# 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_spkb39612 # _entry.id spkb39612 # 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 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" "C4 H9 N O3" 119.119 THR y THREONINE C[C@H]([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 LYS 2 1 n LEU 3 1 n ILE 4 1 n ILE 5 1 n LEU 6 1 n VAL 7 1 n ALA 8 1 n LEU 9 1 n THR 10 1 n LEU 11 1 n ALA 12 1 n ALA 13 1 n VAL 14 1 n VAL 15 1 n ALA 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 @ 2025-07-04 03:27:37)" _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 96.87 _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 90.99 1 1 A LYS 2 2 94.53 1 2 A LEU 3 2 97.42 1 3 A ILE 4 2 97.97 1 4 A ILE 5 2 98.19 1 5 A LEU 6 2 97.25 1 6 A VAL 7 2 98.35 1 7 A ALA 8 2 98.66 1 8 A LEU 9 2 97.66 1 9 A THR 10 2 97.64 1 10 A LEU 11 2 96.62 1 11 A ALA 12 2 98.52 1 12 A ALA 13 2 98.66 1 13 A VAL 14 2 97.81 1 14 A VAL 15 2 97.04 1 15 A ALA 16 2 94.79 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 LYS . 2 A 2 A 3 1 n LEU . 3 A 3 A 4 1 n ILE . 4 A 4 A 5 1 n ILE . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n VAL . 7 A 7 A 8 1 n ALA . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n THR . 10 A 10 A 11 1 n LEU . 11 A 11 A 12 1 n ALA . 12 A 12 A 13 1 n ALA . 13 A 13 A 14 1 n VAL . 14 A 14 A 15 1 n VAL . 15 A 15 A 16 1 n ALA . 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 ? 6.233 5.104 8.368 1.00 95.60 1 A 1 ATOM 2 C CA . MET A 1 1 ? 5.628 3.775 8.559 1.00 96.07 1 A 1 ATOM 3 C C . MET A 1 1 ? 5.875 2.882 7.349 1.00 96.38 1 A 1 ATOM 4 O O . MET A 1 1 ? 6.182 3.365 6.264 1.00 94.67 1 A 1 ATOM 5 C CB . MET A 1 1 ? 4.124 3.908 8.769 1.00 93.75 1 A 1 ATOM 6 C CG . MET A 1 1 ? 3.796 4.543 10.108 1.00 89.74 1 A 1 ATOM 7 S SD . MET A 1 1 ? 2.029 4.677 10.371 1.00 86.11 1 A 1 ATOM 8 C CE . MET A 1 1 ? 2.020 5.342 12.032 1.00 75.56 1 A 1 ATOM 9 N N . LYS A 1 2 ? 5.729 1.574 7.539 1.00 98.09 2 A 1 ATOM 10 C CA . LYS A 1 2 ? 5.928 0.615 6.457 1.00 98.22 2 A 1 ATOM 11 C C . LYS A 1 2 ? 4.615 -0.048 6.047 1.00 98.43 2 A 1 ATOM 12 O O . LYS A 1 2 ? 4.494 -0.549 4.930 1.00 98.25 2 A 1 ATOM 13 C CB . LYS A 1 2 ? 6.947 -0.439 6.884 1.00 97.81 2 A 1 ATOM 14 C CG . LYS A 1 2 ? 