# 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_spkb41891 # _entry.id spkb41891 # 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" "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" "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 ILE 2 1 n ALA 3 1 n LEU 4 1 n LEU 5 1 n ILE 6 1 n LEU 7 1 n SER 8 1 n LEU 9 1 n THR 10 1 n CYS 11 1 n SER 12 1 n ALA 13 1 n SER 14 1 n THR 15 # _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 @ 2025-07-10 04:03:41)" _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 94.45 _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 89.02 1 1 A ILE 2 2 95.21 1 2 A ALA 3 2 97.67 1 3 A LEU 4 2 95.58 1 4 A LEU 5 2 95.36 1 5 A ILE 6 2 96.82 1 6 A LEU 7 2 96.13 1 7 A SER 8 2 96.63 1 8 A LEU 9 2 95.86 1 9 A THR 10 2 95.49 1 10 A CYS 11 2 94.51 1 11 A SER 12 2 93.02 1 12 A ALA 13 2 94.43 1 13 A SER 14 2 92.95 1 14 A THR 15 2 89.18 1 15 # _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 ILE . 2 A 2 A 3 1 n ALA . 3 A 3 A 4 1 n LEU . 4 A 4 A 5 1 n LEU . 5 A 5 A 6 1 n ILE . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n SER . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n THR . 10 A 10 A 11 1 n CYS . 11 A 11 A 12 1 n SER . 12 A 12 A 13 1 n ALA . 13 A 13 A 14 1 n SER . 14 A 14 A 15 1 n THR . 15 A 15 # _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 ? -11.827 2.899 4.701 1.00 93.92 1 A 1 ATOM 2 C CA . MET A 1 1 ? -10.451 3.320 4.399 1.00 94.28 1 A 1 ATOM 3 C C . MET A 1 1 ? -9.493 2.133 4.507 1.00 94.33 1 A 1 ATOM 4 O O . MET A 1 1 ? -8.358 2.271 4.955 1.00 93.99 1 A 1 ATOM 5 C CB . MET A 1 1 ? -10.012 4.421 5.369 1.00 90.94 1 A 1 ATOM 6 C CG . MET A 1 1 ? -10.924 5.632 5.332 1.00 85.59 1 A 1 ATOM 7 S SD . MET A 1 1 ? -10.530 6.803 6.638 1.00 83.86 1 A 1 ATOM 8 C CE . MET A 1 1 ? -11.802 8.029 6.358 1.00 75.27 1 A 1 ATOM 9 N N . ILE A 1 2 ? -9.980 0.971 4.103 1.00 95.90 2 A 1 ATOM 10 C CA . ILE A 1 2 ? -9.188 -0.256 4.188 1.00 97.07 2 A 1 ATOM 11 C C . ILE A 1 2 ? -8.084 -0.265 3.133 1.00 97.83 2 A 1 ATOM 12 O O . ILE A 1 2 ? -6.951 -0.668 3.401 1.00 97.65 2 A 1 ATOM 13 C CB . ILE A 1 2 ? -10.091 -1.482 4.009 1.00 96.54 2 A 1 ATOM 14 C CG1 . ILE A 1 2 ? -11.264 -1.430 4.986 1.00 94.26 2 A 1 ATOM 15 C CG2 . ILE A 1 2 ? -9.276 -2.755 4.235 1.00 93.22 2 A 1 ATOM 16 C CD1 . ILE A 1 2 ? -12.383 -2.364 4.597 1.00 89.22 2 A 1 ATOM 17 N N . ALA A 1 3 ? -8.429 0.181 1.923 1.00 97.55 3 A 1 ATOM 18 C CA . ALA A 1 3 ? -7.464 0.207 0.825 1.00 97.75 3 A 1 ATOM 19 C C . ALA A 1 3 ? -6.274 1.110 1.147 1.00 98.08 3 A 1 ATOM 20 O O . ALA A 1 3 ? -5.144 0.834 0.742 1.00 97.69 3 A 1 ATOM 21 C CB . ALA A 1 3 ? -8.155 0.676 -0.451 1.00 97.28 3 A 1 ATOM 22 N N . LEU A 1 4 ? -6.531 