# 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_spkb33612 # _entry.id spkb33612 # 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" "C2 H5 N O2" 75.067 GLY y GLYCINE C(C(=O)O)N ? "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 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 MET 3 1 n ILE 4 1 n LEU 5 1 n ALA 6 1 n LEU 7 1 n VAL 8 1 n VAL 9 1 n LEU 10 1 n GLY 11 1 n LEU 12 1 n VAL 13 1 n LEU 14 1 n VAL 15 1 n ALA 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 @ 2025-07-13 01:01:35)" _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 95.92 _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 88.95 1 1 A LYS 2 2 93.08 1 2 A MET 3 2 94.24 1 3 A ILE 4 2 97.00 1 4 A LEU 5 2 95.27 1 5 A ALA 6 2 98.54 1 6 A LEU 7 2 96.83 1 7 A VAL 8 2 98.21 1 8 A VAL 9 2 98.03 1 9 A LEU 10 2 96.23 1 10 A GLY 11 2 98.47 1 11 A LEU 12 2 96.45 1 12 A VAL 13 2 98.04 1 13 A LEU 14 2 96.00 1 14 A VAL 15 2 97.47 1 15 A ALA 16 2 98.08 1 16 A ALA 17 2 93.68 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 MET . 3 A 3 A 4 1 n ILE . 4 A 4 A 5 1 n LEU . 5 A 5 A 6 1 n ALA . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n VAL . 8 A 8 A 9 1 n VAL . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n GLY . 11 A 11 A 12 1 n LEU . 12 A 12 A 13 1 n VAL . 13 A 13 A 14 1 n LEU . 14 A 14 A 15 1 n VAL . 15 A 15 A 16 1 n ALA . 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 ? -2.739 -11.363 7.318 1.00 94.79 1 A 1 ATOM 2 C CA . MET A 1 1 ? -2.355 -9.963 7.538 1.00 95.35 1 A 1 ATOM 3 C C . MET A 1 1 ? -2.306 -9.192 6.216 1.00 95.80 1 A 1 ATOM 4 O O . MET A 1 1 ? -1.367 -8.445 5.945 1.00 93.78 1 A 1 ATOM 5 C CB . MET A 1 1 ? -0.987 -9.886 8.221 1.00 91.95 1 A 1 ATOM 6 C CG . MET A 1 1 ? -1.023 -10.345 9.667 1.00 86.92 1 A 1 ATOM 7 S SD . MET A 1 1 ? -1.592 -9.056 10.761 1.00 81.69 1 A 1 ATOM 8 C CE . MET A 1 1 ? -1.424 -9.872 12.340 1.00 71.30 1 A 1 ATOM 9 N N . LYS A 1 2 ? -3.325 -9.397 5.408 1.00 97.69 2 A 1 ATOM 10 C CA . LYS A 1 2 ? -3.404 -8.728 4.111 1.00 97.99 2 A 1 ATOM 11 C C . LYS A 1 2 ? -3.944 -7.308 4.250 1.00 98.18 2 A 1 ATOM 12 O O . LYS A 1 2 ? -3.764 -6.483 3.357 1.00 97.71 2 A 1 ATOM 13 C CB . LYS A 1 2 ? -4.291 -9.537 3.166 1.00 97.37 2 A 1 ATOM 14 C CG . LYS A 1 2 ? -3.765 -10.939 2.881 1.00 94.18 2 A 1 ATOM 15 C CD . LYS A 1 2 ? -2.530 -10.911 1.999 1.00 90.53 2 A 1 ATOM 16 C CE . LYS A 1 2 ? -2.097 -12.316 1.614 1.00 85.03 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? -0.900 -12.301 0.739 1.00 79.06 2 A 1 ATOM 18 N N . MET A 1 3 ? -4.617 -7.038 5.373 1.00 97.95 3 A 1 ATOM 19 C CA . MET A 1 3 ? -5.218 -5.722 5.614 1.00 98.14 3 A 1 ATOM 20 C C . MET A 1 3 ? -4.149 -4.634 5.685 1.00 98.37 3 A 1 ATOM 21 O O . MET A 1 3 ? -4.298 -3.561 5.103 1.00 97.85 3 A 1 ATOM 22 C CB . MET A 1 3 ? -6.035 -5.751 6.908 1.00 97.56 3 A 1 ATOM 23 C CG . MET A 1 3 ? -7.201 -6.719 6.846 1.00 94.47 3 A 1 ATOM 24 S SD . MET A 1 3 ? -8.474 -6.227 5.691 1.00 89.74 3 A 1 ATOM 25 C CE . MET A 1 3 ? -9.340 -5.008 6.658 1.00 79.84 3 A 1 ATOM 26 N N . ILE A 1 4 ? -3.074 -4.932 6.400 1.00 98.05 4 A 1 ATOM 27 C CA . ILE A 1 4 ? -1.972 -3.981 6.535 1.00 98.13 4 A 1 ATOM 28 C C . ILE A 1 4 ? -1.324 -3.733 5.177 1.00 98.29 4 A 1 ATOM 29 O O . ILE A 1 4 ? -1.039 -2.593 4.804 1.00 98.07 4 A 1 ATOM 30 C CB . ILE A 1 4 ? -0.925 -4.487 7.546 1.00 98.08 4 A 1 ATOM 31 C CG1 . ILE A 1 4 ? -1.556 -4.632 8.937 1.00 96.60 4 A 1 ATOM 32 C CG2 . ILE A 1 4 ? 0.260 -3.523 7.606 1.00 95.96 4 A 1 ATOM 33 C CD1 . ILE A 1 4 ? -0.655 -5.349 9.926 1.00 92.78 4 A 1 ATOM 34 N N . LEU A 1 5 ? -1.101 -4.813 4.440 1.00 98.15 5 A 1 ATOM 35 C CA . LEU A 1 5 ? -0.500 -4.717 3.112 1.00 98.18 5 A 1 ATOM 36 C C . LEU A 1 5 ? -1.380 -3.881 2.190 1.00 98.36 5 A 1 ATOM 37 O O . LEU A 1 5 ? -0.881 -3.071 1.408 1.00 98.29 5 A 1 ATOM 38 C CB . LEU A 1 5 ? -0.299 -6.119 2.530 1.00 97.97 5 A 1 ATOM 39 C CG . LEU A 1 5 ? 0.568 -6.141 1.277 1.00 91.67 5 A 1 ATOM 40 C CD1 . LEU A 1 5 ? 2.014 -5.821 1.609 1.00 89.18 5 A 1 ATOM 41 C CD2 . LEU A 1 5 ? 0.473 -7.498 0.593 1.00 90.32 5 A 1 ATOM 42 N N . ALA A 1 6 ? -2.684 -4.078 2.292 1.00 98.59 6 A 1 ATOM 43 C CA . ALA A 1 6 ? -3.641 -3.336 1.477 1.00 98.60 6 A 1 ATOM 44 C C . ALA A 1 6 ? -3.560 -1.837 1.761 1.00 98.66 6 A 1 ATOM 45 O O . ALA A 1 6 ? -3.611 -1.020 0.843 1.00 98.46 6 A 1 ATOM 46 C CB . ALA A 1 6 ? -5.054 -3.847 1.743 1.00 98.41 6 A 1 ATOM 47 N N . LEU A 1 7 ? -3.423 -1.495 3.040 1.00 98.63 7 A 1 ATOM 48 C CA . LEU A 1 7 ? -3.312 -0.094 3.440 1.00 98.66 7 A 1 ATOM 49 C C . LEU A 1 7 ? -2.034 0.528 2.888 1.00 98.75 7 A 1 ATOM 50 O O . LEU A 1 7 ? -2.047 1.658 2.395 1.00 98.66 7 A 1 ATOM 51 C CB . LEU A 1 7 ? -3.329 0.012 4.966 1.00 98.53 7 A 1 ATOM 52 C CG . LEU A 1 7 ? -4.706 -0.213 5.590 1.00 94.88 7 A 1 ATOM 53 C CD1 . LEU A 1 7 ? -4.584 -0.397 7.092 1.00 92.73 7 A 1 ATOM 54 C CD2 . LEU A 1 7 ? -5.633 0.956 5.277 1.00 93.77 7 A 1 ATOM 55 N N . VAL A 1 8 ? -0.950 -0.219 2.971 1.00 98.58 8 A 1 ATOM 56 C CA . VAL A 1 8 ? 