# 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_spkb39256 # _entry.id spkb39256 # 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" "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" "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 ALA 2 1 n ARG 3 1 n TYR 4 1 n PHE 5 1 n ILE 6 1 n LEU 7 1 n ALA 8 1 n VAL 9 1 n ALA 10 1 n LEU 11 1 n LEU 12 1 n LEU 13 1 n THR 14 1 n ALA 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 @ 2025-07-08 14:56:37)" _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 95.46 _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 87.31 1 1 A ALA 2 2 95.37 1 2 A ARG 3 2 91.13 1 3 A TYR 4 2 95.98 1 4 A PHE 5 2 96.36 1 5 A ILE 6 2 97.40 1 6 A LEU 7 2 96.47 1 7 A ALA 8 2 98.42 1 8 A VAL 9 2 98.01 1 9 A ALA 10 2 98.44 1 10 A LEU 11 2 97.22 1 11 A LEU 12 2 97.08 1 12 A LEU 13 2 96.92 1 13 A THR 14 2 95.36 1 14 A ALA 15 2 93.47 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 ALA . 2 A 2 A 3 1 n ARG . 3 A 3 A 4 1 n TYR . 4 A 4 A 5 1 n PHE . 5 A 5 A 6 1 n ILE . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n ALA . 8 A 8 A 9 1 n VAL . 9 A 9 A 10 1 n ALA . 10 A 10 A 11 1 n LEU . 11 A 11 A 12 1 n LEU . 12 A 12 A 13 1 n LEU . 13 A 13 A 14 1 n THR . 14 A 14 A 15 1 n ALA . 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 ? -8.863 7.005 5.344 1.00 92.51 1 A 1 ATOM 2 C CA . MET A 1 1 ? -7.385 6.990 5.368 1.00 93.45 1 A 1 ATOM 3 C C . MET A 1 1 ? -6.834 6.539 4.014 1.00 94.16 1 A 1 ATOM 4 O O . MET A 1 1 ? -6.786 5.347 3.724 1.00 92.80 1 A 1 ATOM 5 C CB . MET A 1 1 ? -6.876 6.047 6.452 1.00 89.73 1 A 1 ATOM 6 C CG . MET A 1 1 ? -7.145 6.577 7.855 1.00 83.78 1 A 1 ATOM 7 S SD . MET A 1 1 ? -8.862 6.375 8.331 1.00 80.71 1 A 1 ATOM 8 C CE . MET A 1 1 ? -8.760 6.827 10.058 1.00 71.36 1 A 1 ATOM 9 N N . ALA A 1 2 ? -6.428 7.499 3.203 1.00 93.26 2 A 1 ATOM 10 C CA . ALA A 1 2 ? -5.881 7.196 1.881 1.00 96.08 2 A 1 ATOM 11 C C . ALA A 1 2 ? -4.453 6.661 1.970 1.00 97.21 2 A 1 ATOM 12 O O . ALA A 1 2 ? -3.981 5.969 1.069 1.00 96.03 2 A 1 ATOM 13 C CB . ALA A 1 2 ? -5.918 8.451 1.019 1.00 94.25 2 A 1 ATOM 14 N N . ARG A 1 3 ? -3.775 6.985 3.064 1.00 97.50 3 A 1 ATOM 15 C CA . ARG A 1 3 ? -2.389 6.550 3.268 1.00 97.89 3 A 1 ATOM 16 C C . ARG A 1 3 ? -2.285 5.027 3.253 1.00 98.22 3 A 1 ATOM 17 O O . ARG A 1 3 ? -1.373 4.468 2.651 1.00 97.72 3 A 1 ATOM 18 C CB . ARG A 1 3 ? -1.867 7.102 4.599 1.00 97.18 3 A 1 ATOM 19 C CG . ARG A 1 3 ? -0.576 7.870 4.423 1.00 93.10 3 A 1 ATOM 20 C CD . ARG A 1 3 ? 