# 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_spkb41697 # _entry.id spkb41697 # 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" "C6 H15 N4 O2" 175.209 ARG y ARGININE C(C[C@@H](C(=O)O)N)CNC(=[NH2+])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" "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 ILE 2 1 n ARG 3 1 n ARG 4 1 n VAL 5 1 n LEU 6 1 n LEU 7 1 n LEU 8 1 n SER 9 1 n LEU 10 1 n ALA 11 1 n LEU 12 1 n LEU 13 1 n LEU 14 1 n ALA 15 1 n GLY 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 @ 2025-07-03 00:07:57)" _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 95.79 _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 91.75 1 1 A ILE 2 2 95.92 1 2 A ARG 3 2 92.36 1 3 A ARG 4 2 91.44 1 4 A VAL 5 2 98.04 1 5 A LEU 6 2 97.28 1 6 A LEU 7 2 97.72 1 7 A LEU 8 2 97.38 1 8 A SER 9 2 97.84 1 9 A LEU 10 2 96.78 1 10 A ALA 11 2 98.69 1 11 A LEU 12 2 97.47 1 12 A LEU 13 2 97.27 1 13 A LEU 14 2 97.29 1 14 A ALA 15 2 98.11 1 15 A GLY 16 2 91.31 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 ILE . 2 A 2 A 3 1 n ARG . 3 A 3 A 4 1 n ARG . 4 A 4 A 5 1 n VAL . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n SER . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n ALA . 11 A 11 A 12 1 n LEU . 12 A 12 A 13 1 n LEU . 13 A 13 A 14 1 n LEU . 14 A 14 A 15 1 n ALA . 15 A 15 A 16 1 n GLY . 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 ? 3.512 2.923 11.388 1.00 95.95 1 A 1 ATOM 2 C CA . MET A 1 1 ? 3.821 2.943 9.948 1.00 96.77 1 A 1 ATOM 3 C C . MET A 1 1 ? 2.599 2.491 9.137 1.00 97.25 1 A 1 ATOM 4 O O . MET A 1 1 ? 2.660 1.526 8.379 1.00 95.88 1 A 1 ATOM 5 C CB . MET A 1 1 ? 5.011 2.038 9.653 1.00 94.48 1 A 1 ATOM 6 C CG . MET A 1 1 ? 6.313 2.598 10.226 1.00 88.03 1 A 1 ATOM 7 S SD . MET A 1 1 ? 6.333 2.539 12.011 1.00 86.94 1 A 1 ATOM 8 C CE . MET A 1 1 ? 7.956 3.179 12.334 1.00 78.71 1 A 1 ATOM 9 N N . ILE A 1 2 ? 1.515 3.194 9.322 1.00 98.08 2 A 1 ATOM 10 C CA . ILE A 1 2 ? 0.269 2.873 8.621 1.00 98.15 2 A 1 ATOM 11 C C . ILE A 1 2 ? 0.371 3.222 7.136 1.00 98.31 2 A 1 ATOM 12 O O . ILE A 1 2 ? -0.370 2.687 6.310 1.00 97.69 2 A 1 ATOM 13 C CB . ILE A 1 2 ? -0.886 3.637 9.282 1.00 97.74 2 A 1 ATOM 14 C CG1 . ILE A 1 2 ? -1.049 3.207 10.739 1.00 94.41 2 A 1 ATOM 15 C CG2 . ILE A 1 2 ? -2.196 3.401 8.527 1.00 93.80 2 A 1 ATOM 16 C CD1 . ILE A 1 2 ? -0.961 4.375 11.677 1.00 89.16 2 A 1 ATOM 17 N N . ARG A 1 3 ? 