# 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_spkb30904 # _entry.id spkb30904 # 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" "C5 H10 N2 O3" 146.144 GLN y GLUTAMINE C(CC(=O)N)[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" "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 ILE 2 1 n THR 3 1 n VAL 4 1 n PHE 5 1 n VAL 6 1 n ALA 7 1 n CYS 8 1 n LEU 9 1 n PHE 10 1 n GLN 11 1 n CYS 12 1 n VAL 13 1 n SER 14 1 n SER 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 @ 2025-07-13 05:50:29)" _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 92.59 _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 86.25 1 1 A ILE 2 2 90.92 1 2 A THR 3 2 94.04 1 3 A VAL 4 2 95.27 1 4 A PHE 5 2 92.85 1 5 A VAL 6 2 96.46 1 6 A ALA 7 2 96.99 1 7 A CYS 8 2 95.73 1 8 A LEU 9 2 94.66 1 9 A PHE 10 2 92.78 1 10 A GLN 11 2 92.29 1 11 A CYS 12 2 95.10 1 12 A VAL 13 2 93.57 1 13 A SER 14 2 91.42 1 14 A SER 15 2 83.04 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 THR . 3 A 3 A 4 1 n VAL . 4 A 4 A 5 1 n PHE . 5 A 5 A 6 1 n VAL . 6 A 6 A 7 1 n ALA . 7 A 7 A 8 1 n CYS . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n PHE . 10 A 10 A 11 1 n GLN . 11 A 11 A 12 1 n CYS . 12 A 12 A 13 1 n VAL . 13 A 13 A 14 1 n SER . 14 A 14 A 15 1 n SER . 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 ? 3.320 -1.738 10.746 1.00 90.96 1 A 1 ATOM 2 C CA . MET A 1 1 ? 3.261 -0.311 10.373 1.00 92.19 1 A 1 ATOM 3 C C . MET A 1 1 ? 3.481 -0.138 8.870 1.00 92.02 1 A 1 ATOM 4 O O . MET A 1 1 ? 2.781 0.635 8.216 1.00 91.35 1 A 1 ATOM 5 C CB . MET A 1 1 ? 4.308 0.492 11.159 1.00 88.39 1 A 1 ATOM 6 C CG . MET A 1 1 ? 3.964 0.605 12.641 1.00 82.90 1 A 1 ATOM 7 S SD . MET A 1 1 ? 5.231 1.469 13.575 1.00 80.26 1 A 1 ATOM 8 C CE . MET A 1 1 ? 4.455 1.553 15.191 1.00 71.95 1 A 1 ATOM 9 N N . ILE A 1 2 ? 4.430 -0.871 8.345 1.00 90.80 2 A 1 ATOM 10 C CA . ILE A 1 2 ? 4.710 -0.816 6.914 1.00 93.92 2 A 1 ATOM 11 C C . ILE A 1 2 ? 3.675 -1.601 6.111 1.00 95.54 2 A 1 ATOM 12 O O . ILE A 1 2 ? 3.424 -1.308 4.939 1.00 94.90 2 A 1 ATOM 13 C CB . ILE A 1 2 ? 6.123 -1.356 6.606 1.00 92.86 2 A 1 ATOM 14 C CG1 . ILE A 1 2 ? 