0.622 6.945 4.309 1.00 91.48 3 A 1 ATOM 21 N NE . ARG A 1 3 ? 1.499 7.350 3.209 1.00 86.85 3 A 1 ATOM 22 C CZ . ARG A 1 3 ? 2.740 6.903 3.030 1.00 85.63 3 A 1 ATOM 23 N NH1 . ARG A 1 3 ? 3.273 6.047 3.876 1.00 78.43 3 A 1 ATOM 24 N NH2 . ARG A 1 3 ? 3.447 7.320 1.991 1.00 78.48 3 A 1 ATOM 25 N N . TYR A 1 4 ? -3.229 4.370 3.894 1.00 98.09 4 A 1 ATOM 26 C CA . TYR A 1 4 ? -3.231 2.908 3.945 1.00 98.19 4 A 1 ATOM 27 C C . TYR A 1 4 ? -3.477 2.315 2.559 1.00 98.27 4 A 1 ATOM 28 O O . TYR A 1 4 ? -2.909 1.284 2.200 1.00 98.00 4 A 1 ATOM 29 C CB . TYR A 1 4 ? -4.308 2.428 4.920 1.00 97.88 4 A 1 ATOM 30 C CG . TYR A 1 4 ? -3.953 2.708 6.362 1.00 96.73 4 A 1 ATOM 31 C CD1 . TYR A 1 4 ? -2.823 2.139 6.935 1.00 95.06 4 A 1 ATOM 32 C CD2 . TYR A 1 4 ? -4.753 3.531 7.145 1.00 94.74 4 A 1 ATOM 33 C CE1 . TYR A 1 4 ? -2.492 2.391 8.260 1.00 94.09 4 A 1 ATOM 34 C CE2 . TYR A 1 4 ? -4.431 3.788 8.471 1.00 93.62 4 A 1 ATOM 35 C CZ . TYR A 1 4 ? -3.299 3.212 9.023 1.00 94.09 4 A 1 ATOM 36 O OH . TYR A 1 4 ? -2.978 3.461 10.335 1.00 92.98 4 A 1 ATOM 37 N N . PHE A 1 5 ? -4.313 2.975 1.774 1.00 98.33 5 A 1 ATOM 38 C CA . PHE A 1 5 ? -4.610 2.526 0.414 1.00 98.37 5 A 1 ATOM 39 C C . PHE A 1 5 ? -3.359 2.604 -0.457 1.00 98.51 5 A 1 ATOM 40 O O . PHE A 1 5 ? -3.065 1.685 -1.224 1.00 98.31 5 A 1 ATOM 41 C CB . PHE A 1 5 ? -5.719 3.387 -0.181 1.00 98.14 5 A 1 ATOM 42 C CG . PHE A 1 5 ? -6.170 2.886 -1.526 1.00 96.84 5 A 1 ATOM 43 C CD1 . PHE A 1 5 ? -5.602 3.381 -2.694 1.00 94.92 5 A 1 ATOM 44 C CD2 . PHE A 1 5 ? -7.156 1.912 -1.616 1.00 94.95 5 A 1 ATOM 45 C CE1 . PHE A 1 5 ? -6.010 2.912 -3.935 1.00 93.94 5 A 1 ATOM 46 C CE2 . PHE A 1 5 ? -7.566 1.438 -2.857 1.00 93.71 5 A 1 ATOM 47 C CZ . PHE A 1 5 ? -6.991 1.937 -4.017 1.00 93.91 5 A 1 ATOM 48 N N . ILE A 1 6 ? -2.636 3.695 -0.331 1.00 98.47 6 A 1 ATOM 49 C CA . ILE A 1 6 ? -1.405 3.895 -1.098 1.00 98.46 6 A 1 ATOM 50 C C . ILE A 1 6 ? -0.372 2.837 -0.726 1.00 98.57 6 A 1 ATOM 51 O O . ILE A 1 6 ? 