# 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_spkb11663 # _entry.id spkb11663 # 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" "C2 H5 N O2" 75.067 GLY y GLYCINE C(C(=O)O)N ? "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" "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 LYS 4 1 n THR 5 1 n LEU 6 1 n ALA 7 1 n LEU 8 1 n SER 9 1 n LEU 10 1 n LEU 11 1 n ALA 12 1 n ALA 13 1 n GLY 14 1 n VAL 15 1 n LEU 16 1 n ALA 17 1 n GLY 18 # _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 15:57:29)" _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 95.44 _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 84.41 1 1 A LYS 2 2 92.45 1 2 A LEU 3 2 96.28 1 3 A LYS 4 2 93.48 1 4 A THR 5 2 96.29 1 5 A LEU 6 2 95.54 1 6 A ALA 7 2 98.38 1 7 A LEU 8 2 96.64 1 8 A SER 9 2 97.25 1 9 A LEU 10 2 97.24 1 10 A LEU 11 2 96.30 1 11 A ALA 12 2 98.38 1 12 A ALA 13 2 98.51 1 13 A GLY 14 2 98.64 1 14 A VAL 15 2 97.76 1 15 A LEU 16 2 96.08 1 16 A ALA 17 2 98.16 1 17 A GLY 18 2 92.46 1 18 # _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 LYS . 4 A 4 A 5 1 n THR . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n ALA . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n SER . 9 A 9 A 10 1 n LEU . 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 GLY . 14 A 14 A 15 1 n VAL . 15 A 15 A 16 1 n LEU . 16 A 16 A 17 1 n ALA . 17 A 17 A 18 1 n GLY . 18 A 18 # _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 ? -4.620 10.787 8.787 1.00 88.55 1 A 1 ATOM 2 C CA . MET A 1 1 ? -4.715 9.445 8.200 1.00 92.08 1 A 1 ATOM 3 C C . MET A 1 1 ? -4.251 8.392 9.202 1.00 93.74 1 A 1 ATOM 4 O O . MET A 1 1 ? -3.506 8.688 10.134 1.00 89.66 1 A 1 ATOM 5 C CB . MET A 1 1 ? -3.869 9.340 6.931 1.00 85.42 1 A 1 ATOM 6 C CG . MET A 1 1 ? -2.394 9.611 7.171 1.00 81.04 1 A 1 ATOM 7 S SD . MET A 1 1 ? -1.403 9.566 5.667 1.00 77.38 1 A 1 ATOM 8 C CE . MET A 1 1 ? -1.986 11.040 4.855 1.00 67.44 1 A 1 ATOM 9 N N . LYS A 1 2 ? -4.684 7.166 9.021 1.00 96.64 2 A 1 ATOM 10 C CA . LYS A 1 2 ? -4.337 6.066 9.917 1.00 97.20 2 A 1 ATOM 11 C C . LYS A 1 2 ? -3.073 5.357 9.433 1.00 97.63 2 A 1 ATOM 12 O O . LYS A 1 2 ? -2.806 5.288 8.233 1.00 97.17 2 A 1 ATOM 13 C CB . LYS A 1 2 ? -5.496 5.077 9.999 1.00 96.30 2 A 1 ATOM 14 C CG . LYS A 1 2 ? -6.766 5.685 10.584 1.00 91.99 2 A 1 ATOM 15 C CD . LYS A 1 2 ? -7.890 4.660 