# 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_spkb09033 # _entry.id spkb09033 # 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" "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" "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 ASN 2 1 n GLY 3 1 n LYS 4 1 n LEU 5 1 n GLY 6 1 n ALA 7 1 n VAL 8 1 n LEU 9 1 n ALA 10 1 n LEU 11 1 n LEU 12 1 n LEU 13 1 n VAL 14 1 n SER 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 @ 2025-07-05 12:58:09)" _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 92.89 _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 79.57 1 1 A ASN 2 2 84.59 1 2 A GLY 3 2 93.06 1 3 A LYS 4 2 91.37 1 4 A LEU 5 2 93.53 1 5 A GLY 6 2 96.48 1 6 A ALA 7 2 96.79 1 7 A VAL 8 2 96.09 1 8 A LEU 9 2 94.76 1 9 A ALA 10 2 97.23 1 10 A LEU 11 2 95.43 1 11 A LEU 12 2 96.09 1 12 A LEU 13 2 95.62 1 13 A VAL 14 2 96.00 1 14 A SER 15 2 95.66 1 15 A ALA 16 2 89.93 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 ASN . 2 A 2 A 3 1 n GLY . 3 A 3 A 4 1 n LYS . 4 A 4 A 5 1 n LEU . 5 A 5 A 6 1 n GLY . 6 A 6 A 7 1 n ALA . 7 A 7 A 8 1 n VAL . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n ALA . 10 A 10 A 11 1 n LEU . 11 A 11 A 12 1 n LEU . 12 A 12 A 13 1 n LEU . 13 A 13 A 14 1 n VAL . 14 A 14 A 15 1 n SER . 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 ? 1.258 8.132 16.817 1.00 83.92 1 A 1 ATOM 2 C CA . MET A 1 1 ? 0.626 7.147 15.924 1.00 86.25 1 A 1 ATOM 3 C C . MET A 1 1 ? 0.794 7.568 14.472 1.00 87.54 1 A 1 ATOM 4 O O . MET A 1 1 ? 0.183 8.537 14.026 1.00 84.01 1 A 1 ATOM 5 C CB . MET A 1 1 ? -0.858 7.014 16.263 1.00 81.39 1 A 1 ATOM 6 C CG . MET A 1 1 ? -1.484 5.788 15.656 1.00 78.80 1 A 1 ATOM 7 S SD . MET A 1 1 ? -3.208 5.565 16.122 1.00 71.84 1 A 1 ATOM 8 C CE . MET A 1 1 ? -3.027 5.185 17.854 1.00 62.84 1 A 1 ATOM 9 N N . ASN A 1 2 ? 1.632 6.866 13.741 1.00 85.59 2 A 1 ATOM 10 C CA . ASN A 1 2 ? 1.909 7.187 12.347 1.00 88.89 2 A 1 ATOM 11 C C . ASN A 1 2 ? 1.136 6.264 11.409 1.00 90.21 2 A 1 ATOM 12 O O . ASN A 1 2 ? 0.959 5.080 11.697 1.00 88.19 2 A 1 ATOM 13 C CB . ASN A 1 2 ? 3.410 7.066 12.078 1.00 85.43 2 A 1 ATOM 14 C CG . ASN A 1 2 ? 4.215 8.063 12.886 1.00 82.49 2 A 1 ATOM 15 O OD1 . ASN A 1 2 ? 3.732 9.131 13.241 1.00 79.17 2 A 1 ATOM 16 N ND2 . ASN A 1 2 ? 5.458 7.719 13.175 1.00 76.78 2 A 1 ATOM 17 N N . GLY A 1 3 ? 0.674 6.810 10.290 1.00 91.20 3 A 1 ATOM 18 C CA . GLY A 1 3 ? -0.072 6.034 9.303 1.00 93.02 3 A 1 ATOM 19 C C . GLY A 1 3 ? 0.763 5.723 8.072 1.00 94.80 3 A 1 ATOM 20 O O . GLY A 1 3 ? 0.261 5.767 6.953 1.00 93.23 3 A 1 ATOM 21 N N . LYS A 1 4 ? 2.034 5.424 8.290 1.00 95.55 4 A 1 ATOM 22 C CA . LYS A 1 4 ? 2.957 5.144 7.192 1.00 96.50 4 A 1 ATOM 23 C C . LYS A 1 4 ? 2.557 3.865 6.466 1.00 96.89 4 A 1 ATOM 24 O O . LYS A 1 4 ? 