0.331 2.305 -1.585 1.00 98.44 6 A 1 ATOM 52 C CB . ILE A 1 6 ? -0.834 5.303 -0.845 1.00 98.27 6 A 1 ATOM 53 C CG1 . ILE A 1 6 ? -1.853 6.388 -1.230 1.00 97.16 6 A 1 ATOM 54 C CG2 . ILE A 1 6 ? 0.465 5.500 -1.630 1.00 96.89 6 A 1 ATOM 55 C CD1 . ILE A 1 6 ? -2.240 6.363 -2.701 1.00 92.94 6 A 1 ATOM 56 N N . LEU A 1 7 ? -0.282 2.552 0.555 1.00 98.40 7 A 1 ATOM 57 C CA . LEU A 1 7 ? 0.665 1.551 1.042 1.00 98.31 7 A 1 ATOM 58 C C . LEU A 1 7 ? 0.343 0.177 0.463 1.00 98.48 7 A 1 ATOM 59 O O . LEU A 1 7 ? 1.239 -0.559 0.049 1.00 98.34 7 A 1 ATOM 60 C CB . LEU A 1 7 ? 0.619 1.490 2.570 1.00 98.04 7 A 1 ATOM 61 C CG . LEU A 1 7 ? 1.932 1.020 3.189 1.00 94.25 7 A 1 ATOM 62 C CD1 . LEU A 1 7 ? 2.617 2.166 3.926 1.00 92.82 7 A 1 ATOM 63 C CD2 . LEU A 1 7 ? 1.698 -0.138 4.143 1.00 93.16 7 A 1 ATOM 64 N N . ALA A 1 8 ? -0.930 -0.158 0.430 1.00 98.40 8 A 1 ATOM 65 C CA . ALA A 1 8 ? -1.368 -1.444 -0.103 1.00 98.47 8 A 1 ATOM 66 C C . ALA A 1 8 ? -1.076 -1.550 -1.596 1.00 98.59 8 A 1 ATOM 67 O O . ALA A 1 8 ? -0.620 -2.588 -2.075 1.00 98.41 8 A 1 ATOM 68 C CB . ALA A 1 8 ? -2.861 -1.617 0.157 1.00 98.25 8 A 1 ATOM 69 N N . VAL A 1 9 ? -1.333 -0.477 -2.321 1.00 98.59 9 A 1 ATOM 70 C CA . VAL A 1 9 ? -1.090 -0.448 -3.763 1.00 98.53 9 A 1 ATOM 71 C C . VAL A 1 9 ? 0.400 -0.585 -4.059 1.00 98.63 9 A 1 ATOM 72 O O . VAL A 1 9 ? 0.796 -1.311 -4.972 1.00 98.47 9 A 1 ATOM 73 C CB . VAL A 1 9 ? -1.630 0.854 -4.381 1.00 98.17 9 A 1 ATOM 74 C CG1 . VAL A 1 9 ? -1.262 0.944 -5.853 1.00 96.87 9 A 1 ATOM 75 C CG2 . VAL A 1 9 ? -3.137 0.922 -4.220 1.00 96.79 9 A 1 ATOM 76 N N . ALA A 1 10 ? 1.213 0.108 -3.282 1.00 98.48 10 A 1 ATOM 77 C CA . ALA A 1 10 ? 2.661 0.060 -3.466 1.00 98.49 10 A 1 ATOM 78 C C . ALA A 1 10 ? 3.194 -1.355 -3.253 1.00 98.62 10 A 1 ATOM 79 O O . ALA A 1 10 ? 4.049 -1.822 -4.004 1.00 98.36 10 A 1 ATOM 80 C CB . ALA A 1 10 ? 3.335 1.022 -2.495 1.00 98.24 10 A 1 ATOM 81 N N . LEU A 1 11 ? 2.686 -2.019 -2.236 1.00 98.69 11 A 1 ATOM 82 C CA . LEU A 1 11 ? 3.109 -3.384 -1.929 1.00 98.63 11 A 1 ATOM 83 C C . LEU A 1 11 ? 2.666 -4.348 -3.022 1.00 98.70 11 A 1 ATOM 84 O O . LEU A 1 11 ? 3.415 -5.242 -3.418 1.00 98.44 11 A 1 ATOM 85 C CB . LEU A 1 11 ? 