1.296 4.116 6.822 1.00 98.42 3 A 1 ATOM 18 C CA . ARG A 1 3 ? 1.484 4.553 5.434 1.00 98.46 3 A 1 ATOM 19 C C . ARG A 1 3 ? 1.779 3.372 4.513 1.00 98.59 3 A 1 ATOM 20 O O . ARG A 1 3 ? 1.188 3.249 3.446 1.00 98.13 3 A 1 ATOM 21 C CB . ARG A 1 3 ? 2.636 5.572 5.388 1.00 98.02 3 A 1 ATOM 22 C CG . ARG A 1 3 ? 2.640 6.386 4.128 1.00 94.51 3 A 1 ATOM 23 C CD . ARG A 1 3 ? 1.965 7.729 4.339 1.00 93.25 3 A 1 ATOM 24 N NE . ARG A 1 3 ? 0.522 7.594 4.485 1.00 88.37 3 A 1 ATOM 25 C CZ . ARG A 1 3 ? -0.307 8.624 4.539 1.00 87.30 3 A 1 ATOM 26 N NH1 . ARG A 1 3 ? 0.134 9.862 4.464 1.00 80.21 3 A 1 ATOM 27 N NH2 . ARG A 1 3 ? -1.593 8.411 4.672 1.00 80.69 3 A 1 ATOM 28 N N . ARG A 1 4 ? 2.691 2.502 4.942 1.00 98.29 4 A 1 ATOM 29 C CA . ARG A 1 4 ? 3.069 1.335 4.138 1.00 98.45 4 A 1 ATOM 30 C C . ARG A 1 4 ? 1.893 0.385 3.961 1.00 98.67 4 A 1 ATOM 31 O O . ARG A 1 4 ? 1.619 -0.065 2.849 1.00 98.38 4 A 1 ATOM 32 C CB . ARG A 1 4 ? 4.228 0.589 4.797 1.00 98.14 4 A 1 ATOM 33 C CG . ARG A 1 4 ? 5.544 0.857 4.094 1.00 94.37 4 A 1 ATOM 34 C CD . ARG A 1 4 ? 6.153 2.155 4.571 1.00 91.87 4 A 1 ATOM 35 N NE . ARG A 1 4 ? 7.088 2.708 3.584 1.00 87.27 4 A 1 ATOM 36 C CZ . ARG A 1 4 ? 7.009 3.921 3.079 1.00 84.58 4 A 1 ATOM 37 N NH1 . ARG A 1 4 ? 6.039 4.746 3.426 1.00 77.87 4 A 1 ATOM 38 N NH2 . ARG A 1 4 ? 7.915 4.330 2.214 1.00 77.97 4 A 1 ATOM 39 N N . VAL A 1 5 ? 1.206 0.099 5.043 1.00 98.67 5 A 1 ATOM 40 C CA . VAL A 1 5 ? 0.057 -0.812 5.011 1.00 98.72 5 A 1 ATOM 41 C C . VAL A 1 5 ? -1.040 -0.256 4.102 1.00 98.76 5 A 1 ATOM 42 O O . VAL A 1 5 ? -1.647 -0.994 3.321 1.00 98.52 5 A 1 ATOM 43 C CB . VAL A 1 5 ? -0.492 -1.035 6.430 1.00 98.51 5 A 1 ATOM 44 C CG1 . VAL A 1 5 ? -1.675 -1.982 6.406 1.00 96.73 5 A 1 ATOM 45 C CG2 . VAL A 1 5 ? 0.601 -1.570 7.338 1.00 96.40 5 A 1 ATOM 46 N N . LEU A 1 6 ? -1.276 1.027 4.213 1.00 98.72 6 A 1 ATOM 47 C CA . LEU A 1 6 ? -2.293 1.693 3.400 1.00 98.73 6 A 1 ATOM 48 C C . LEU A 1 6 ? -1.934 1.609 1.918 1.00 98.77 6 A 1 ATOM 49 O O . LEU A 1 6 ? -2.786 1.294 1.083 1.00 98.65 6 A 1 ATOM 50 C CB . LEU A 1 6 ? -2.416 3.154 3.850 1.00 98.65 6 A 1 ATOM 51 C CG . LEU A 1 6 ? -3.689 3.836 3.357 1.00 96.91 6 A 1 ATOM 52 C CD1 . LEU A 1 6 ? -4.165 4.864 4.376 1.00 93.61 6 A 1 ATOM 53 C CD2 . LEU A 1 6 ? -3.452 4.523 2.020 1.00 94.19 6 A 1 ATOM 54 N N . LEU A 1 7 ? -0.680 1.887 1.599 1.00 98.67 7 A 1 ATOM 55 C CA . LEU A 1 7 ? -0.214 1.841 0.213 1.00 98.71 7 A 1 ATOM 56 C C . LEU A 1 7 ? -0.319 0.426 -0.352 1.00 98.74 7 A 1 ATOM 57 O O . LEU A 1 7 ? -0.747 0.244 -1.493 1.00 98.64 7 A 1 ATOM 58 C CB . LEU A 1 7 ? 