# 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_spkb12169 # _entry.id spkb12169 # 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" "C4 H8 N2 O3" 132.118 ASN y ASPARAGINE C([C@@H](C(=O)O)N)C(=O)N ? "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" "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 LYS 2 1 n ASN 3 1 n LEU 4 1 n PRO 5 1 n ILE 6 1 n LEU 7 1 n LEU 8 1 n LEU 9 1 n LEU 10 1 n CYS 11 1 n VAL 12 1 n ALA 13 1 n ALA 14 1 n CYS 15 1 n SER 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 @ 2025-07-03 15:04:06)" _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 94.53 _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 87.90 1 1 A LYS 2 2 87.34 1 2 A ASN 3 2 92.51 1 3 A LEU 4 2 94.16 1 4 A PRO 5 2 96.88 1 5 A ILE 6 2 96.11 1 6 A LEU 7 2 95.83 1 7 A LEU 8 2 95.56 1 8 A LEU 9 2 95.74 1 9 A LEU 10 2 95.89 1 10 A CYS 11 2 96.68 1 11 A VAL 12 2 97.25 1 12 A ALA 13 2 98.34 1 13 A ALA 14 2 98.10 1 14 A CYS 15 2 96.28 1 15 A SER 16 2 94.81 1 16 A ALA 17 2 92.43 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 ASN . 3 A 3 A 4 1 n LEU . 4 A 4 A 5 1 n PRO . 5 A 5 A 6 1 n ILE . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n CYS . 11 A 11 A 12 1 n VAL . 12 A 12 A 13 1 n ALA . 13 A 13 A 14 1 n ALA . 14 A 14 A 15 1 n CYS . 15 A 15 A 16 1 n SER . 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 ? -11.207 -3.643 3.779 1.00 93.68 1 A 1 ATOM 2 C CA . MET A 1 1 ? -9.953 -4.267 4.248 1.00 94.13 1 A 1 ATOM 3 C C . MET A 1 1 ? -9.067 -3.260 4.975 1.00 94.24 1 A 1 ATOM 4 O O . MET A 1 1 ? -9.002 -2.097 4.582 1.00 91.64 1 A 1 ATOM 5 C CB . MET A 1 1 ? -9.173 -4.830 3.068 1.00 91.74 1 A 1 ATOM 6 C CG . MET A 1 1 ? -9.801 -6.107 2.528 1.00 87.08 1 A 1 ATOM 7 S SD . MET A 1 1 ? -8.806 -6.818 1.213 1.00 80.06 1 A 1 ATOM 8 C CE . MET A 1 1 ? -9.765 -8.262 0.829 1.00 70.59 1 A 1 ATOM 9 N N . LYS A 1 2 ? -8.391 -3.702 6.022 1.00 93.57 2 A 1 ATOM 10 C CA . LYS A 1 2 ? -7.497 -2.833 6.799 1.00 94.26 2 A 1 ATOM 11 C C . LYS A 1 2 ? -6.120 -2.739 6.135 1.00 94.50 2 A 1 ATOM 12 O O . LYS A 1 2 ? -5.242 -2.019 6.612 1.00 93.51 2 A 1 ATOM 13 C CB . LYS A 1 2 ? -7.349 -3.378 8.216 1.00 92.34 2 A 1 ATOM 14 C CG . LYS A 1 2 ? -8.602 -3.279 9.064 1.00 85.60 2 A 1 ATOM 15 C CD . LYS A 1 2 ? -8.977 -1.838 9.347 1.00 83.16 