0.340 0.254 2.469 1.00 98.60 8 A 1 ATOM 57 C C . VAL A 1 8 ? 0.280 0.459 0.959 1.00 98.67 8 A 1 ATOM 58 O O . VAL A 1 8 ? 0.739 1.482 0.441 1.00 98.52 8 A 1 ATOM 59 C CB . VAL A 1 8 ? 1.462 -0.733 2.826 1.00 98.45 8 A 1 ATOM 60 C CG1 . VAL A 1 8 ? 2.776 -0.320 2.172 1.00 97.48 8 A 1 ATOM 61 C CG2 . VAL A 1 8 ? 1.636 -0.810 4.336 1.00 97.17 8 A 1 ATOM 62 N N . VAL A 1 9 ? -0.291 -0.516 0.266 1.00 98.55 9 A 1 ATOM 63 C CA . VAL A 1 9 ? -0.418 -0.443 -1.188 1.00 98.49 9 A 1 ATOM 64 C C . VAL A 1 9 ? -1.295 0.739 -1.584 1.00 98.56 9 A 1 ATOM 65 O O . VAL A 1 9 ? -0.967 1.478 -2.518 1.00 98.43 9 A 1 ATOM 66 C CB . VAL A 1 9 ? -0.995 -1.753 -1.752 1.00 98.18 9 A 1 ATOM 67 C CG1 . VAL A 1 9 ? -1.319 -1.612 -3.233 1.00 97.06 9 A 1 ATOM 68 C CG2 . VAL A 1 9 ? -0.011 -2.895 -1.549 1.00 96.97 9 A 1 ATOM 69 N N . LEU A 1 10 ? -2.390 0.918 -0.863 1.00 98.41 10 A 1 ATOM 70 C CA . LEU A 1 10 ? -3.305 2.024 -1.137 1.00 98.36 10 A 1 ATOM 71 C C . LEU A 1 10 ? -2.591 3.363 -1.002 1.00 98.54 10 A 1 ATOM 72 O O . LEU A 1 10 ? -2.767 4.258 -1.834 1.00 98.37 10 A 1 ATOM 73 C CB . LEU A 1 10 ? -4.492 1.962 -0.176 1.00 98.02 10 A 1 ATOM 74 C CG . LEU A 1 10 ? -5.595 2.978 -0.472 1.00 93.86 10 A 1 ATOM 75 C CD1 . LEU A 1 10 ? -6.250 2.690 -1.813 1.00 91.95 10 A 1 ATOM 76 C CD2 . LEU A 1 10 ? -6.636 2.963 0.635 1.00 92.35 10 A 1 ATOM 77 N N . GLY A 1 11 ? -1.800 3.490 0.050 1.00 98.43 11 A 1 ATOM 78 C CA . GLY A 1 11 ? -1.032 4.713 0.268 1.00 98.46 11 A 1 ATOM 79 C C . GLY A 1 11 ? -0.036 4.948 -0.850 1.00 98.60 11 A 1 ATOM 80 O O . GLY A 1 11 ? 0.124 6.074 -1.329 1.00 98.38 11 A 1 ATOM 81 N N . LEU A 1 12 ? 0.622 3.876 -1.276 1.00 98.49 12 A 1 ATOM 82 C CA . LEU A 1 12 ? 1.602 3.954 -2.359 1.00 98.48 12 A 1 ATOM 83 C C . LEU A 1 12 ? 0.930 4.374 -3.662 1.00 98.62 12 A 1 ATOM 84 O O . LEU A 1 12 ? 1.477 5.179 -4.421 1.00 98.31 12 A 1 ATOM 85 C CB . LEU A 1 12 ? 2.289 2.599 -2.527 1.00 98.17 12 A 1 ATOM 86 C CG . LEU A 1 12 ? 3.489 2.618 -3.474 1.00 94.72 12 A 1 ATOM 87 C CD1 . LEU A 1 12 ? 