1.235 2.328 0.150 1.00 98.65 7 A 1 ATOM 59 C CG . LEU A 1 7 ? 1.376 3.836 0.362 1.00 97.39 7 A 1 ATOM 60 C CD1 . LEU A 1 7 ? 2.823 4.193 0.652 1.00 95.56 7 A 1 ATOM 61 C CD2 . LEU A 1 7 ? 0.895 4.594 -0.874 1.00 95.44 7 A 1 ATOM 62 N N . LEU A 1 8 ? 0.059 -0.554 0.444 1.00 98.70 8 A 1 ATOM 63 C CA . LEU A 1 8 ? 0.004 -1.951 0.014 1.00 98.67 8 A 1 ATOM 64 C C . LEU A 1 8 ? -1.438 -2.381 -0.243 1.00 98.74 8 A 1 ATOM 65 O O . LEU A 1 8 ? -1.726 -3.030 -1.249 1.00 98.60 8 A 1 ATOM 66 C CB . LEU A 1 8 ? 0.640 -2.836 1.086 1.00 98.57 8 A 1 ATOM 67 C CG . LEU A 1 8 ? 2.160 -2.716 1.144 1.00 96.98 8 A 1 ATOM 68 C CD1 . LEU A 1 8 ? 2.683 -3.310 2.445 1.00 94.22 8 A 1 ATOM 69 C CD2 . LEU A 1 8 ? 2.795 -3.435 -0.044 1.00 94.59 8 A 1 ATOM 70 N N . SER A 1 9 ? -2.327 -2.016 0.648 1.00 98.74 9 A 1 ATOM 71 C CA . SER A 1 9 ? -3.737 -2.376 0.500 1.00 98.73 9 A 1 ATOM 72 C C . SER A 1 9 ? -4.337 -1.709 -0.737 1.00 98.80 9 A 1 ATOM 73 O O . SER A 1 9 ? -5.087 -2.338 -1.486 1.00 98.68 9 A 1 ATOM 74 C CB . SER A 1 9 ? -4.510 -1.962 1.755 1.00 98.52 9 A 1 ATOM 75 O OG . SER A 1 9 ? -4.457 -0.571 1.939 1.00 93.58 9 A 1 ATOM 76 N N . LEU A 1 10 ? -3.991 -0.463 -0.950 1.00 98.67 10 A 1 ATOM 77 C CA . LEU A 1 10 ? -4.477 0.277 -2.116 1.00 98.63 10 A 1 ATOM 78 C C . LEU A 1 10 ? -3.956 -0.350 -3.403 1.00 98.73 10 A 1 ATOM 79 O O . LEU A 1 10 ? -4.709 -0.515 -4.368 1.00 98.58 10 A 1 ATOM 80 C CB . LEU A 1 10 ? -4.026 1.737 -2.019 1.00 98.42 10 A 1 ATOM 81 C CG . LEU A 1 10 ? -4.682 2.643 -3.058 1.00 95.75 10 A 1 ATOM 82 C CD1 . LEU A 1 10 ? -6.139 2.904 -2.690 1.00 92.13 10 A 1 ATOM 83 C CD2 . LEU A 1 10 ? -3.932 3.959 -3.163 1.00 93.35 10 A 1 ATOM 84 N N . ALA A 1 11 ? -2.680 -0.688 -3.414 1.00 98.76 11 A 1 ATOM 85 C CA . ALA A 1 11 ? -2.059 -1.311 -4.584 1.00 98.74 11 A 1 ATOM 86 C C . ALA A 1 11 ? -2.731 -2.644 -4.902 1.00 98.79 11 A 1 ATOM 87 O O . ALA A 1 11 ? -2.993 -2.950 -6.067 1.00 98.56 11 A 1 ATOM 88 C CB . ALA A 1 11 ? -0.571 -1.510 -4.330 1.00 