2.707 3.764 5.249 1.00 96.26 4 A 1 ATOM 25 C CB . LYS A 1 4 ? 4.388 5.033 7.728 1.00 95.74 4 A 1 ATOM 26 C CG . LYS A 1 4 ? 5.417 5.388 6.673 1.00 91.87 4 A 1 ATOM 27 C CD . LYS A 1 4 ? 6.560 6.200 7.265 1.00 88.13 4 A 1 ATOM 28 C CE . LYS A 1 4 ? 7.363 6.893 6.177 1.00 83.58 4 A 1 ATOM 29 N NZ . LYS A 1 4 ? 8.415 7.786 6.763 1.00 77.79 4 A 1 ATOM 30 N N . LEU A 1 5 ? 2.028 2.895 7.209 1.00 95.16 5 A 1 ATOM 31 C CA . LEU A 1 5 ? 1.583 1.632 6.628 1.00 95.79 5 A 1 ATOM 32 C C . LEU A 1 5 ? 0.475 1.868 5.606 1.00 96.37 5 A 1 ATOM 33 O O . LEU A 1 5 ? 0.432 1.215 4.563 1.00 96.06 5 A 1 ATOM 34 C CB . LEU A 1 5 ? 1.094 0.696 7.736 1.00 95.19 5 A 1 ATOM 35 C CG . LEU A 1 5 ? 2.204 0.175 8.650 1.00 92.40 5 A 1 ATOM 36 C CD1 . LEU A 1 5 ? 1.605 -0.587 9.821 1.00 89.45 5 A 1 ATOM 37 C CD2 . LEU A 1 5 ? 3.163 -0.711 7.876 1.00 87.83 5 A 1 ATOM 38 N N . GLY A 1 6 ? -0.419 2.811 5.915 1.00 95.90 6 A 1 ATOM 39 C CA . GLY A 1 6 ? -1.510 3.147 5.003 1.00 96.15 6 A 1 ATOM 40 C C . GLY A 1 6 ? -0.993 3.724 3.699 1.00 96.97 6 A 1 ATOM 41 O O . GLY A 1 6 ? -1.470 3.382 2.618 1.00 96.90 6 A 1 ATOM 42 N N . ALA A 1 7 ? 0.002 4.602 3.797 1.00 96.24 7 A 1 ATOM 43 C CA . ALA A 1 7 ? 0.604 5.221 2.618 1.00 96.89 7 A 1 ATOM 44 C C . ALA A 1 7 ? 1.306 4.175 1.752 1.00 97.56 7 A 1 ATOM 45 O O . ALA A 1 7 ? 1.185 4.190 0.525 1.00 96.98 7 A 1 ATOM 46 C CB . ALA A 1 7 ? 1.595 6.298 3.045 1.00 96.28 7 A 1 ATOM 47 N N . VAL A 1 8 ? 2.026 3.269 2.400 1.00 96.42 8 A 1 ATOM 48 C CA . VAL A 1 8 ? 2.741 2.205 1.695 1.00 96.86 8 A 1 ATOM 49 C C . VAL A 1 8 ? 1.757 1.271 1.006 1.00 97.30 8 A 1 ATOM 50 O O . VAL A 1 8 ? 1.979 0.846 -0.132 1.00 96.95 8 A 1 ATOM 51 C CB . VAL A 1 8 ? 3.638 1.409 2.660 1.00 96.43 8 A 1 ATOM 52 C CG1 . VAL A 1 8 ? 4.263 0.210 1.957 1.00 94.58 8 A 1 ATOM 53 C CG2 . VAL A 1 8 ? 4.729 2.308 3.223 1.00 94.10 8 A 1 ATOM 54 N N . LEU A 1 9 ? 0.669 0.957 1.697 1.00 97.02 9 A 1 ATOM 55 C CA . LEU A 1 9 ? -0.359 0.074 1.150 1.00 96.89 9 A 1 ATOM 56 C C . LEU A 1 9 ? -0.980 0.681 -0.101 1.00 97.45 9 A 1 ATOM 57 O O . LEU A 1 9 ? -1.197 -0.013 -1.097 1.00 97.59 9 A 1 ATOM 58 C CB . LEU A 1 9 ? -1.438 -0.178 2.201 1.00 96.37 9 A 1 ATOM 59 C CG . LEU A 1 9 ? -2.507 -1.172 1.768 1.00 91.79 9 A 1 ATOM 60 C CD1 . LEU A 1 9 ? -1.927 -2.567 1.637 1.00 90.24 9 A 1 ATOM 61 C CD2 . LEU A 1 9 ? -3.668 -1.174 2.753 1.00 90.73 9 A 1 ATOM 62 N N . ALA A 1 10 ? -1.268 1.976 -0.046 1.00 97.06 10 A 1 ATOM 63 C CA . ALA A 1 10 ? -1.854 2.682 -1.183 1.00 97.31 10 A 1 ATOM 64 C C . ALA A 1 10 ? -0.901 2.675 -2.376 1.00 97.78 10 A 1 ATOM 65 O O . ALA A 1 10 ? -1.316 2.432 -3.510 1.00 97.20 10 A 1 ATOM 66 C CB . ALA A 1 10 ? -2.191 4.115 -0.786 1.00 96.81 10 A 1 ATOM 67 N N . LEU A 1 11 ? 0.368 2.926 -2.108 1.00 97.40 11 A 1 ATOM 68 C CA . LEU A 1 11 ? 