10.622 1.00 90.05 2 A 1 ATOM 16 C CE . LYS A 1 2 ? -9.160 5.266 11.188 1.00 85.00 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? -10.284 4.289 11.194 1.00 80.03 2 A 1 ATOM 18 N N . LEU A 1 3 ? -2.314 4.790 10.383 1.00 97.83 3 A 1 ATOM 19 C CA . LEU A 1 3 ? -1.100 4.047 10.049 1.00 98.19 3 A 1 ATOM 20 C C . LEU A 1 3 ? -1.440 2.812 9.222 1.00 98.37 3 A 1 ATOM 21 O O . LEU A 1 3 ? -0.683 2.407 8.340 1.00 97.81 3 A 1 ATOM 22 C CB . LEU A 1 3 ? -0.368 3.633 11.329 1.00 97.93 3 A 1 ATOM 23 C CG . LEU A 1 3 ? 0.212 4.798 12.128 1.00 96.09 3 A 1 ATOM 24 C CD1 . LEU A 1 3 ? 0.785 4.296 13.443 1.00 92.70 3 A 1 ATOM 25 C CD2 . LEU A 1 3 ? 1.291 5.517 11.331 1.00 91.31 3 A 1 ATOM 26 N N . LYS A 1 4 ? -2.605 2.214 9.512 1.00 97.96 4 A 1 ATOM 27 C CA . LYS A 1 4 ? -3.060 1.032 8.782 1.00 98.06 4 A 1 ATOM 28 C C . LYS A 1 4 ? -3.276 1.360 7.311 1.00 98.19 4 A 1 ATOM 29 O O . LYS A 1 4 ? -2.988 0.544 6.436 1.00 98.00 4 A 1 ATOM 30 C CB . LYS A 1 4 ? -4.348 0.496 9.399 1.00 97.91 4 A 1 ATOM 31 C CG . LYS A 1 4 ? -4.144 -0.043 10.807 1.00 94.79 4 A 1 ATOM 32 C CD . LYS A 1 4 ? -5.446 -0.573 11.386 1.00 90.99 4 A 1 ATOM 33 C CE . LYS A 1 4 ? -5.238 -1.122 12.789 1.00 86.27 4 A 1 ATOM 34 N NZ . LYS A 1 4 ? -6.515 -1.617 13.381 1.00 79.15 4 A 1 ATOM 35 N N . THR A 1 5 ? -3.777 2.543 7.040 1.00 97.71 5 A 1 ATOM 36 C CA . THR A 1 5 ? -4.017 2.984 5.670 1.00 97.82 5 A 1 ATOM 37 C C . THR A 1 5 ? -2.694 3.118 4.923 1.00 97.99 5 A 1 ATOM 38 O O . THR A 1 5 ? -2.577 2.710 3.765 1.00 97.64 5 A 1 ATOM 39 C CB . THR A 1 5 ? -4.753 4.329 5.650 1.00 97.84 5 A 1 ATOM 40 O OG1 . THR A 1 5 ? -5.984 4.212 6.358 1.00 93.76 5 A 1 ATOM 41 C CG2 . THR A 1 5 ? -5.045 4.765 4.220 1.00 91.26 5 A 1 ATOM 42 N N . LEU A 1 6 ? -1.687 3.686 5.598 1.00 97.89 6 A 1 ATOM 43 C CA . LEU A 1 6 ? -0.368 3.865 5.005 1.00 97.90 6 A 1 ATOM 44 C C . LEU A 1 6 ? 0.257 2.509 4.704 1.00 98.20 6 A 1 ATOM 45 O O . LEU A 1 6 ? 0.792 2.286 3.612 1.00 97.96 6 A 1 ATOM 46 C CB . LEU A 1 6 ? 0.515 4.689 5.945 1.00 97.93 6 A 1 ATOM 47 C CG . LEU A 1 6 ? 1.826 5.189 5.334 1.00 94.27 6 A 1 ATOM 48 C CD1 . LEU A 1 6 ? 2.360 6.364 6.149 1.00 89.48 6 A 1 ATOM 49 C CD2 . LEU A 1 6 ? 2.877 4.092 5.287 1.00 90.66 6 A 1 ATOM 50 N N . ALA A 1 7 ? 0.186 1.594 5.678 1.00 98.34 7 A 1 ATOM 51 C CA . ALA A 1 7 ? 0.749 0.257 5.515 1.00 98.41 7 A 1 ATOM 52 C C . ALA A 1 7 ? 