98.58 11 A 1 ATOM 89 N N . LEU A 1 12 ? -3.016 -3.417 -3.873 1.00 98.73 12 A 1 ATOM 90 C CA . LEU A 1 12 ? -3.678 -4.711 -4.040 1.00 98.69 12 A 1 ATOM 91 C C . LEU A 1 12 ? -5.075 -4.522 -4.628 1.00 98.75 12 A 1 ATOM 92 O O . LEU A 1 12 ? -5.493 -5.270 -5.514 1.00 98.48 12 A 1 ATOM 93 C CB . LEU A 1 12 ? -3.764 -5.409 -2.685 1.00 98.47 12 A 1 ATOM 94 C CG . LEU A 1 12 ? -4.163 -6.872 -2.795 1.00 97.08 12 A 1 ATOM 95 C CD1 . LEU A 1 12 ? -2.997 -7.704 -3.323 1.00 94.86 12 A 1 ATOM 96 C CD2 . LEU A 1 12 ? -4.601 -7.399 -1.442 1.00 94.66 12 A 1 ATOM 97 N N . LEU A 1 13 ? -5.778 -3.536 -4.138 1.00 98.66 13 A 1 ATOM 98 C CA . LEU A 1 13 ? -7.123 -3.228 -4.628 1.00 98.63 13 A 1 ATOM 99 C C . LEU A 1 13 ? -7.081 -2.831 -6.100 1.00 98.71 13 A 1 ATOM 100 O O . LEU A 1 13 ? -7.936 -3.247 -6.890 1.00 98.41 13 A 1 ATOM 101 C CB . LEU A 1 13 ? -7.725 -2.101 -3.786 1.00 98.44 13 A 1 ATOM 102 C CG . LEU A 1 13 ? -9.234 -1.966 -3.977 1.00 96.99 13 A 1 ATOM 103 C CD1 . LEU A 1 13 ? -9.938 -1.923 -2.630 1.00 94.35 13 A 1 ATOM 104 C CD2 . LEU A 1 13 ? -9.566 -0.716 -4.772 1.00 93.97 13 A 1 ATOM 105 N N . LEU A 1 14 ? -6.094 -2.023 -6.465 1.00 98.61 14 A 1 ATOM 106 C CA . LEU A 1 14 ? -5.935 -1.580 -7.849 1.00 98.55 14 A 1 ATOM 107 C C . LEU A 1 14 ? -5.586 -2.752 -8.755 1.00 98.61 14 A 1 ATOM 108 O O . LEU A 1 14 ? -6.084 -2.834 -9.881 1.00 98.15 14 A 1 ATOM 109 C CB . LEU A 1 14 ? -4.838 -0.512 -7.919 1.00 98.30 14 A 1 ATOM 110 C CG . LEU A 1 14 ? -5.263 0.831 -7.318 1.00 97.25 14 A 1 ATOM 111 C CD1 . LEU A 1 14 ? -4.048 1.709 -7.081 1.00 94.60 14 A 1 ATOM 112 C CD2 . LEU A 1 14 ? -6.243 1.543 -8.247 1.00 94.23 14 A 1 ATOM 113 N N . ALA A 1 15 ? -4.741 -3.643 -8.273 1.00 98.59 15 A 1 ATOM 114 C CA . ALA A 1 15 ? -4.340 -4.827 -9.039 1.00 98.42 15 A 1 ATOM 115 C C . ALA A 1 15 ? -5.546 -5.710 -9.335 1.00 98.41 15 A 1 ATOM 116 O O . ALA A 1 15 ? -5.727 -6.158 -10.467 1.00 97.26 15 A 1 ATOM 117 C CB . ALA A 1 15 ? -3.280 -5.603 -8.265 1.00 97.85 15 A 1 ATOM 118 N N . GLY A 1 16 ? -6.365 -5.959 -8.299 1.00 96.39 16 A 1 ATOM 119 C CA . GLY A 1 16 ? -7.581 -6.765 -8.449 1.00 93.67 16 A 1 ATOM 120 C C . GLY A 1 16 ? -7.395 -7.984 -9.342 1.00 90.84 16 A 1 ATOM 121 O O . GLY A 1 16 ? -8.380 -8.444 -9.939 1.00 85.41 16 A 1 ATOM 122 O OXT . GLY A 1 16 ? -6.293 -8.433 -9.555 1.00 90.23 16 A 1 #