1.388 2.947 -3.156 1.00 97.39 11 A 1 ATOM 69 C C . LEU A 1 11 ? 1.545 1.572 -3.791 1.00 97.85 11 A 1 ATOM 70 O O . LEU A 1 11 ? 1.658 1.449 -5.014 1.00 97.46 11 A 1 ATOM 71 C CB . LEU A 1 11 ? 2.724 3.410 -2.573 1.00 96.91 11 A 1 ATOM 72 C CG . LEU A 1 11 ? 3.829 3.610 -3.608 1.00 92.84 11 A 1 ATOM 73 C CD1 . LEU A 1 11 ? 3.482 4.764 -4.546 1.00 91.51 11 A 1 ATOM 74 C CD2 . LEU A 1 11 ? 5.161 3.879 -2.926 1.00 92.07 11 A 1 ATOM 75 N N . LEU A 1 12 ? 1.550 0.542 -2.947 1.00 97.84 12 A 1 ATOM 76 C CA . LEU A 1 12 ? 1.687 -0.835 -3.416 1.00 97.92 12 A 1 ATOM 77 C C . LEU A 1 12 ? 0.495 -1.241 -4.272 1.00 98.19 12 A 1 ATOM 78 O O . LEU A 1 12 ? 0.654 -1.898 -5.303 1.00 97.97 12 A 1 ATOM 79 C CB . LEU A 1 12 ? 1.817 -1.777 -2.220 1.00 97.70 12 A 1 ATOM 80 C CG . LEU A 1 12 ? 2.187 -3.209 -2.595 1.00 94.68 12 A 1 ATOM 81 C CD1 . LEU A 1 12 ? 3.610 -3.278 -3.129 1.00 91.87 12 A 1 ATOM 82 C CD2 . LEU A 1 12 ? 2.040 -4.127 -1.389 1.00 92.53 12 A 1 ATOM 83 N N . LEU A 1 13 ? -0.695 -0.844 -3.847 1.00 97.87 13 A 1 ATOM 84 C CA . LEU A 1 13 ? -1.924 -1.162 -4.572 1.00 97.84 13 A 1 ATOM 85 C C . LEU A 1 13 ? -1.919 -0.529 -5.958 1.00 98.03 13 A 1 ATOM 86 O O . LEU A 1 13 ? -2.319 -1.156 -6.941 1.00 97.61 13 A 1 ATOM 87 C CB . LEU A 1 13 ? -3.137 -0.675 -3.778 1.00 97.47 13 A 1 ATOM 88 C CG . LEU A 1 13 ? -4.482 -1.091 -4.364 1.00 93.36 13 A 1 ATOM 89 C CD1 . LEU A 1 13 ? -4.671 -2.597 -4.256 1.00 91.31 13 A 1 ATOM 90 C CD2 . LEU A 1 13 ? -5.621 -0.369 -3.658 1.00 91.47 13 A 1 ATOM 91 N N . VAL A 1 14 ? -1.464 0.715 -6.042 1.00 97.99 14 A 1 ATOM 92 C CA . VAL A 1 14 ? -1.390 1.431 -7.318 1.00 97.76 14 A 1 ATOM 93 C C . VAL A 1 14 ? -0.378 0.772 -8.251 1.00 97.87 14 A 1 ATOM 94 O O . VAL A 1 14 ? -0.568 0.745 -9.473 1.00 96.73 14 A 1 ATOM 95 C CB . VAL A 1 14 ? -1.021 2.907 -7.091 1.00 96.69 14 A 1 ATOM 96 C CG1 . VAL A 1 14 ? -0.768 3.619 -8.415 1.00 91.83 14 A 1 ATOM 97 C CG2 . VAL A 1 14 ? -2.124 3.618 -6.329 1.00 93.10 14 A 1 ATOM 98 N N . SER A 1 15 ? 0.685 0.232 -7.679 1.00 97.62 15 A 1 ATOM 99 C CA . SER A 1 15 ? 1.729 -0.434 -8.460 1.00 97.49 15 A 1 ATOM 100 C C . SER A 1 15 ? 1.190 -1.667 -9.183 1.00 97.51 15 A 1 ATOM 101 O O . SER A 1 15 ? 1.652 -2.002 -10.277 1.00 95.92 15 A 1 ATOM 102 C CB . SER A 1 15 ? 2.888 -0.833 -7.550 1.00 96.37 15 A 1 ATOM 103 O OG . SER A 1 15 ? 3.499 0.314 -6.993 1.00 89.06 15 A 1 ATOM 104 N N . ALA A 1 16 ? 0.205 -2.331 -8.571 1.00 94.95 16 A 1 ATOM 105 C CA . ALA A 1 16 ? -0.386 -3.540 -9.132 1.00 93.58 16 A 1 ATOM 106 C C . ALA A 1 16 ? -1.909 -3.426 -9.168 1.00 91.87 16 A 1 ATOM 107 O O . ALA A 1 16 ? -2.532 -3.310 -8.109 1.00 88.31 16 A 1 ATOM 108 C CB . ALA A 1 16 ? 0.032 -4.755 -8.322 1.00 89.81 16 A 1 ATOM 109 O OXT . ALA A 1 16 ? -2.491 -3.443 -10.255 1.00 81.05 16 A 1 #