0.047 -0.500 4.392 1.00 98.50 7 A 1 ATOM 53 O O . ALA A 1 7 ? 0.691 -1.176 3.588 1.00 98.32 7 A 1 ATOM 54 C CB . ALA A 1 7 ? 0.629 -0.516 6.825 1.00 98.33 7 A 1 ATOM 55 N N . LEU A 1 8 ? -1.279 -0.379 4.335 1.00 98.64 8 A 1 ATOM 56 C CA . LEU A 1 8 ? -2.064 -1.053 3.307 1.00 98.60 8 A 1 ATOM 57 C C . LEU A 1 8 ? -1.703 -0.531 1.925 1.00 98.65 8 A 1 ATOM 58 O O . LEU A 1 8 ? -1.635 -1.296 0.958 1.00 98.46 8 A 1 ATOM 59 C CB . LEU A 1 8 ? -3.556 -0.846 3.574 1.00 98.44 8 A 1 ATOM 60 C CG . LEU A 1 8 ? -4.472 -1.590 2.603 1.00 95.77 8 A 1 ATOM 61 C CD1 . LEU A 1 8 ? -4.278 -3.089 2.720 1.00 91.89 8 A 1 ATOM 62 C CD2 . LEU A 1 8 ? -5.926 -1.226 2.868 1.00 92.68 8 A 1 ATOM 63 N N . SER A 1 9 ? -1.468 0.767 1.827 1.00 98.51 9 A 1 ATOM 64 C CA . SER A 1 9 ? -1.103 1.386 0.558 1.00 98.47 9 A 1 ATOM 65 C C . SER A 1 9 ? 0.230 0.839 0.051 1.00 98.59 9 A 1 ATOM 66 O O . SER A 1 9 ? 0.383 0.554 -1.136 1.00 98.45 9 A 1 ATOM 67 C CB . SER A 1 9 ? -1.015 2.901 0.714 1.00 98.21 9 A 1 ATOM 68 O OG . SER A 1 9 ? -2.279 3.441 1.058 1.00 91.30 9 A 1 ATOM 69 N N . LEU A 1 10 ? 1.191 0.677 0.966 1.00 98.41 10 A 1 ATOM 70 C CA . LEU A 1 10 ? 2.497 0.143 0.610 1.00 98.41 10 A 1 ATOM 71 C C . LEU A 1 10 ? 2.383 -1.308 0.161 1.00 98.53 10 A 1 ATOM 72 O O . LEU A 1 10 ? 3.030 -1.722 -0.808 1.00 98.33 10 A 1 ATOM 73 C CB . LEU A 1 10 ? 3.450 0.247 1.803 1.00 98.28 10 A 1 ATOM 74 C CG . LEU A 1 10 ? 3.843 1.680 2.171 1.00 97.01 10 A 1 ATOM 75 C CD1 . LEU A 1 10 ? 4.658 1.683 3.458 1.00 94.22 10 A 1 ATOM 76 C CD2 . LEU A 1 10 ? 4.637 2.333 1.051 1.00 94.76 10 A 1 ATOM 77 N N . LEU A 1 11 ? 1.552 -2.081 0.865 1.00 98.44 11 A 1 ATOM 78 C CA . LEU A 1 11 ? 1.346 -3.484 0.523 1.00 98.35 11 A 1 ATOM 79 C C . LEU A 1 11 ? 0.683 -3.610 -0.843 1.00 98.51 11 A 1 ATOM 80 O O . LEU A 1 11 ? 1.067 -4.458 -1.654 1.00 98.30 11 A 1 ATOM 81 C CB . LEU A 1 11 ? 0.485 -4.161 1.587 1.00 98.09 11 A 1 ATOM 82 C CG . LEU A 1 11 ? 1.183 -4.342 2.936 1.00 94.87 11 A 1 ATOM 83 C CD1 . LEU A 1 11 ? 0.194 -4.850 3.976 1.00 91.30 11 A 1 ATOM 84 C CD2 . LEU A 1 11 ? 2.352 -5.309 2.813 1.00 92.55 11 A 1 ATOM 85 N N . ALA A 1 12 ? -0.307 -2.764 -1.099 1.00 98.53 12 A 1 ATOM 86 C CA . ALA A 1 12 ? -1.006 -2.772 -2.379 1.00 98.48 12 A 1 ATOM 87 C C . ALA A 1 12 ? -0.040 -2.466 -3.518 1.00 98.59 12 A 1 ATOM 88 O O . ALA A 1 12 ? -0.086 -3.100 -4.575 1.00 98.19 12 A 1 ATOM 89 C CB . ALA A 1 12 ? -2.139 -1.750 -2.356 1.00 98.09 12 A 1 ATOM 90 N N . ALA A 1 13 ? 