4.633 3.425 -2.891 1.00 92.46 12 A 1 ATOM 88 C CD2 . LEU A 1 12 ? 3.951 1.199 -3.771 1.00 92.33 12 A 1 ATOM 89 N N . VAL A 1 13 ? -0.253 3.833 -3.908 1.00 98.63 13 A 1 ATOM 90 C CA . VAL A 1 13 ? -1.014 4.170 -5.111 1.00 98.64 13 A 1 ATOM 91 C C . VAL A 1 13 ? -1.387 5.648 -5.113 1.00 98.72 13 A 1 ATOM 92 O O . VAL A 1 13 ? -1.312 6.316 -6.147 1.00 98.43 13 A 1 ATOM 93 C CB . VAL A 1 13 ? -2.278 3.301 -5.219 1.00 98.32 13 A 1 ATOM 94 C CG1 . VAL A 1 13 ? -3.172 3.782 -6.357 1.00 96.84 13 A 1 ATOM 95 C CG2 . VAL A 1 13 ? -1.899 1.847 -5.446 1.00 96.68 13 A 1 ATOM 96 N N . LEU A 1 14 ? -1.776 6.155 -3.947 1.00 98.36 14 A 1 ATOM 97 C CA . LEU A 1 14 ? -2.141 7.564 -3.817 1.00 98.36 14 A 1 ATOM 98 C C . LEU A 1 14 ? -0.959 8.463 -4.160 1.00 98.48 14 A 1 ATOM 99 O O . LEU A 1 14 ? -1.125 9.500 -4.810 1.00 98.15 14 A 1 ATOM 100 C CB . LEU A 1 14 ? -2.618 7.848 -2.392 1.00 98.11 14 A 1 ATOM 101 C CG . LEU A 1 14 ? -4.016 7.306 -2.089 1.00 94.33 14 A 1 ATOM 102 C CD1 . LEU A 1 14 ? -4.297 7.369 -0.598 1.00 91.22 14 A 1 ATOM 103 C CD2 . LEU A 1 14 ? -5.070 8.095 -2.856 1.00 90.95 14 A 1 ATOM 104 N N . VAL A 1 15 ? 0.224 8.066 -3.713 1.00 98.53 15 A 1 ATOM 105 C CA . VAL A 1 15 ? 1.439 8.827 -4.003 1.00 98.45 15 A 1 ATOM 106 C C . VAL A 1 15 ? 1.780 8.744 -5.486 1.00 98.53 15 A 1 ATOM 107 O O . VAL A 1 15 ? 2.212 9.732 -6.092 1.00 98.10 15 A 1 ATOM 108 C CB . VAL A 1 15 ? 2.619 8.315 -3.162 1.00 97.87 15 A 1 ATOM 109 C CG1 . VAL A 1 15 ? 3.904 9.045 -3.535 1.00 95.07 15 A 1 ATOM 110 C CG2 . VAL A 1 15 ? 2.329 8.493 -1.683 1.00 95.73 15 A 1 ATOM 111 N N . ALA A 1 16 ? 1.596 7.561 -6.062 1.00 98.34 16 A 1 ATOM 112 C CA . ALA A 1 16 ? 1.894 7.333 -7.475 1.00 98.24 16 A 1 ATOM 113 C C . ALA A 1 16 ? 0.844 7.952 -8.392 1.00 98.33 16 A 1 ATOM 114 O O . ALA A 1 16 ? 1.103 8.177 -9.577 1.00 97.75 16 A 1 ATOM 115 C CB . ALA A 1 16 ? 2.007 5.835 -7.747 1.00 97.76 16 A 1 ATOM 116 N N . ALA A 1 17 ? -0.343 8.221 -7.847 1.00 97.23 17 A 1 ATOM 117 C CA . ALA A 1 17 ? -1.440 8.782 -8.621 1.00 96.34 17 A 1 ATOM 118 C C . ALA A 1 17 ? -1.215 10.262 -8.934 1.00 95.44 17 A 1 ATOM 119 O O . ALA A 1 17 ? -0.462 10.933 -8.205 1.00 92.10 17 A 1 ATOM 120 C CB . ALA A 1 17 ? -2.761 8.588 -7.883 1.00 94.18 17 A 1 ATOM 121 O OXT . ALA A 1 17 ? -1.805 10.760 -9.898 1.00 86.80 17 A 1 #