2.180 1.875 1.00 97.97 4 A 1 ATOM 23 C CA . LEU A 1 4 ? -5.474 3.120 2.249 1.00 97.89 4 A 1 ATOM 24 C C . LEU A 1 4 ? -4.426 2.440 3.121 1.00 98.07 4 A 1 ATOM 25 O O . LEU A 1 4 ? -3.225 2.659 2.947 1.00 97.78 4 A 1 ATOM 26 C CB . LEU A 1 4 ? -6.084 4.312 2.992 1.00 97.47 4 A 1 ATOM 27 C CG . LEU A 1 4 ? -6.849 5.278 2.089 1.00 92.90 4 A 1 ATOM 28 C CD1 . LEU A 1 4 ? -7.688 6.237 2.930 1.00 91.35 4 A 1 ATOM 29 C CD2 . LEU A 1 4 ? -5.884 6.066 1.214 1.00 91.17 4 A 1 ATOM 30 N N . LEU A 1 5 ? -4.877 1.612 4.051 1.00 97.68 5 A 1 ATOM 31 C CA . LEU A 1 5 ? -3.970 0.887 4.937 1.00 97.61 5 A 1 ATOM 32 C C . LEU A 1 5 ? -3.138 -0.118 4.150 1.00 97.95 5 A 1 ATOM 33 O O . LEU A 1 5 ? -1.938 -0.265 4.380 1.00 97.81 5 A 1 ATOM 34 C CB . LEU A 1 5 ? -4.759 0.171 6.033 1.00 97.37 5 A 1 ATOM 35 C CG . LEU A 1 5 ? -5.010 1.027 7.274 1.00 92.61 5 A 1 ATOM 36 C CD1 . LEU A 1 5 ? -6.076 2.084 6.998 1.00 90.64 5 A 1 ATOM 37 C CD2 . LEU A 1 5 ? -5.425 0.155 8.448 1.00 91.21 5 A 1 ATOM 38 N N . ILE A 1 6 ? -3.785 -0.807 3.219 1.00 97.97 6 A 1 ATOM 39 C CA . ILE A 1 6 ? -3.105 -1.800 2.393 1.00 97.90 6 A 1 ATOM 40 C C . ILE A 1 6 ? -2.043 -1.130 1.526 1.00 97.97 6 A 1 ATOM 41 O O . ILE A 1 6 ? -0.924 -1.636 1.392 1.00 97.68 6 A 1 ATOM 42 C CB . ILE A 1 6 ? -4.116 -2.548 1.507 1.00 97.74 6 A 1 ATOM 43 C CG1 . ILE A 1 6 ? -5.162 -3.256 2.369 1.00 96.45 6 A 1 ATOM 44 C CG2 . ILE A 1 6 ? -3.384 -3.567 0.626 1.00 96.12 6 A 1 ATOM 45 C CD1 . ILE A 1 6 ? -6.335 -3.780 1.563 1.00 92.77 6 A 1 ATOM 46 N N . LEU A 1 7 ? -2.397 0.003 0.936 1.00 98.12 7 A 1 ATOM 47 C CA . LEU A 1 7 ? -1.465 0.743 0.089 1.00 97.80 7 A 1 ATOM 48 C C . LEU A 1 7 ? -0.263 1.219 0.893 1.00 97.94 7 A 1 ATOM 49 O O . LEU A 1 7 ? 0.875 1.161 0.430 1.00 97.78 7 A 1 ATOM 50 C CB . LEU A 1 7 ? -2.179 1.940 -0.557 1.00 97.52 7 A 1 ATOM 51 C CG . LEU A 1 7 ? -2.678 1.697 -1.982 1.00 94.07 7 A 1 ATOM 52 C CD1 . LEU A 1 7 ? -1.509 1.506 -2.930 1.00 92.64 7 A 1 ATOM 53 C CD2 . LEU A 1 7 ? -3.598 0.493 -2.032 1.00 93.18 7 A 1 ATOM 54 N N . SER A 1 8 ? -0.522 1.689 2.100 1.00 97.61 8 A 1 ATOM 55 C CA . SER A 1 8 ? 0.541 2.170 2.979 1.00 97.35 8 A 1 ATOM 56 C C . SER A 1 8 ? 1.527 1.046 3.291 1.00 97.51 8 A 1 ATOM 57 O O . SER A 1 8 ? 2.743 1.251 3.274 1.00 97.05 8 A 1 ATOM 58 C CB . SER A 1 8 ? -0.059 2.724 4.275 1.00 96.93 8 A 1 ATOM 59 O OG . SER A 1 8 ? 0.943 3.350 5.045 1.00 93.32 8 A 1 ATOM 60 N N . LEU A 1 9 ? 1.006 -0.154 3.558 1.00 97.79 9 A 1 ATOM 61 C CA . LEU A 1 9 ? 1.848 -1.312 3.855 1.00 97.60 9 A 1 ATOM 62 C C . LEU A 1 9 ? 2.587 -1.774 2.607 1.00 97.79 9 A 1 ATOM 63 O O . LEU A 1 9 ? 3.756 -2.155 2.667 1.00 97.25 9 A 1 ATOM 64 C CB . LEU A 1 9 ? 0.991 -2.454 4.417 1.00 97.37 9 A 1 ATOM 65 C CG . LEU A 1 9 ? 