0.846 -1.503 -3.295 1.00 98.68 13 A 1 ATOM 91 C CA . ALA A 1 13 ? 1.848 -1.142 -4.291 1.00 98.62 13 A 1 ATOM 92 C C . ALA A 1 13 ? 2.800 -2.308 -4.539 1.00 98.71 13 A 1 ATOM 93 O O . ALA A 1 13 ? 3.212 -2.557 -5.674 1.00 98.28 13 A 1 ATOM 94 C CB . ALA A 1 13 ? 2.626 0.085 -3.825 1.00 98.24 13 A 1 ATOM 95 N N . GLY A 1 14 ? 3.145 -3.031 -3.473 1.00 98.66 14 A 1 ATOM 96 C CA . GLY A 1 14 ? 4.024 -4.189 -3.582 1.00 98.64 14 A 1 ATOM 97 C C . GLY A 1 14 ? 3.413 -5.291 -4.423 1.00 98.74 14 A 1 ATOM 98 O O . GLY A 1 14 ? 4.095 -5.930 -5.225 1.00 98.51 14 A 1 ATOM 99 N N . VAL A 1 15 ? 2.105 -5.517 -4.260 1.00 98.61 15 A 1 ATOM 100 C CA . VAL A 1 15 ? 1.388 -6.532 -5.033 1.00 98.58 15 A 1 ATOM 101 C C . VAL A 1 15 ? 1.438 -6.197 -6.517 1.00 98.66 15 A 1 ATOM 102 O O . VAL A 1 15 ? 1.652 -7.073 -7.360 1.00 98.22 15 A 1 ATOM 103 C CB . VAL A 1 15 ? -0.073 -6.648 -4.570 1.00 98.19 15 A 1 ATOM 104 C CG1 . VAL A 1 15 ? -0.857 -7.597 -5.470 1.00 96.10 15 A 1 ATOM 105 C CG2 . VAL A 1 15 ? -0.122 -7.137 -3.134 1.00 95.99 15 A 1 ATOM 106 N N . LEU A 1 16 ? 1.235 -4.933 -6.838 1.00 98.47 16 A 1 ATOM 107 C CA . LEU A 1 16 ? 1.269 -4.485 -8.225 1.00 98.34 16 A 1 ATOM 108 C C . LEU A 1 16 ? 2.676 -4.580 -8.796 1.00 98.40 16 A 1 ATOM 109 O O . LEU A 1 16 ? 2.855 -4.899 -9.974 1.00 97.94 16 A 1 ATOM 110 C CB . LEU A 1 16 ? 0.767 -3.041 -8.322 1.00 98.01 16 A 1 ATOM 111 C CG . LEU A 1 16 ? -0.712 -2.870 -7.983 1.00 95.20 16 A 1 ATOM 112 C CD1 . LEU A 1 16 ? -1.077 -1.392 -7.958 1.00 91.10 16 A 1 ATOM 113 C CD2 . LEU A 1 16 ? -1.585 -3.610 -8.982 1.00 91.18 16 A 1 ATOM 114 N N . ALA A 1 17 ? 3.679 -4.310 -7.970 1.00 98.44 17 A 1 ATOM 115 C CA . ALA A 1 17 ? 5.078 -4.385 -8.382 1.00 98.34 17 A 1 ATOM 116 C C . ALA A 1 17 ? 5.483 -5.822 -8.683 1.00 98.45 17 A 1 ATOM 117 O O . ALA A 1 17 ? 6.233 -6.077 -9.632 1.00 97.77 17 A 1 ATOM 118 C CB . ALA A 1 17 ? 5.978 -3.793 -7.299 1.00 97.80 17 A 1 ATOM 119 N N . GLY A 1 18 ? 4.952 -6.768 -7.877 1.00 96.51 18 A 1 ATOM 120 C CA . GLY A 1 18 ? 5.254 -8.188 -8.053 1.00 95.08 18 A 1 ATOM 121 C C . GLY A 1 18 ? 6.664 -8.536 -7.622 1.00 92.93 18 A 1 ATOM 122 O O . GLY A 1 18 ? 7.205 -9.547 -8.115 1.00 85.10 18 A 1 ATOM 123 O OXT . GLY A 1 18 ? 7.240 -7.854 -6.766 1.00 92.67 18 A 1 #