6.336 -2.730 7.242 1.00 88.65 2 A 1 ATOM 15 C CG2 . ILE A 1 2 ? 7.183 -0.360 7.077 1.00 87.78 2 A 1 ATOM 16 C CD1 . ILE A 1 2 ? 7.474 -3.504 6.613 1.00 82.90 2 A 1 ATOM 17 N N . THR A 1 3 ? 3.072 -2.584 6.751 1.00 95.46 3 A 1 ATOM 18 C CA . THR A 1 3 ? 2.055 -3.415 6.113 1.00 96.20 3 A 1 ATOM 19 C C . THR A 1 3 ? 0.847 -2.573 5.705 1.00 96.71 3 A 1 ATOM 20 O O . THR A 1 3 ? 0.233 -2.802 4.658 1.00 96.06 3 A 1 ATOM 21 C CB . THR A 1 3 ? 1.592 -4.544 7.056 1.00 95.49 3 A 1 ATOM 22 O OG1 . THR A 1 3 ? 2.593 -4.831 8.032 1.00 89.35 3 A 1 ATOM 23 C CG2 . THR A 1 3 ? 1.276 -5.805 6.268 1.00 89.00 3 A 1 ATOM 24 N N . VAL A 1 4 ? 0.513 -1.608 6.525 1.00 96.86 4 A 1 ATOM 25 C CA . VAL A 1 4 ? -0.611 -0.709 6.255 1.00 96.82 4 A 1 ATOM 26 C C . VAL A 1 4 ? -0.307 0.166 5.040 1.00 97.12 4 A 1 ATOM 27 O O . VAL A 1 4 ? -1.200 0.503 4.257 1.00 96.36 4 A 1 ATOM 28 C CB . VAL A 1 4 ? -0.925 0.177 7.481 1.00 95.95 4 A 1 ATOM 29 C CG1 . VAL A 1 4 ? -2.178 1.016 7.241 1.00 91.68 4 A 1 ATOM 30 C CG2 . VAL A 1 4 ? -1.098 -0.673 8.732 1.00 92.13 4 A 1 ATOM 31 N N . PHE A 1 5 ? 0.956 0.520 4.883 1.00 94.76 5 A 1 ATOM 32 C CA . PHE A 1 5 ? 1.392 1.336 3.754 1.00 95.22 5 A 1 ATOM 33 C C . PHE A 1 5 ? 1.164 0.602 2.441 1.00 96.18 5 A 1 ATOM 34 O O . PHE A 1 5 ? 0.680 1.182 1.467 1.00 95.80 5 A 1 ATOM 35 C CB . PHE A 1 5 ? 2.875 1.693 3.906 1.00 95.34 5 A 1 ATOM 36 C CG . PHE A 1 5 ? 3.103 3.111 4.378 1.00 93.53 5 A 1 ATOM 37 C CD1 . PHE A 1 5 ? 2.823 3.479 5.683 1.00 90.66 5 A 1 ATOM 38 C CD2 . PHE A 1 5 ? 3.599 4.065 3.497 1.00 90.92 5 A 1 ATOM 39 C CE1 . PHE A 1 5 ? 3.026 4.783 6.113 1.00 89.82 5 A 1 ATOM 40 C CE2 . PHE A 1 5 ? 3.810 5.370 3.925 1.00 89.13 5 A 1 ATOM 41 C CZ . PHE A 1 5 ? 3.524 5.731 5.230 1.00 89.94 5 A 1 ATOM 42 N N . VAL A 1 6 ? 1.494 -0.674 2.432 1.00 97.30 6 A 1 ATOM 43 C CA . VAL A 1 6 ? 1.325 -1.504 1.243 1.00 97.50 6 A 1 ATOM 44 C C . VAL A 1 6 ? -0.154 -1.654 0.900 1.00 97.73 6 A 1 ATOM 45 O O . VAL A 1 6 ? -0.541 -1.626 -0.270 1.00 97.33 6 A 1 ATOM 46 C CB . VAL A 1 6 ? 1.953 -2.896 1.447 1.00 97.10 6 A 1 ATOM 47 C CG1 . VAL A 1 6 ? 1.873 -3.712 0.167 1.00 93.96 6 A 1 ATOM 48 C CG2 . VAL A 1 6 ? 