2 A 1 ATOM 16 C CE . LYS A 1 2 ? -9.706 -1.701 10.666 1.00 77.20 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? -10.860 -2.636 10.758 1.00 71.89 2 A 1 ATOM 18 N N . ASN A 1 3 ? -5.926 -3.466 5.059 1.00 95.14 3 A 1 ATOM 19 C CA . ASN A 1 3 ? -4.643 -3.493 4.363 1.00 96.25 3 A 1 ATOM 20 C C . ASN A 1 3 ? -4.502 -2.307 3.414 1.00 96.77 3 A 1 ATOM 21 O O . ASN A 1 3 ? -3.425 -2.067 2.864 1.00 96.20 3 A 1 ATOM 22 C CB . ASN A 1 3 ? -4.493 -4.796 3.576 1.00 95.42 3 A 1 ATOM 23 C CG . ASN A 1 3 ? -4.846 -6.020 4.398 1.00 91.18 3 A 1 ATOM 24 O OD1 . ASN A 1 3 ? -5.850 -6.060 5.088 1.00 85.87 3 A 1 ATOM 25 N ND2 . ASN A 1 3 ? -4.019 -7.053 4.309 1.00 83.28 3 A 1 ATOM 26 N N . LEU A 1 4 ? -5.584 -1.580 3.224 1.00 96.98 4 A 1 ATOM 27 C CA . LEU A 1 4 ? -5.572 -0.423 2.335 1.00 97.19 4 A 1 ATOM 28 C C . LEU A 1 4 ? -4.564 0.640 2.782 1.00 97.69 4 A 1 ATOM 29 O O . LEU A 1 4 ? -3.804 1.153 1.958 1.00 97.23 4 A 1 ATOM 30 C CB . LEU A 1 4 ? -6.976 0.180 2.236 1.00 96.81 4 A 1 ATOM 31 C CG . LEU A 1 4 ? -7.397 0.489 0.804 1.00 92.97 4 A 1 ATOM 32 C CD1 . LEU A 1 4 ? -7.603 -0.801 0.024 1.00 87.54 4 A 1 ATOM 33 C CD2 . LEU A 1 4 ? -8.665 1.329 0.804 1.00 86.83 4 A 1 ATOM 34 N N . PRO A 1 5 ? -4.558 0.983 4.059 1.00 96.99 5 A 1 ATOM 35 C CA . PRO A 1 5 ? -3.620 2.000 4.570 1.00 97.26 5 A 1 ATOM 36 C C . PRO A 1 5 ? -2.165 1.623 4.318 1.00 97.74 5 A 1 ATOM 37 O O . PRO A 1 5 ? -1.315 2.490 4.104 1.00 97.46 5 A 1 ATOM 38 C CB . PRO A 1 5 ? -3.913 2.038 6.074 1.00 96.51 5 A 1 ATOM 39 C CG . PRO A 1 5 ? -5.296 1.495 6.210 1.00 95.53 5 A 1 ATOM 40 C CD . PRO A 1 5 ? -5.464 0.503 5.094 1.00 96.64 5 A 1 ATOM 41 N N . ILE A 1 6 ? -1.886 0.336 4.347 1.00 97.46 6 A 1 ATOM 42 C CA . ILE A 1 6 ? -0.526 -0.150 4.122 1.00 97.40 6 A 1 ATOM 43 C C . ILE A 1 6 ? -0.068 0.196 2.709 1.00 97.62 6 A 1 ATOM 44 O O . ILE A 1 6 ? 1.092 0.554 2.482 1.00 97.30 6 A 1 ATOM 45 C CB . ILE A 1 6 ? -0.449 -1.671 4.342 1.00 97.39 6 A 1 ATOM 46 C CG1 . ILE A 1 6 ? -0.879 -2.018 5.771 1.00 95.61 6 A 1 ATOM 47 C CG2 . ILE A 1 6 ? 0.969 -2.172 4.081 1.00 95.24 6 A 1 ATOM 48 C CD1 . ILE A 1 6 ? -0.988 -3.509 6.016 1.00 90.86 6 A 1 ATOM 49 N N . LEU A 1 7 ? -0.989 0.085 1.765 1.00 97.77 7 A 1 ATOM 50 C CA . LEU A 1 7 ? -0.675 0.400 0.374 1.00 97.76 7 A 1 ATOM 51 C C . LEU A 1 7 ? -0.287 1.868 0.240 1.00 97.98 7 A 1 ATOM 52 O O . LEU A 1 7 ? 