2.530 -3.804 -0.578 1.00 98.41 11 A 1 ATOM 86 C CG . LEU A 1 11 ? 3.390 -4.836 0.142 1.00 96.10 11 A 1 ATOM 87 C CD1 . LEU A 1 11 ? 3.540 -4.480 1.612 1.00 94.32 11 A 1 ATOM 88 C CD2 . LEU A 1 11 ? 2.799 -6.226 0.007 1.00 94.46 11 A 1 ATOM 89 N N . LEU A 1 12 ? 1.460 -4.156 -3.520 1.00 98.65 12 A 1 ATOM 90 C CA . LEU A 1 12 ? 0.911 -5.004 -4.577 1.00 98.55 12 A 1 ATOM 91 C C . LEU A 1 12 ? 1.688 -4.820 -5.876 1.00 98.56 12 A 1 ATOM 92 O O . LEU A 1 12 ? 1.910 -5.775 -6.624 1.00 98.16 12 A 1 ATOM 93 C CB . LEU A 1 12 ? -0.565 -4.662 -4.785 1.00 98.29 12 A 1 ATOM 94 C CG . LEU A 1 12 ? -1.433 -5.873 -5.114 1.00 96.24 12 A 1 ATOM 95 C CD1 . LEU A 1 12 ? -2.874 -5.628 -4.709 1.00 94.29 12 A 1 ATOM 96 C CD2 . LEU A 1 12 ? -1.361 -6.210 -6.596 1.00 93.88 12 A 1 ATOM 97 N N . LEU A 1 13 ? 2.097 -3.592 -6.147 1.00 98.38 13 A 1 ATOM 98 C CA . LEU A 1 13 ? 2.857 -3.281 -7.359 1.00 98.14 13 A 1 ATOM 99 C C . LEU A 1 13 ? 4.234 -3.930 -7.324 1.00 98.13 13 A 1 ATOM 100 O O . LEU A 1 13 ? 4.746 -4.378 -8.352 1.00 97.25 13 A 1 ATOM 101 C CB . LEU A 1 13 ? 2.993 -1.762 -7.501 1.00 97.73 13 A 1 ATOM 102 C CG . LEU A 1 13 ? 3.360 -1.323 -8.916 1.00 96.73 13 A 1 ATOM 103 C CD1 . LEU A 1 13 ? 2.272 -0.427 -9.496 1.00 94.77 13 A 1 ATOM 104 C CD2 . LEU A 1 13 ? 4.689 -0.606 -8.932 1.00 94.22 13 A 1 ATOM 105 N N . THR A 1 14 ? 4.833 -3.966 -6.150 1.00 97.83 14 A 1 ATOM 106 C CA . THR A 1 14 ? 6.160 -4.567 -5.984 1.00 97.51 14 A 1 ATOM 107 C C . THR A 1 14 ? 6.076 -6.088 -5.908 1.00 97.50 14 A 1 ATOM 108 O O . THR A 1 14 ? 6.959 -6.795 -6.401 1.00 95.32 14 A 1 ATOM 109 C CB . THR A 1 14 ? 6.834 -4.026 -4.715 1.00 96.14 14 A 1 ATOM 110 O OG1 . THR A 1 14 ? 6.926 -2.598 -4.792 1.00 92.05 14 A 1 ATOM 111 C CG2 . THR A 1 14 ? 8.239 -4.584 -4.558 1.00 91.14 14 A 1 ATOM 112 N N . ALA A 1 15 ? 5.024 -6.574 -5.286 1.00 97.24 15 A 1 ATOM 113 C CA . ALA A 1 15 ? 4.837 -8.008 -5.115 1.00 96.17 15 A 1 ATOM 114 C C . ALA A 1 15 ? 4.084 -8.621 -6.298 1.00 94.90 15 A 1 ATOM 115 O O . ALA A 1 15 ? 3.787 -7.906 -7.276 1.00 91.30 15 A 1 ATOM 116 C CB . ALA A 1 15 ? 4.099 -8.273 -3.803 1.00 94.43 15 A 1 ATOM 117 O OXT . ALA A 1 15 ? 3.774 -9.815 -6.264 1.00 86.80 15 A 1 #