3.399 -2.765 1.902 1.00 94.27 6 A 1 ATOM 49 N N . ALA A 1 7 ? -0.972 -1.823 1.928 1.00 97.38 7 A 1 ATOM 50 C CA . ALA A 1 7 ? -2.412 -1.970 1.748 1.00 97.07 7 A 1 ATOM 51 C C . ALA A 1 7 ? -3.030 -0.693 1.177 1.00 97.28 7 A 1 ATOM 52 O O . ALA A 1 7 ? -3.885 -0.746 0.294 1.00 96.54 7 A 1 ATOM 53 C CB . ALA A 1 7 ? -3.064 -2.325 3.082 1.00 96.68 7 A 1 ATOM 54 N N . CYS A 1 8 ? -2.588 0.435 1.686 1.00 96.74 8 A 1 ATOM 55 C CA . CYS A 1 8 ? -3.086 1.728 1.231 1.00 96.70 8 A 1 ATOM 56 C C . CYS A 1 8 ? -2.686 1.985 -0.220 1.00 97.15 8 A 1 ATOM 57 O O . CYS A 1 8 ? -3.487 2.463 -1.022 1.00 96.22 8 A 1 ATOM 58 C CB . CYS A 1 8 ? -2.551 2.844 2.138 1.00 95.83 8 A 1 ATOM 59 S SG . CYS A 1 8 ? -3.415 4.409 1.912 1.00 91.72 8 A 1 ATOM 60 N N . LEU A 1 9 ? -1.444 1.649 -0.542 1.00 96.19 9 A 1 ATOM 61 C CA . LEU A 1 9 ? -0.938 1.822 -1.901 1.00 96.47 9 A 1 ATOM 62 C C . LEU A 1 9 ? -1.675 0.914 -2.876 1.00 97.07 9 A 1 ATOM 63 O O . LEU A 1 9 ? -2.024 1.323 -3.984 1.00 96.76 9 A 1 ATOM 64 C CB . LEU A 1 9 ? 0.567 1.523 -1.940 1.00 96.21 9 A 1 ATOM 65 C CG . LEU A 1 9 ? 1.456 2.748 -1.753 1.00 92.88 9 A 1 ATOM 66 C CD1 . LEU A 1 9 ? 2.861 2.330 -1.325 1.00 90.90 9 A 1 ATOM 67 C CD2 . LEU A 1 9 ? 1.527 3.553 -3.048 1.00 90.84 9 A 1 ATOM 68 N N . PHE A 1 10 ? -1.915 -0.324 -2.449 1.00 95.80 10 A 1 ATOM 69 C CA . PHE A 1 10 ? -2.619 -1.298 -3.274 1.00 95.56 10 A 1 ATOM 70 C C . PHE A 1 10 ? -4.035 -0.821 -3.582 1.00 96.08 10 A 1 ATOM 71 O O . PHE A 1 10 ? -4.528 -0.980 -4.698 1.00 95.31 10 A 1 ATOM 72 C CB . PHE A 1 10 ? -2.665 -2.648 -2.559 1.00 95.48 10 A 1 ATOM 73 C CG . PHE A 1 10 ? -3.011 -3.785 -3.487 1.00 92.68 10 A 1 ATOM 74 C CD1 . PHE A 1 10 ? -4.333 -4.149 -3.693 1.00 90.18 10 A 1 ATOM 75 C CD2 . PHE A 1 10 ? -2.012 -4.474 -4.155 1.00 90.51 10 A 1 ATOM 76 C CE1 . PHE A 1 10 ? -4.658 -5.184 -4.556 1.00 89.45 10 A 1 ATOM 77 C CE2 . PHE A 1 10 ? -2.335 -5.515 -5.021 1.00 89.73 10 A 1 ATOM 78 C CZ . PHE A 1 10 ? -3.655 -5.867 -5.219 1.00 89.81 10 A 1 ATOM 79 N N . GLN A 1 11 ? -4.685 -0.247 -2.584 1.00 97.34 11 A 1 ATOM 80 C CA . GLN A 1 11 ? -6.039 0.274 -2.750 1.00 97.01 11 A 1 ATOM 81 C C . GLN A 1 11 ? -6.057 1.494 -3.661 1.00 