CG2 . VAL A 1 14 ? -5.005 -3.014 -5.682 1.00 87.28 14 A 1 ATOM 115 N N . VAL A 1 15 ? -3.094 -3.718 -8.047 1.00 94.75 15 A 1 ATOM 116 C CA . VAL A 1 15 ? -2.733 -3.042 -9.292 1.00 92.15 15 A 1 ATOM 117 C C . VAL A 1 15 ? -1.970 -3.967 -10.232 1.00 90.97 15 A 1 ATOM 118 O O . VAL A 1 15 ? -1.994 -3.793 -11.451 1.00 85.58 15 A 1 ATOM 119 C CB . VAL A 1 15 ? -1.884 -1.784 -9.009 1.00 89.21 15 A 1 ATOM 120 C CG1 . VAL A 1 15 ? -0.470 -2.175 -8.588 1.00 82.81 15 A 1 ATOM 121 C CG2 . VAL A 1 15 ? -1.832 -0.892 -10.233 1.00 84.29 15 A 1 ATOM 122 N N . SER A 1 16 ? -1.293 -4.959 -9.659 1.00 90.69 16 A 1 ATOM 123 C CA . SER A 1 16 ? -0.493 -5.893 -10.435 1.00 88.37 16 A 1 ATOM 124 C C . SER A 1 16 ? -1.362 -6.860 -11.235 1.00 83.97 16 A 1 ATOM 125 O O . SER A 1 16 ? -2.348 -7.367 -10.691 1.00 77.03 16 A 1 ATOM 126 C CB . SER A 1 16 ? 0.452 -6.672 -9.529 1.00 82.76 16 A 1 ATOM 127 O OG . SER A 1 16 ? 1.327 -7.467 -10.300 1.00 74.09 16 A 1 ATOM 128 O OXT . SER A 1 16 ? -1.035 -7.117 -12.400 1.00 75.11 16 A 1 #