0.614 2.217 -0.534 1.00 97.90 7 A 1 ATOM 53 C CB . LEU A 1 7 ? -1.886 0.094 -0.513 1.00 97.71 7 A 1 ATOM 54 C CG . LEU A 1 7 ? -2.317 -1.371 -0.504 1.00 93.81 7 A 1 ATOM 55 C CD1 . LEU A 1 7 ? -3.635 -1.538 -1.250 1.00 91.32 7 A 1 ATOM 56 C CD2 . LEU A 1 7 ? -1.240 -2.247 -1.136 1.00 92.42 7 A 1 ATOM 57 N N . LEU A 1 8 ? -0.964 2.709 0.988 1.00 97.60 8 A 1 ATOM 58 C CA . LEU A 1 8 ? -0.683 4.141 0.965 1.00 97.61 8 A 1 ATOM 59 C C . LEU A 1 8 ? 0.722 4.414 1.489 1.00 97.98 8 A 1 ATOM 60 O O . LEU A 1 8 ? 1.460 5.232 0.933 1.00 97.94 8 A 1 ATOM 61 C CB . LEU A 1 8 ? -1.721 4.895 1.811 1.00 97.55 8 A 1 ATOM 62 C CG . LEU A 1 8 ? -2.883 5.481 1.008 1.00 92.67 8 A 1 ATOM 63 C CD1 . LEU A 1 8 ? -2.375 6.562 0.073 1.00 90.74 8 A 1 ATOM 64 C CD2 . LEU A 1 8 ? -3.579 4.387 0.218 1.00 92.37 8 A 1 ATOM 65 N N . LEU A 1 9 ? 1.082 3.720 2.555 1.00 97.45 9 A 1 ATOM 66 C CA . LEU A 1 9 ? 2.406 3.881 3.148 1.00 97.52 9 A 1 ATOM 67 C C . LEU A 1 9 ? 3.490 3.446 2.170 1.00 97.94 9 A 1 ATOM 68 O O . LEU A 1 9 ? 4.551 4.074 2.088 1.00 97.82 9 A 1 ATOM 69 C CB . LEU A 1 9 ? 2.497 3.046 4.427 1.00 97.26 9 A 1 ATOM 70 C CG . LEU A 1 9 ? 1.638 3.577 5.568 1.00 93.15 9 A 1 ATOM 71 C CD1 . LEU A 1 9 ? 1.597 2.569 6.707 1.00 91.98 9 A 1 ATOM 72 C CD2 . LEU A 1 9 ? 2.177 4.906 6.068 1.00 92.80 9 A 1 ATOM 73 N N . LEU A 1 10 ? 3.219 2.381 1.433 1.00 97.82 10 A 1 ATOM 74 C CA . LEU A 1 10 ? 4.169 1.874 0.452 1.00 97.81 10 A 1 ATOM 75 C C . LEU A 1 10 ? 4.383 2.894 -0.659 1.00 98.14 10 A 1 ATOM 76 O O . LEU A 1 10 ? 5.506 3.111 -1.119 1.00 97.88 10 A 1 ATOM 77 C CB . LEU A 1 10 ? 3.660 0.550 -0.132 1.00 97.55 10 A 1 ATOM 78 C CG . LEU A 1 10 ? 4.340 -0.688 0.450 1.00 93.66 10 A 1 ATOM 79 C CD1 . LEU A 1 10 ? 5.799 -0.713 0.049 1.00 91.95 10 A 1 ATOM 80 C CD2 . LEU A 1 10 ? 4.203 -0.702 1.963 1.00 92.35 10 A 1 ATOM 81 N N . CYS A 1 11 ? 3.300 3.512 -1.076 1.00 97.63 11 A 1 ATOM 82 C CA . CYS A 1 11 ? 3.369 4.515 -2.132 1.00 97.79 11 A 1 ATOM 83 C C . CYS A 1 11 ? 4.187 5.723 -1.680 1.00 98.08 11 A 1 ATOM 84 O O . CYS A 1 11 ? 5.008 6.252 -2.430 1.00 97.39 11 A 1 ATOM 85 C CB . CYS A 1 11 ? 1.957 4.955 -2.525 1.00 97.11 11 A 1 ATOM 86 S SG . CYS A 1 11 ? 1.921 5.882 -4.068 1.00 92.09 11 A 1 ATOM 87 N N . VAL A 1 12 ? 