1.001 -2.547 5.942 1.00 94.84 9 A 1 ATOM 66 C CD1 . LEU A 1 9 ? 2.375 -2.943 6.443 1.00 92.28 9 A 1 ATOM 67 C CD2 . LEU A 1 9 ? 0.568 -1.234 6.569 1.00 91.93 9 A 1 ATOM 68 N N . THR A 1 10 ? 1.890 -1.740 1.472 1.00 97.68 10 A 1 ATOM 69 C CA . THR A 1 10 ? 2.480 -2.161 0.203 1.00 97.33 10 A 1 ATOM 70 C C . THR A 1 10 ? 3.632 -1.242 -0.194 1.00 96.98 10 A 1 ATOM 71 O O . THR A 1 10 ? 4.618 -1.691 -0.779 1.00 95.43 10 A 1 ATOM 72 C CB . THR A 1 10 ? 1.423 -2.155 -0.907 1.00 96.49 10 A 1 ATOM 73 O OG1 . THR A 1 10 ? 0.289 -2.908 -0.501 1.00 92.42 10 A 1 ATOM 74 C CG2 . THR A 1 10 ? 1.992 -2.767 -2.184 1.00 92.07 10 A 1 ATOM 75 N N . CYS A 1 11 ? 3.513 0.041 0.122 1.00 96.13 11 A 1 ATOM 76 C CA . CYS A 1 11 ? 4.561 1.008 -0.200 1.00 95.80 11 A 1 ATOM 77 C C . CYS A 1 11 ? 5.876 0.629 0.478 1.00 95.75 11 A 1 ATOM 78 O O . CYS A 1 11 ? 6.940 0.690 -0.130 1.00 94.85 11 A 1 ATOM 79 C CB . CYS A 1 11 ? 4.129 2.410 0.236 1.00 94.32 11 A 1 ATOM 80 S SG . CYS A 1 11 ? 2.912 3.135 -0.876 1.00 90.20 11 A 1 ATOM 81 N N . SER A 1 12 ? 5.786 0.239 1.738 1.00 95.06 12 A 1 ATOM 82 C CA . SER A 1 12 ? 6.965 -0.168 2.497 1.00 95.48 12 A 1 ATOM 83 C C . SER A 1 12 ? 7.515 -1.491 1.980 1.00 95.97 12 A 1 ATOM 84 O O . SER A 1 12 ? 8.728 -1.691 1.910 1.00 94.89 12 A 1 ATOM 85 C CB . SER A 1 12 ? 6.623 -0.294 3.977 1.00 93.65 12 A 1 ATOM 86 O OG . SER A 1 12 ? 7.796 -0.547 4.720 1.00 83.05 12 A 1 ATOM 87 N N . ALA A 1 13 ? 6.614 -2.407 1.614 1.00 95.07 13 A 1 ATOM 88 C CA . ALA A 1 13 ? 7.001 -3.720 1.102 1.00 94.67 13 A 1 ATOM 89 C C . ALA A 1 13 ? 7.582 -3.624 -0.305 1.00 95.19 13 A 1 ATOM 90 O O . ALA A 1 13 ? 8.369 -4.475 -0.716 1.00 94.32 13 A 1 ATOM 91 C CB . ALA A 1 13 ? 5.791 -4.655 1.108 1.00 92.88 13 A 1 ATOM 92 N N . SER A 1 14 ? 7.180 -2.596 -1.045 1.00 95.27 14 A 1 ATOM 93 C CA . SER A 1 14 ? 7.667 -2.390 -2.408 1.00 95.28 14 A 1 ATOM 94 C C . SER A 1 14 ? 9.158 -2.078 -2.416 1.00 95.27 14 A 1 ATOM 95 O O . SER A 1 14 ? 9.887 -2.468 -3.326 1.00 92.41 14 A 1 ATOM 96 C CB . SER A 1 14 ? 6.902 -1.255 -3.079 1.00 93.64 14 A 1 ATOM 97 O OG . SER A 1 14 ? 7.289 -1.134 -4.425 1.00 85.83 14 A 1 ATOM 98 N N . THR A 1 15 ? 9.610 -1.375 -1.393 1.00 95.14 15 A 1 ATOM 99 C CA . THR A 1 15 ? 11.012 -0.990 -1.279 1.00 94.22 15 A 1 ATOM 100 C C . THR A 1 15 ? 11.848 -2.089 -0.636 1.00 92.70 15 A 1 ATOM 101 O O . THR A 1 15 ? 11.319 -2.800 0.240 1.00 88.21 15 A 1 ATOM 102 C CB . THR A 1 15 ? 11.155 0.289 -0.444 1.00 90.16 15 A 1 ATOM 103 O OG1 . THR A 1 15 ? 10.478 0.134 0.799 1.00 84.06 15 A 1 ATOM 104 C CG2 . THR A 1 15 ? 10.583 1.472 -1.190 1.00 85.44 15 A 1 ATOM 105 O OXT . THR A 1 15 ? 13.042 -2.220 -0.982 1.00 83.54 15 A 1 #