# 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_spkb16362 # _entry.id spkb16362 # 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" "C4 H7 N O4" 133.103 ASP y "ASPARTIC ACID" C([C@@H](C(=O)O)N)C(=O)O ? "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 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" "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" # _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 ALA 3 1 n ARG 4 1 n LEU 5 1 n LEU 6 1 n ILE 7 1 n LEU 8 1 n LEU 9 1 n CYS 10 1 n ALA 11 1 n LEU 12 1 n SER 13 1 n ALA 14 1 n THR 15 1 n ASP 16 1 n ALA 17 # _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 @ 2025-07-07 07:42:34)" _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 89.37 _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 83.57 1 1 A LYS 2 2 86.79 1 2 A ALA 3 2 95.35 1 3 A ARG 4 2 85.16 1 4 A LEU 5 2 92.09 1 5 A LEU 6 2 93.04 1 6 A ILE 7 2 95.00 1 7 A LEU 8 2 93.06 1 8 A LEU 9 2 92.32 1 9 A CYS 10 2 93.38 1 10 A ALA 11 2 95.12 1 11 A LEU 12 2 92.34 1 12 A SER 13 2 92.44 1 13 A ALA 14 2 93.61 1 14 A THR 15 2 85.32 1 15 A ASP 16 2 77.59 1 16 A ALA 17 2 79.98 1 17 # _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 ALA . 3 A 3 A 4 1 n ARG . 4 A 4 A 5 1 n LEU . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n ILE . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n CYS . 10 A 10 A 11 1 n ALA . 11 A 11 A 12 1 n LEU . 12 A 12 A 13 1 n SER . 13 A 13 A 14 1 n ALA . 14 A 14 A 15 1 n THR . 15 A 15 A 16 1 n ASP . 16 A 16 A 17 1 n ALA . 17 A 17 # _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 ? 3.583 -0.183 12.756 1.00 88.76 1 A 1 ATOM 2 C CA . MET A 1 1 ? 3.791 1.008 11.910 1.00 90.40 1 A 1 ATOM 3 C C . MET A 1 1 ? 2.680 1.106 10.875 1.00 92.32 1 A 1 ATOM 4 O O . MET A 1 1 ? 2.373 0.128 10.200 1.00 89.18 1 A 1 ATOM 5 C CB . MET A 1 1 ? 5.144 0.927 11.203 1.00 86.12 1 A 1 ATOM 6 C CG . MET A 1 1 ? 6.305 0.887 12.190 1.00 80.65 1 A 1 ATOM 7 S SD . MET A 1 1 ? 7.903 0.748 11.375 1.00 75.83 1 A 1 ATOM 8 C CE . MET A 1 1 ? 8.980 0.732 12.789 1.00 65.30 1 A 1 ATOM 9 N N . LYS A 1 2 ? 2.076 2.279 10.752 1.00 92.31 2 A 1 ATOM 10 C CA . LYS A 1 2 ? 0.957 2.491 9.837 1.00 93.13 2 A 1 ATOM 11 C C . LYS A 1 2 ? 1.426 2.667 8.398 1.00 93.73 2 A 1 ATOM 12 O O . LYS A 1 2 ? 0.609 2.721 7.481 1.00 93.31 2 A 1 ATOM 13 C CB . LYS A 1 2 ? 0.151 3.707 10.279 1.00 92.06 2 A 1 ATOM 14 C CG . LYS A 1 2 ? -0.718 3.438 11.492 1.00 85.74 2 A 1 ATOM 15 C CD . LYS A 1 2 ? 