6.759 -0.889 8.328 1.00 95.50 2 A 1 ATOM 15 C CD . LYS A 1 2 ? 7.908 -1.751 8.791 1.00 92.61 2 A 1 ATOM 16 C CE . LYS A 1 2 ? 7.985 -1.789 10.315 1.00 88.09 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? 9.164 -1.049 10.784 1.00 83.73 2 A 1 ATOM 18 N N . LEU A 1 3 ? 3.634 -0.054 6.929 1.00 98.42 3 A 1 ATOM 19 C CA . LEU A 1 3 ? 2.332 -0.650 6.633 1.00 98.56 3 A 1 ATOM 20 C C . LEU A 1 3 ? 1.621 0.116 5.523 1.00 98.71 3 A 1 ATOM 21 O O . LEU A 1 3 ? 1.037 -0.474 4.618 1.00 98.51 3 A 1 ATOM 22 C CB . LEU A 1 3 ? 1.458 -0.679 7.891 1.00 98.37 3 A 1 ATOM 23 C CG . LEU A 1 3 ? 1.735 -1.889 8.785 1.00 96.97 3 A 1 ATOM 24 C CD1 . LEU A 1 3 ? 3.030 -1.694 9.559 1.00 95.14 3 A 1 ATOM 25 C CD2 . LEU A 1 3 ? 0.579 -2.120 9.744 1.00 94.65 3 A 1 ATOM 26 N N . ILE A 1 4 ? 1.672 1.431 5.594 1.00 98.62 4 A 1 ATOM 27 C CA . ILE A 1 4 ? 1.023 2.270 4.589 1.00 98.68 4 A 1 ATOM 28 C C . ILE A 1 4 ? 1.589 1.994 3.197 1.00 98.73 4 A 1 ATOM 29 O O . ILE A 1 4 ? 0.865 2.009 2.204 1.00 98.62 4 A 1 ATOM 30 C CB . ILE A 1 4 ? 1.183 3.761 4.936 1.00 98.61 4 A 1 ATOM 31 C CG1 . ILE A 1 4 ? 2.659 4.104 5.164 1.00 97.75 4 A 1 ATOM 32 C CG2 . ILE A 1 4 ? 0.351 4.091 6.168 1.00 97.28 4 A 1 ATOM 33 C CD1 . ILE A 1 4 ? 2.897 5.597 5.272 1.00 95.49 4 A 1 ATOM 34 N N . ILE A 1 5 ? 2.874 1.746 3.128 1.00 98.75 5 A 1 ATOM 35 C CA . ILE A 1 5 ? 3.535 1.490 1.850 1.00 98.71 5 A 1 ATOM 36 C C . ILE A 1 5 ? 3.039 0.175 1.249 1.00 98.74 5 A 1 ATOM 37 O O . ILE A 1 5 ? 2.648 0.117 0.081 1.00 98.69 5 A 1 ATOM 38 C CB . ILE A 1 5 ? 5.064 1.441 2.027 1.00 98.66 5 A 1 ATOM 39 C CG1 . ILE A 1 5 ? 5.577 2.779 2.576 1.00 98.05 5 A 1 ATOM 40 C CG2 . ILE A 1 5 ? 5.733 1.139 0.685 1.00 97.72 5 A 1 ATOM 41 C CD1 . ILE A 1 5 ? 7.029 2.715 3.017 1.00 96.21 5 A 1 ATOM 42 N N . LEU A 1 6 ? 3.050 -0.875 2.042 1.00 98.74 6 A 1 ATOM 43 C CA . LEU A 1 6 ? 2.615 -2.187 1.573 1.00 98.73 6 A 1 ATOM 44 C C . LEU A 1 6 ? 1.134 -2.172 1.209 1.00 98.80 6 A 1 ATOM 45 O O . LEU A 1 6 ? 0.728 -2.736 0.193 1.00 98.76 6 A 1 ATOM 46 C CB . LEU A 1 6 ? 2.870 -3.231 2.661 1.00 98.60 6 A 1 ATOM 47 C CG . LEU A 1 6 ? 4.353 -3.447 2.962 1.00 95.42 6 A 1 ATOM 48 C CD1 . LEU A 1 6 ? 