# 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_spkb30334 # _entry.id spkb30334 # 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" "C5 H10 N2 O3" 146.144 GLN y GLUTAMINE C(CC(=O)N)[C@@H](C(=O)O)N ? "L-PEPTIDE LINKING" "C5 H9 N O4" 147.129 GLU y "GLUTAMIC ACID" C(CC(=O)O)[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" "C5 H11 N O2 S" 149.211 MET y METHIONINE CSCC[C@@H](C(=O)O)N ? "L-PEPTIDE LINKING" "C9 H11 N O2" 165.189 PHE y PHENYLALANINE c1ccc(cc1)C[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" "C9 H11 N O3" 181.189 TYR y TYROSINE c1cc(ccc1C[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 PHE 2 1 n LEU 3 1 n ILE 4 1 n TYR 5 1 n LEU 6 1 n LEU 7 1 n VAL 8 1 n GLN 9 1 n THR 10 1 n ALA 11 1 n GLU 12 1 n SER 13 # _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 @ 2025-07-12 15:04:41)" _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 93.56 _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 91.45 1 1 A PHE 2 2 94.03 1 2 A LEU 3 2 94.47 1 3 A ILE 4 2 96.20 1 4 A TYR 5 2 94.96 1 5 A LEU 6 2 96.28 1 6 A LEU 7 2 96.28 1 7 A VAL 8 2 97.18 1 8 A GLN 9 2 94.26 1 9 A THR 10 2 95.34 1 10 A ALA 11 2 96.48 1 11 A GLU 12 2 85.75 1 12 A SER 13 2 84.21 1 13 # _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 PHE . 2 A 2 A 3 1 n LEU . 3 A 3 A 4 1 n ILE . 4 A 4 A 5 1 n TYR . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n VAL . 8 A 8 A 9 1 n GLN . 9 A 9 A 10 1 n THR . 10 A 10 A 11 1 n ALA . 11 A 11 A 12 1 n GLU . 12 A 12 A 13 1 n SER . 13 A 13 # _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 ? 4.913 7.334 4.451 1.00 94.65 1 A 1 ATOM 2 C CA . MET A 1 1 ? 4.519 5.999 4.951 1.00 95.81 1 A 1 ATOM 3 C C . MET A 1 1 ? 4.285 5.030 3.793 1.00 96.32 1 A 1 ATOM 4 O O . MET A 1 1 ? 3.785 5.422 2.749 1.00 95.01 1 A 1 ATOM 5 C CB . MET A 1 1 ? 3.237 6.088 5.777 1.00 93.14 1 A 1 ATOM 6 C CG . MET A 1 1 ? 3.470 6.611 7.190 1.00 89.30 1 A 1 ATOM 7 S SD . MET A 1 1 ? 3.709 8.376 7.234 1.00 87.88 1 A 1 ATOM 8 C CE . MET A 1 1 ? 3.681 8.656 9.000 1.00 79.46 1 A 1 ATOM 9 N N . PHE A 1 2 ? 4.647 3.767 3.995 1.00 96.09 2 A 1 ATOM 10 C CA . PHE A 1 2 ? 4.444 2.732 2.984 1.00 97.07 2 A 1 ATOM 11 C C . PHE A 1 2 ? 3.400 1.711 3.441 1.00 97.87 2 A 1 ATOM 12 O O . PHE A 1 2 ? 2.808 1.016 2.619 1.00 97.60 2 A 1 ATOM 13 C CB . PHE A 1 2 ? 5.766 2.031 2.680 1.00 96.34 2 A 1 ATOM 14 C CG . PHE A 1 2 ? 6.168 1.024 3.722 1.00 94.69 2 A 1 ATOM 15 C CD1 . PHE A 1 2 ? 6.688 1.432 4.932 1.00 92.39 2 A 1 ATOM 16 C CD2 . PHE A 1 2 ? 6.010 -0.321 3.477 1.00 92.00 2 A 1 ATOM 17 C CE1 . PHE A 1 2 ? 7.056 0.511 5.890 1.00 90.78 2 A 1 ATOM 18 C CE2 . PHE A 1 2 ? 6.376 -1.255 4.434 1.00 89.59 2 A 1 ATOM 19 C CZ . PHE A 1 2 ? 6.899 -0.834 5.637 1.00 89.96 2 A 1 ATOM 20 N N . LEU A 1 3 ? 3.196 1.610 4.739 1.00 97.07 3 A 1 ATOM 21 C CA . LEU A 1 3 ? 