0.102 3.363 12.779 1.00 83.04 2 A 1 ATOM 16 C CE . LYS A 1 2 ? 0.621 4.725 13.184 1.00 77.05 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? 1.323 4.671 14.485 1.00 70.71 2 A 1 ATOM 18 N N . ALA A 1 3 ? 2.730 2.761 8.194 1.00 95.11 3 A 1 ATOM 19 C CA . ALA A 1 3 ? 3.284 2.943 6.853 1.00 95.81 3 A 1 ATOM 20 C C . ALA A 1 3 ? 2.921 1.774 5.940 1.00 96.48 3 A 1 ATOM 21 O O . ALA A 1 3 ? 2.825 1.930 4.724 1.00 95.03 3 A 1 ATOM 22 C CB . ALA A 1 3 ? 4.797 3.096 6.932 1.00 94.31 3 A 1 ATOM 23 N N . ARG A 1 4 ? 2.714 0.601 6.538 1.00 96.04 4 A 1 ATOM 24 C CA . ARG A 1 4 ? 2.367 -0.591 5.765 1.00 96.60 4 A 1 ATOM 25 C C . ARG A 1 4 ? 1.053 -0.383 5.029 1.00 97.04 4 A 1 ATOM 26 O O . ARG A 1 4 ? 0.892 -0.819 3.891 1.00 95.76 4 A 1 ATOM 27 C CB . ARG A 1 4 ? 2.273 -1.803 6.690 1.00 96.04 4 A 1 ATOM 28 C CG . ARG A 1 4 ? 3.539 -2.042 7.491 1.00 90.36 4 A 1 ATOM 29 C CD . ARG A 1 4 ? 4.708 -2.391 6.582 1.00 84.80 4 A 1 ATOM 30 N NE . ARG A 1 4 ? 4.524 -3.684 5.923 1.00 76.88 4 A 1 ATOM 31 C CZ . ARG A 1 4 ? 5.387 -4.205 5.062 1.00 72.62 4 A 1 ATOM 32 N NH1 . ARG A 1 4 ? 6.474 -3.548 4.727 1.00 66.12 4 A 1 ATOM 33 N NH2 . ARG A 1 4 ? 5.149 -5.394 4.521 1.00 64.53 4 A 1 ATOM 34 N N . LEU A 1 5 ? 0.108 0.287 5.676 1.00 95.27 5 A 1 ATOM 35 C CA . LEU A 1 5 ? -1.181 0.565 5.057 1.00 95.64 5 A 1 ATOM 36 C C . LEU A 1 5 ? -1.013 1.474 3.848 1.00 96.13 5 A 1 ATOM 37 O O . LEU A 1 5 ? -1.664 1.285 2.820 1.00 95.42 5 A 1 ATOM 38 C CB . LEU A 1 5 ? -2.110 1.222 6.069 1.00 95.52 5 A 1 ATOM 39 C CG . LEU A 1 5 ? -3.494 1.497 5.503 1.00 88.10 5 A 1 ATOM 40 C CD1 . LEU A 1 5 ? -4.184 0.196 5.119 1.00 84.75 5 A 1 ATOM 41 C CD2 . LEU A 1 5 ? -4.333 2.255 6.518 1.00 85.86 5 A 1 ATOM 42 N N . LEU A 1 6 ? -0.150 2.455 3.974 1.00 96.35 6 A 1 ATOM 43 C CA . LEU A 1 6 ? 0.104 3.383 2.874 1.00 96.02 6 A 1 ATOM 44 C C . LEU A 1 6 ? 0.697 2.642 1.684 1.00 96.23 6 A 1 ATOM 45 O O . LEU A 1 6 ? 0.376 2.934 0.532 1.00 95.93 6 A 1 ATOM 46 C CB . LEU A 1 6 ? 1.060 4.488 3.331 1.00 95.88 6 A 1 ATOM 47 C CG . LEU A 1 6 ? 0.480 5.388 4.420 1.00 89.58 6 A 1 ATOM 48 C CD1 . LEU A 1 6 ? 1.524 6.387 4.895 1.00 87.08 6 A 1 ATOM 49 C CD2 . LEU A 1 6 ? -0.754 6.121 3.907 1.00 87.25 6 A 1 ATOM 50 N N . ILE A 1 7 ? 1.561 1.686 1.971 1.00 96.21 7 A 1 ATOM 51 C CA . ILE A 1 7 ? 2.181 0.896 0.909 1.00 95.99 7 A 1 ATOM 52 C C . ILE A 1 7 ? 