4.516 -4.333 4.190 1.00 94.33 6 A 1 ATOM 49 C CD2 . LEU A 1 6 ? 5.053 -4.075 1.764 1.00 94.65 6 A 1 ATOM 50 N N . VAL A 1 7 ? 0.337 -1.529 2.034 1.00 98.71 7 A 1 ATOM 51 C CA . VAL A 1 7 ? -1.102 -1.441 1.792 1.00 98.71 7 A 1 ATOM 52 C C . VAL A 1 7 ? -1.382 -0.665 0.511 1.00 98.77 7 A 1 ATOM 53 O O . VAL A 1 7 ? -2.243 -1.045 -0.286 1.00 98.71 7 A 1 ATOM 54 C CB . VAL A 1 7 ? -1.813 -0.771 2.979 1.00 98.59 7 A 1 ATOM 55 C CG1 . VAL A 1 7 ? -3.284 -0.531 2.669 1.00 97.57 7 A 1 ATOM 56 C CG2 . VAL A 1 7 ? -1.683 -1.644 4.220 1.00 97.36 7 A 1 ATOM 57 N N . ALA A 1 8 ? -0.671 0.425 0.322 1.00 98.69 8 A 1 ATOM 58 C CA . ALA A 1 8 ? -0.855 1.258 -0.863 1.00 98.70 8 A 1 ATOM 59 C C . ALA A 1 8 ? -0.554 0.470 -2.136 1.00 98.76 8 A 1 ATOM 60 O O . ALA A 1 8 ? -1.302 0.534 -3.111 1.00 98.61 8 A 1 ATOM 61 C CB . ALA A 1 8 ? 0.045 2.484 -0.779 1.00 98.56 8 A 1 ATOM 62 N N . LEU A 1 9 ? 0.530 -0.276 -2.126 1.00 98.80 9 A 1 ATOM 63 C CA . LEU A 1 9 ? 0.922 -1.069 -3.287 1.00 98.75 9 A 1 ATOM 64 C C . LEU A 1 9 ? -0.085 -2.180 -3.547 1.00 98.80 9 A 1 ATOM 65 O O . LEU A 1 9 ? -0.425 -2.469 -4.694 1.00 98.67 9 A 1 ATOM 66 C CB . LEU A 1 9 ? 2.310 -1.668 -3.058 1.00 98.60 9 A 1 ATOM 67 C CG . LEU A 1 9 ? 3.425 -0.626 -3.035 1.00 96.63 9 A 1 ATOM 68 C CD1 . LEU A 1 9 ? 4.731 -1.261 -2.586 1.00 95.42 9 A 1 ATOM 69 C CD2 . LEU A 1 9 ? 3.591 0.009 -4.406 1.00 95.64 9 A 1 ATOM 70 N N . THR A 1 10 ? -0.559 -2.790 -2.486 1.00 98.61 10 A 1 ATOM 71 C CA . THR A 1 10 ? -1.530 -3.875 -2.603 1.00 98.56 10 A 1 ATOM 72 C C . THR A 1 10 ? -2.830 -3.367 -3.217 1.00 98.66 10 A 1 ATOM 73 O O . THR A 1 10 ? -3.374 -3.979 -4.136 1.00 98.43 10 A 1 ATOM 74 C CB . THR A 1 10 ? -1.825 -4.483 -1.230 1.00 98.31 10 A 1 ATOM 75 O OG1 . THR A 1 10 ? -0.613 -4.941 -0.642 1.00 95.91 10 A 1 ATOM 76 C CG2 . THR A 1 10 ? -2.787 -5.658 -1.369 1.00 94.98 10 A 1 ATOM 77 N N . LEU A 1 11 ? -3.325 -2.252 -2.718 1.00 98.71 11 A 1 ATOM 78 C CA . LEU A 1 11 ? -4.567 -1.672 -3.222 1.00 98.64 11 A 1 ATOM 79 C C . LEU A 1 11 ? -4.409 -1.243 -4.671 1.00 98.71 11 A 1 ATOM 80 O O . LEU A 1 11 ? -5.309 -1.441 -5.488 1.00 98.55 11 A 1 ATOM 81 C CB . LEU A 1 11 ? -4.959 -0.473 -2.366 1.00 98.36 11 A 1 ATOM 82 C CG . LEU A 1 11 ? -5.420 -0.861 -0.962 1.00 94.02 11 A 1 ATOM 83 C CD1 . LEU A 1 11 ? -5.564 0.374 -0.098 1.00 92.37 11 A 1 ATOM 84 C CD2 . LEU A 1 11 ? -6.737 -1.619 -1.028 1.00 93.59 11 A 1 ATOM 85 N N . ALA A 1 12 ? -3.275 -0.653 -4.989 1.00 98.65 12 A 1 ATOM 86 C CA . ALA A 1 12 ? -3.006 -0.198 -6.349 1.00 98.59 12 A 1 ATOM 87 C C . ALA A 1 12 ? -3.016 -1.369 -7.325 1.00 98.67 12 A 1 ATOM 88 O O . ALA A 1 12 ? -3.549 -1.268 -8.427 1.00 98.39 12 A 1 ATOM 89 C CB . ALA A 1 12 ? -1.661 0.513 -6.403 1.00 98.29 12 A 1 ATOM 90 N N . ALA A 1 13 ? -2.429 -2.480 -6.918 1.00 98.77 13 A 1 ATOM 91 C CA . ALA A 1 13 ? -2.369 -3.667 -7.764 1.00 98.73 13 A 1 ATOM 92 C C . ALA A 1 13 ? -3.753 -4.270 -7.966 1.00 98.80 13 A 1 ATOM 93 O O . ALA A 1 13 ? -4.087 -4.726 -9.058 1.00 98.52 13 A 1 ATOM 94 C CB . ALA A 1 13 ? -1.432 -4.696 -7.142 1.00 98.49 13 A 1 ATOM 95 N N . VAL A 1 14 ? -4.561 -4.275 -6.920 1.00 98.65 14 A 1 ATOM 96 C CA . VAL A 1 14 ? -5.912 -4.831 -6.993 1.00 98.59 14 A 1 ATOM 97 C C . VAL A 1 14 ? -6.808 -3.978 -7.877 1.00 98.65 14 A 1 ATOM 98 O O . VAL A 1 14 ? -7.566 -4.498 -8.700 1.00 98.20 14 A 1 ATOM 99 C CB . VAL A 1 14 ? -6.526 -4.949 -5.594 1.00 98.16 14 A 1 ATOM 100 C CG1 . VAL A 1 14 ? -7.981 -5.384 -5.687 1.00 96.04 14 A 1 ATOM 101 C CG2 . VAL A 1 14 ? -5.736 -5.938 -4.764 1.00 96.38 14 A 1 ATOM 102 N N . VAL A 1 15 ? -6.747 -2.677 -7.697 1.00 98.39 15 A 1 ATOM 103 C CA . VAL A 1 15 ? -7.567 -1.750 -8.475 1.00 98.30 15 A 1 ATOM 104 C C . VAL A 1 15 ? -7.192 -1.781 -9.948 1.00 98.39 15 A 1 ATOM 105 O O . VAL A 1 15 ? -8.057 -1.835 -10.823 1.00 97.90 15 A 1 ATOM 106 C CB . VAL A 1 15 ? -7.425 -0.318 -7.944 1.00 97.56 15 A 1 ATOM 107 C CG1 . VAL A 1 15 ? -8.157 0.660 -8.847 1.00 94.14 15 A 1 ATOM 108 C CG2 . VAL A 1 15 ? -7.963 -0.237 -6.532 1.00 94.58 15 A 1 ATOM 109 N N . ALA A 1 16 ? -5.906 -1.717 -10.225 1.00 97.85 16 A 1 ATOM 110 C CA . ALA A 1 16 ? -5.424 -1.706 -11.597 1.00 97.21 16 A 1 ATOM 111 C C . ALA A 1 16 ? -5.539 -3.083 -12.239 1.00 96.52 16 A 1 ATOM 112 O O . ALA A 1 16 ? -5.431 -4.096 -11.527 1.00 93.48 16 A 1 ATOM 113 C CB . ALA A 1 16 ? -3.983 -1.212 -11.643 1.00 95.70 16 A 1 ATOM 114 O OXT . ALA A 1 16 ? -5.706 -3.159 -13.456 1.00 87.95 16 A 1 #