2.209 0.688 5.299 1.00 97.49 3 A 1 ATOM 22 C C . LEU A 1 3 ? 0.816 1.013 4.774 1.00 97.88 3 A 1 ATOM 23 O O . LEU A 1 3 ? 0.054 0.133 4.383 1.00 97.54 3 A 1 ATOM 24 C CB . LEU A 1 3 ? 2.224 0.759 6.833 1.00 97.02 3 A 1 ATOM 25 C CG . LEU A 1 3 ? 2.851 -0.452 7.525 1.00 91.29 3 A 1 ATOM 26 C CD1 . LEU A 1 3 ? 2.079 -1.707 7.228 1.00 88.90 3 A 1 ATOM 27 C CD2 . LEU A 1 3 ? 4.304 -0.599 7.108 1.00 88.55 3 A 1 ATOM 28 N N . ILE A 1 4 ? 0.507 2.302 4.769 1.00 97.91 4 A 1 ATOM 29 C CA . ILE A 1 4 ? -0.784 2.767 4.272 1.00 98.06 4 A 1 ATOM 30 C C . ILE A 1 4 ? -0.900 2.501 2.773 1.00 98.22 4 A 1 ATOM 31 O O . ILE A 1 4 ? -1.967 2.143 2.270 1.00 97.82 4 A 1 ATOM 32 C CB . ILE A 1 4 ? -0.968 4.267 4.555 1.00 97.71 4 A 1 ATOM 33 C CG1 . ILE A 1 4 ? -0.833 4.555 6.051 1.00 95.16 4 A 1 ATOM 34 C CG2 . ILE A 1 4 ? -2.341 4.726 4.056 1.00 94.43 4 A 1 ATOM 35 C CD1 . ILE A 1 4 ? -0.712 6.035 6.351 1.00 90.28 4 A 1 ATOM 36 N N . TYR A 1 5 ? 0.204 2.665 2.067 1.00 97.67 5 A 1 ATOM 37 C CA . TYR A 1 5 ? 0.243 2.428 0.626 1.00 97.64 5 A 1 ATOM 38 C C . TYR A 1 5 ? -0.080 0.969 0.310 1.00 97.78 5 A 1 ATOM 39 O O . TYR A 1 5 ? -0.879 0.675 -0.583 1.00 97.59 5 A 1 ATOM 40 C CB . TYR A 1 5 ? 1.627 2.785 0.094 1.00 97.38 5 A 1 ATOM 41 C CG . TYR A 1 5 ? 1.703 2.695 -1.409 1.00 96.08 5 A 1 ATOM 42 C CD1 . TYR A 1 5 ? 1.899 1.474 -2.039 1.00 94.12 5 A 1 ATOM 43 C CD2 . TYR A 1 5 ? 1.574 3.838 -2.192 1.00 93.74 5 A 1 ATOM 44 C CE1 . TYR A 1 5 ? 1.952 1.391 -3.420 1.00 92.49 5 A 1 ATOM 45 C CE2 . TYR A 1 5 ? 1.634 3.757 -3.574 1.00 92.30 5 A 1 ATOM 46 C CZ . TYR A 1 5 ? 1.820 2.532 -4.178 1.00 91.92 5 A 1 ATOM 47 O OH . TYR A 1 5 ? 1.874 2.446 -5.543 1.00 90.83 5 A 1 ATOM 48 N N . LEU A 1 6 ? 0.530 0.070 1.037 1.00 97.87 6 A 1 ATOM 49 C CA . LEU A 1 6 ? 0.304 -1.359 0.846 1.00 97.84 6 A 1 ATOM 50 C C . LEU A 1 6 ? -1.132 -1.737 1.190 1.00 98.08 6 A 1 ATOM 51 O O . LEU A 1 6 ? -1.750 -2.562 0.527 1.00 97.81 6 A 1 ATOM 52 C CB . LEU A 1 6 ? 1.270 -2.155 1.720 1.00 97.55 6 A 1 ATOM 53 C CG . LEU A 1 6 ? 2.094 -3.186 0.962 1.00 95.28 6 A 1 ATOM 54 C CD1 . LEU A 1 6 ? 1.209 -4.251 0.353 1.00 93.03 6 A 1 ATOM 55 C CD2 . LEU A 1 6 ? 2.914 -2.497 -0.121 1.00 92.81 6 A 1 ATOM 56 N N . LEU A 1 7 ? -1.642 -1.130 2.241 1.00 97.92 7 A 1 ATOM 57 C CA . LEU A 1 7 ? -3.007 -1.390 2.690 1.00 97.87 7 A 1 ATOM 58 C C . LEU A 1 7 ? -4.017 -0.968 1.631 1.00 97.85 7 A 1 ATOM 59 O O . LEU A 1 7 ? -4.983 -1.687 1.358 1.00 97.35 7 A 1 ATOM 60 C CB . LEU A 1 7 ? -3.270 -0.652 4.009 1.00 97.66 7 A 1 ATOM 61 C CG . LEU A 1 7 ? -4.557 -1.059 4.727 1.00 94.78 7 A 1 ATOM 62 C CD1 . LEU A 1 7 ? -4.384 -0.905 6.231 1.00 93.41 7 A 1 ATOM 63 C CD2 . LEU A 1 7 ? -5.735 -0.219 4.258 1.00 93.42 7 A 1 ATOM 64 N N . VAL A 1 8 ? -3.793 0.192 1.038 1.00 98.03 8 A 1 ATOM 65 C CA . VAL A 1 8 ? -4.696 0.697 