1.111 0.121 0.146 1.00 96.00 7 A 1 ATOM 53 O O . ILE A 1 7 ? 1.137 0.047 -1.085 1.00 95.54 7 A 1 ATOM 54 C CB . ILE A 1 7 ? 3.231 -0.067 1.493 1.00 96.21 7 A 1 ATOM 55 C CG1 . ILE A 1 7 ? 4.389 0.724 2.116 1.00 94.96 7 A 1 ATOM 56 C CG2 . ILE A 1 7 ? 3.755 -1.002 0.404 1.00 94.57 7 A 1 ATOM 57 C CD1 . ILE A 1 7 ? 5.356 -0.146 2.899 1.00 90.55 7 A 1 ATOM 58 N N . LEU A 1 8 ? 0.164 -0.446 0.878 1.00 95.97 8 A 1 ATOM 59 C CA . LEU A 1 8 ? -0.913 -1.204 0.253 1.00 95.63 8 A 1 ATOM 60 C C . LEU A 1 8 ? -1.763 -0.299 -0.630 1.00 95.67 8 A 1 ATOM 61 O O . LEU A 1 8 ? -2.145 -0.681 -1.739 1.00 95.09 8 A 1 ATOM 62 C CB . LEU A 1 8 ? -1.784 -1.852 1.328 1.00 95.62 8 A 1 ATOM 63 C CG . LEU A 1 8 ? -1.065 -2.939 2.123 1.00 90.50 8 A 1 ATOM 64 C CD1 . LEU A 1 8 ? -1.947 -3.424 3.270 1.00 87.63 8 A 1 ATOM 65 C CD2 . LEU A 1 8 ? -0.694 -4.110 1.223 1.00 88.33 8 A 1 ATOM 66 N N . LEU A 1 9 ? -2.053 0.893 -0.153 1.00 95.43 9 A 1 ATOM 67 C CA . LEU A 1 9 ? -2.843 1.847 -0.924 1.00 94.94 9 A 1 ATOM 68 C C . LEU A 1 9 ? -2.108 2.245 -2.195 1.00 95.13 9 A 1 ATOM 69 O O . LEU A 1 9 ? -2.712 2.356 -3.264 1.00 94.33 9 A 1 ATOM 70 C CB . LEU A 1 9 ? -3.130 3.082 -0.073 1.00 94.62 9 A 1 ATOM 71 C CG . LEU A 1 9 ? -4.068 2.799 1.098 1.00 90.17 9 A 1 ATOM 72 C CD1 . LEU A 1 9 ? -4.188 4.030 1.984 1.00 86.77 9 A 1 ATOM 73 C CD2 . LEU A 1 9 ? -5.443 2.378 0.593 1.00 87.21 9 A 1 ATOM 74 N N . CYS A 1 10 ? -0.808 2.448 -2.086 1.00 94.79 10 A 1 ATOM 75 C CA . CYS A 1 10 ? -0.004 2.809 -3.247 1.00 94.59 10 A 1 ATOM 76 C C . CYS A 1 10 ? -0.005 1.675 -4.266 1.00 94.64 10 A 1 ATOM 77 O O . CYS A 1 10 ? -0.069 1.909 -5.470 1.00 92.88 10 A 1 ATOM 78 C CB . CYS A 1 10 ? 1.426 3.126 -2.814 1.00 93.80 10 A 1 ATOM 79 S SG . CYS A 1 10 ? 1.540 4.653 -1.868 1.00 89.57 10 A 1 ATOM 80 N N . ALA A 1 11 ? 0.063 0.450 -3.778 1.00 95.53 11 A 1 ATOM 81 C CA . ALA A 1 11 ? 0.059 -0.711 -4.661 1.00 95.50 11 A 1 ATOM 82 C C . ALA A 1 11 ? -1.263 -0.806 -5.418 1.00 95.76 11 A 1 ATOM 83 O O . ALA A 1 11 ? -1.282 -1.075 -6.618 1.00 93.84 11 A 1 ATOM 84 C CB . ALA A 1 11 ? 