97.12 11 A 1 ATOM 82 O O . GLN A 1 11 ? -6.957 1.651 -4.485 1.00 95.48 11 A 1 ATOM 83 C CB . GLN A 1 11 ? -6.630 0.642 -1.383 1.00 96.43 11 A 1 ATOM 84 C CG . GLN A 1 11 ? -7.378 -0.510 -0.736 1.00 91.69 11 A 1 ATOM 85 C CD . GLN A 1 11 ? -8.867 -0.440 -1.058 1.00 89.28 11 A 1 ATOM 86 O OE1 . GLN A 1 11 ? -9.486 0.622 -0.959 1.00 84.66 11 A 1 ATOM 87 N NE2 . GLN A 1 11 ? -9.462 -1.556 -1.431 1.00 81.64 11 A 1 ATOM 88 N N . CYS A 1 12 ? -5.062 2.338 -3.523 1.00 95.90 12 A 1 ATOM 89 C CA . CYS A 1 12 ? -4.964 3.553 -4.327 1.00 96.30 12 A 1 ATOM 90 C C . CYS A 1 12 ? -4.770 3.226 -5.806 1.00 96.61 12 A 1 ATOM 91 O O . CYS A 1 12 ? -5.331 3.892 -6.675 1.00 95.07 12 A 1 ATOM 92 C CB . CYS A 1 12 ? -3.809 4.427 -3.827 1.00 95.24 12 A 1 ATOM 93 S SG . CYS A 1 12 ? -3.860 6.088 -4.508 1.00 91.48 12 A 1 ATOM 94 N N . VAL A 1 13 ? -3.977 2.199 -6.081 1.00 96.24 13 A 1 ATOM 95 C CA . VAL A 1 13 ? -3.698 1.799 -7.459 1.00 95.82 13 A 1 ATOM 96 C C . VAL A 1 13 ? -4.809 0.921 -8.031 1.00 95.73 13 A 1 ATOM 97 O O . VAL A 1 13 ? -5.139 1.015 -9.217 1.00 94.39 13 A 1 ATOM 98 C CB . VAL A 1 13 ? -2.354 1.050 -7.558 1.00 94.66 13 A 1 ATOM 99 C CG1 . VAL A 1 13 ? -2.044 0.699 -9.007 1.00 88.69 13 A 1 ATOM 100 C CG2 . VAL A 1 13 ? -1.228 1.888 -6.980 1.00 89.44 13 A 1 ATOM 101 N N . SER A 1 14 ? -5.369 0.070 -7.183 1.00 95.23 14 A 1 ATOM 102 C CA . SER A 1 14 ? -6.406 -0.863 -7.611 1.00 94.39 14 A 1 ATOM 103 C C . SER A 1 14 ? -7.809 -0.263 -7.526 1.00 92.98 14 A 1 ATOM 104 O O . SER A 1 14 ? -8.767 -0.829 -8.046 1.00 90.12 14 A 1 ATOM 105 C CB . SER A 1 14 ? -6.345 -2.138 -6.769 1.00 92.15 14 A 1 ATOM 106 O OG . SER A 1 14 ? -6.991 -3.203 -7.427 1.00 83.66 14 A 1 ATOM 107 N N . SER A 1 15 ? -7.912 0.873 -6.895 1.00 92.54 15 A 1 ATOM 108 C CA . SER A 1 15 ? -9.213 1.517 -6.708 1.00 89.38 15 A 1 ATOM 109 C C . SER A 1 15 ? -9.281 2.849 -7.453 1.00 85.02 15 A 1 ATOM 110 O O . SER A 1 15 ? -9.881 3.809 -6.949 1.00 77.74 15 A 1 ATOM 111 C CB . SER A 1 15 ? -9.500 1.714 -5.221 1.00 83.91 15 A 1 ATOM 112 O OG . SER A 1 15 ? -10.899 1.753 -4.995 1.00 75.55 15 A 1 ATOM 113 O OXT . SER A 1 15 ? -8.747 2.891 -8.587 1.00 77.12 15 A 1 #