0.009 1.00 97.93 8 A 1 ATOM 66 C C . VAL A 1 8 ? -4.555 -0.105 -1.280 1.00 97.75 8 A 1 ATOM 67 O O . VAL A 1 8 ? -5.535 -0.340 -1.988 1.00 96.99 8 A 1 ATOM 68 C CB . VAL A 1 8 ? -4.432 2.185 -0.269 1.00 97.55 8 A 1 ATOM 69 C CG1 . VAL A 1 8 ? -5.333 2.695 -1.381 1.00 95.87 8 A 1 ATOM 70 C CG2 . VAL A 1 8 ? -4.648 3.007 0.992 1.00 96.11 8 A 1 ATOM 71 N N . GLN A 1 9 ? -3.342 -0.539 -1.577 1.00 97.87 9 A 1 ATOM 72 C CA . GLN A 1 9 ? -3.080 -1.318 -2.785 1.00 97.67 9 A 1 ATOM 73 C C . GLN A 1 9 ? -3.781 -2.667 -2.740 1.00 97.69 9 A 1 ATOM 74 O O . GLN A 1 9 ? -4.393 -3.092 -3.715 1.00 96.88 9 A 1 ATOM 75 C CB . GLN A 1 9 ? -1.582 -1.517 -2.958 1.00 97.24 9 A 1 ATOM 76 C CG . GLN A 1 9 ? -0.863 -0.257 -3.383 1.00 93.95 9 A 1 ATOM 77 C CD . GLN A 1 9 ? -1.245 0.152 -4.794 1.00 93.22 9 A 1 ATOM 78 O OE1 . GLN A 1 9 ? -2.066 1.039 -4.995 1.00 87.70 9 A 1 ATOM 79 N NE2 . GLN A 1 9 ? -0.663 -0.494 -5.779 1.00 86.13 9 A 1 ATOM 80 N N . THR A 1 10 ? -3.693 -3.340 -1.614 1.00 97.65 10 A 1 ATOM 81 C CA . THR A 1 10 ? -4.319 -4.649 -1.456 1.00 97.50 10 A 1 ATOM 82 C C . THR A 1 10 ? -5.835 -4.534 -1.376 1.00 97.24 10 A 1 ATOM 83 O O . THR A 1 10 ? -6.555 -5.439 -1.793 1.00 95.60 10 A 1 ATOM 84 C CB . THR A 1 10 ? -3.802 -5.365 -0.202 1.00 96.53 10 A 1 ATOM 85 O OG1 . THR A 1 10 ? -4.302 -6.704 -0.189 1.00 91.44 10 A 1 ATOM 86 C CG2 . THR A 1 10 ? -4.245 -4.663 1.064 1.00 91.42 10 A 1 ATOM 87 N N . ALA A 1 11 ? -6.322 -3.431 -0.822 1.00 97.58 11 A 1 ATOM 88 C CA . ALA A 1 11 ? -7.757 -3.207 -0.691 1.00 97.05 11 A 1 ATOM 89 C C . ALA A 1 11 ? -8.370 -2.779 -2.016 1.00 96.58 11 A 1 ATOM 90 O O . ALA A 1 11 ? -9.519 -3.100 -2.310 1.00 94.73 11 A 1 ATOM 91 C CB . ALA A 1 11 ? -8.037 -2.152 0.376 1.00 96.44 11 A 1 ATOM 92 N N . GLU A 1 12 ? -7.594 -2.058 -2.813 1.00 95.31 12 A 1 ATOM 93 C CA . GLU A 1 12 ? -8.069 -1.581 -4.110 1.00 93.55 12 A 1 ATOM 94 C C . GLU A 1 12 ? -8.112 -2.711 -5.126 1.00 91.05 12 A 1 ATOM 95 O O . GLU A 1 12 ? -9.102 -2.885 -5.833 1.00 85.25 12 A 1 ATOM 96 C CB . GLU A 1 12 ? -7.178 -0.449 -4.622 1.00 91.04 12 A 1 ATOM 97 C CG . GLU A 1 12 ? -7.602 0.103 -5.970 1.00 83.72 12 A 1 ATOM 98 C CD . GLU A 1 12 ? -8.920 0.856 -5.905 1.00 80.12 12 A 1 ATOM 99 O OE1 . GLU A 1 12 ? -9.884 0.332 -5.330 1.00 75.61 12 A 1 ATOM 100 O OE2 . GLU A 1 12 ? -8.983 1.971 -6.451 1.00 76.11 12 A 1 ATOM 101 N N . SER A 1 13 ? -7.024 -3.462 -5.187 1.00 92.12 13 A 1 ATOM 102 C CA . SER A 1 13 ? -6.921 -4.578 -6.122 1.00 89.48 13 A 1 ATOM 103 C C . SER A 1 13 ? -7.310 -4.159 -7.548 1.00 85.58 13 A 1 ATOM 104 O O . SER A 1 13 ? -8.211 -4.746 -8.147 1.00 79.24 13 A 1 ATOM 105 C CB . SER A 1 13 ? -7.815 -5.727 -5.674 1.00 85.74 13 A 1 ATOM 106 O OG . SER A 1 13 ? -7.598 -6.851 -6.495 1.00 79.94 13 A 1 ATOM 107 O OXT . SER A 1 13 ? -6.701 -3.188 -8.053 1.00 77.38 13 A 1 #