0.306 -1.974 -3.853 1.00 94.98 11 A 1 ATOM 85 N N . LEU A 1 12 ? -2.367 -0.565 -4.728 1.00 95.27 12 A 1 ATOM 86 C CA . LEU A 1 12 ? -3.685 -0.602 -5.354 1.00 94.87 12 A 1 ATOM 87 C C . LEU A 1 12 ? -3.828 0.522 -6.366 1.00 95.22 12 A 1 ATOM 88 O O . LEU A 1 12 ? -4.446 0.348 -7.418 1.00 93.63 12 A 1 ATOM 89 C CB . LEU A 1 12 ? -4.767 -0.487 -4.284 1.00 94.28 12 A 1 ATOM 90 C CG . LEU A 1 12 ? -4.838 -1.696 -3.354 1.00 91.49 12 A 1 ATOM 91 C CD1 . LEU A 1 12 ? -5.829 -1.435 -2.227 1.00 86.83 12 A 1 ATOM 92 C CD2 . LEU A 1 12 ? -5.236 -2.944 -4.125 1.00 87.09 12 A 1 ATOM 93 N N . SER A 1 13 ? -3.263 1.665 -6.053 1.00 95.22 13 A 1 ATOM 94 C CA . SER A 1 13 ? -3.309 2.807 -6.962 1.00 95.23 13 A 1 ATOM 95 C C . SER A 1 13 ? -2.485 2.541 -8.215 1.00 95.32 13 A 1 ATOM 96 O O . SER A 1 13 ? -2.780 3.062 -9.292 1.00 93.49 13 A 1 ATOM 97 C CB . SER A 1 13 ? -2.787 4.055 -6.265 1.00 93.21 13 A 1 ATOM 98 O OG . SER A 1 13 ? -2.830 5.153 -7.146 1.00 82.17 13 A 1 ATOM 99 N N . ALA A 1 14 ? -1.446 1.733 -8.072 1.00 94.55 14 A 1 ATOM 100 C CA . ALA A 1 14 ? -0.571 1.404 -9.194 1.00 94.40 14 A 1 ATOM 101 C C . ALA A 1 14 ? -1.084 0.207 -9.977 1.00 94.72 14 A 1 ATOM 102 O O . ALA A 1 14 ? -0.536 -0.129 -11.030 1.00 91.82 14 A 1 ATOM 103 C CB . ALA A 1 14 ? 0.840 1.129 -8.688 1.00 92.54 14 A 1 ATOM 104 N N . THR A 1 15 ? -2.118 -0.438 -9.474 1.00 90.80 15 A 1 ATOM 105 C CA . THR A 1 15 ? -2.678 -1.613 -10.144 1.00 89.93 15 A 1 ATOM 106 C C . THR A 1 15 ? -3.763 -1.203 -11.133 1.00 89.28 15 A 1 ATOM 107 O O . THR A 1 15 ? -4.814 -1.833 -11.229 1.00 84.65 15 A 1 ATOM 108 C CB . THR A 1 15 ? -3.245 -2.610 -9.134 1.00 86.91 15 A 1 ATOM 109 O OG1 . THR A 1 15 ? -3.668 -3.794 -9.814 1.00 79.22 15 A 1 ATOM 110 C CG2 . THR A 1 15 ? -4.428 -2.023 -8.389 1.00 76.44 15 A 1 ATOM 111 N N . ASP A 1 16 ? -3.517 -0.149 -11.868 1.00 82.18 16 A 1 ATOM 112 C CA . ASP A 1 16 ? -4.470 0.332 -12.857 1.00 82.50 16 A 1 ATOM 113 C C . ASP A 1 16 ? -4.467 -0.562 -14.088 1.00 84.20 16 A 1 ATOM 114 O O . ASP A 1 16 ? -3.421 -0.882 -14.645 1.00 79.93 16 A 1 ATOM 115 C CB . ASP A 1 16 ? -4.133 1.763 -13.261 1.00 78.32 16 A 1 ATOM 116 C CG . ASP A 1 16 ? -2.714 1.879 -13.766 1.00 73.25 16 A 1 ATOM 117 O OD1 . ASP A 1 16 ? -1.948 0.913 -13.650 1.00 69.28 16 A 1 ATOM 118 O OD2 . ASP A 1 16 ? -2.366 2.960 -14.277 1.00 71.07 16 A 1 ATOM 119 N N . ALA A 1 17 ? -5.651 -0.958 -14.526 1.00 86.16 17 A 1 ATOM 120 C CA . ALA A 1 17 ? -5.763 -1.819 -15.691 1.00 85.42 17 A 1 ATOM 121 C C . ALA A 1 17 ? -7.098 -1.588 -16.401 1.00 83.57 17 A 1 ATOM 122 O O . ALA A 1 17 ? -7.946 -0.842 -15.874 1.00 75.91 17 A 1 ATOM 123 C CB . ALA A 1 17 ? -5.616 -3.279 -15.273 1.00 79.43 17 A 1 ATOM 124 O OXT . ALA A 1 17 ? -7.321 -2.162 -17.491 1.00 69.39 17 A 1 #