3.952 6.146 -0.456 1.00 98.18 12 A 1 ATOM 88 C CA . VAL A 1 12 ? 4.678 7.289 0.098 1.00 98.17 12 A 1 ATOM 89 C C . VAL A 1 12 ? 6.156 6.953 0.267 1.00 98.38 12 A 1 ATOM 90 O O . VAL A 1 12 ? 7.031 7.780 -0.004 1.00 97.98 12 A 1 ATOM 91 C CB . VAL A 1 12 ? 4.082 7.712 1.447 1.00 97.57 12 A 1 ATOM 92 C CG1 . VAL A 1 12 ? 4.884 8.857 2.050 1.00 95.07 12 A 1 ATOM 93 C CG2 . VAL A 1 12 ? 2.631 8.125 1.271 1.00 95.42 12 A 1 ATOM 94 N N . ALA A 1 13 ? 6.416 5.739 0.721 1.00 98.47 13 A 1 ATOM 95 C CA . ALA A 1 13 ? 7.792 5.292 0.919 1.00 98.45 13 A 1 ATOM 96 C C . ALA A 1 13 ? 8.546 5.262 -0.407 1.00 98.56 13 A 1 ATOM 97 O O . ALA A 1 13 ? 9.712 5.650 -0.478 1.00 98.10 13 A 1 ATOM 98 C CB . ALA A 1 13 ? 7.799 3.910 1.558 1.00 98.11 13 A 1 ATOM 99 N N . ALA A 1 14 ? 7.877 4.801 -1.450 1.00 98.34 14 A 1 ATOM 100 C CA . ALA A 1 14 ? 8.486 4.728 -2.774 1.00 98.27 14 A 1 ATOM 101 C C . ALA A 1 14 ? 8.723 6.123 -3.342 1.00 98.34 14 A 1 ATOM 102 O O . ALA A 1 14 ? 9.739 6.377 -3.992 1.00 97.71 14 A 1 ATOM 103 C CB . ALA A 1 14 ? 7.595 3.917 -3.708 1.00 97.83 14 A 1 ATOM 104 N N . CYS A 1 15 ? 7.782 7.022 -3.101 1.00 97.40 15 A 1 ATOM 105 C CA . CYS A 1 15 ? 7.898 8.398 -3.576 1.00 97.42 15 A 1 ATOM 106 C C . CYS A 1 15 ? 8.952 9.173 -2.790 1.00 97.65 15 A 1 ATOM 107 O O . CYS A 1 15 ? 9.605 10.068 -3.322 1.00 96.47 15 A 1 ATOM 108 C CB . CYS A 1 15 ? 6.547 9.106 -3.461 1.00 96.32 15 A 1 ATOM 109 S SG . CYS A 1 15 ? 5.675 9.173 -5.042 1.00 92.40 15 A 1 ATOM 110 N N . SER A 1 16 ? 9.088 8.829 -1.527 1.00 97.04 16 A 1 ATOM 111 C CA . SER A 1 16 ? 10.042 9.500 -0.646 1.00 97.04 16 A 1 ATOM 112 C C . SER A 1 16 ? 11.410 8.816 -0.656 1.00 96.89 16 A 1 ATOM 113 O O . SER A 1 16 ? 12.363 9.297 -0.039 1.00 94.75 16 A 1 ATOM 114 C CB . SER A 1 16 ? 9.504 9.529 0.783 1.00 95.83 16 A 1 ATOM 115 O OG . SER A 1 16 ? 10.058 10.601 1.501 1.00 87.30 16 A 1 ATOM 116 N N . ALA A 1 17 ? 11.505 7.706 -1.351 1.00 96.16 17 A 1 ATOM 117 C CA . ALA A 1 17 ? 12.745 6.944 -1.401 1.00 95.41 17 A 1 ATOM 118 C C . ALA A 1 17 ? 13.697 7.526 -2.440 1.00 94.93 17 A 1 ATOM 119 O O . ALA A 1 17 ? 13.265 7.764 -3.578 1.00 91.33 17 A 1 ATOM 120 C CB . ALA A 1 17 ? 12.465 5.478 -1.691 1.00 92.92 17 A 1 ATOM 121 O OXT . ALA A 1 17 ? 14.875 7.720 -2.115 1.00 83.83 17 A 1 #