# 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_spkb07863 # _entry.id spkb07863 # 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" "C3 H7 N O2 S" 121.158 CYS y CYSTEINE C([C@@H](C(=O)O)N)S ? "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" "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" "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 LEU 2 1 n LEU 3 1 n ARG 4 1 n ILE 5 1 n SER 6 1 n VAL 7 1 n LEU 8 1 n PHE 9 1 n LEU 10 1 n LEU 11 1 n LEU 12 1 n GLY 13 1 n SER 14 1 n CYS 15 1 n GLY 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 @ 2025-07-08 07:30:24)" _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 91.20 _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 85.21 1 1 A LEU 2 2 89.69 1 2 A LEU 3 2 92.29 1 3 A ARG 4 2 87.13 1 4 A ILE 5 2 93.14 1 5 A SER 6 2 93.43 1 6 A VAL 7 2 95.98 1 7 A LEU 8 2 92.38 1 8 A PHE 9 2 92.89 1 9 A LEU 10 2 94.60 1 10 A LEU 11 2 95.33 1 11 A LEU 12 2 93.25 1 12 A GLY 13 2 95.28 1 13 A SER 14 2 93.06 1 14 A CYS 15 2 90.24 1 15 A GLY 16 2 85.04 1 16 A ALA 17 2 79.88 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 LEU . 2 A 2 A 3 1 n LEU . 3 A 3 A 4 1 n ARG . 4 A 4 A 5 1 n ILE . 5 A 5 A 6 1 n SER . 6 A 6 A 7 1 n VAL . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n PHE . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n LEU . 11 A 11 A 12 1 n LEU . 12 A 12 A 13 1 n GLY . 13 A 13 A 14 1 n SER . 14 A 14 A 15 1 n CYS . 15 A 15 A 16 1 n GLY . 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 ? -8.027 6.534 7.694 1.00 91.53 1 A 1 ATOM 2 C CA . MET A 1 1 ? -6.586 6.812 7.587 1.00 92.78 1 A 1 ATOM 3 C C . MET A 1 1 ? -6.099 6.549 6.165 1.00 93.95 1 A 1 ATOM 4 O O . MET A 1 1 ? -6.624 5.674 5.486 1.00 91.18 1 A 1 ATOM 5 C CB . MET A 1 1 ? -5.802 5.937 8.562 1.00 86.82 1 A 1 ATOM 6 C CG . MET A 1 1 ? -6.233 6.126 10.010 1.00 79.56 1 A 1 ATOM 7 S SD . MET A 1 1 ? -5.455 4.937 11.102 1.00 77.46 1 A 1 ATOM 8 C CE . MET A 1 1 ? -6.307 5.294 12.634 1.00 68.41 1 A 1 ATOM 9 N N . LEU A 1 2 ? -5.107 7.303 5.722 1.00 93.44 2 A 1 ATOM 10 C CA . LEU A 1 2 ? -4.550 7.159 4.381 1.00 94.84 2 A 1 ATOM 11 C C . LEU A 1 2 ? -3.179 6.489 4.397 1.00 96.37 2 A 1 ATOM 12 O O . LEU A 1 2 ? -2.678 6.074 3.350 1.00 94.73 2 A 1 ATOM 13 C CB . LEU A 1 2 ? -4.455 8.532 3.705 1.00 92.44 2 A 1 ATOM 14 C CG . LEU A 1 2 ? -4.144 9.682 4.657 1.00 84.99 2 A 1 ATOM 15 C CD1 . LEU A 1 2 ? -3.035 10.553 4.103 1.00 80.98 2 A 1 ATOM 16 C CD2 . LEU A 1 2 ? -5.403 10.509 4.881 1.00 79.76 2 A 1 ATOM 17 N N . LEU A 1 3 ? -2.580 6.389 5.572 1.00 96.06 3 A 1 ATOM 18 C CA . LEU A 1 3 ? -1.267 5.765 5.701 1.00 96.54 3 A 1 ATOM 19 C C . LEU A 1 3 ? -1.315 4.279 5.360 1.00 97.19 3 A 1 ATOM 20 O O . LEU A 1 3 ? -0.389 3.739 4.756 1.00 96.17 3 A 1 ATOM 21 C CB . LEU A 1 3 ? -0.713 5.982 7.117 1.00 95.93 3 A 1 ATOM 22 C CG . LEU A 1 3 ? -1.700 5.733 8.253 1.00 88.36 3 A 1 ATOM 23 C CD1 . LEU A 1 3 ? -1.500 4.339 8.840 1.00 84.32 3 A 1 ATOM 24 C CD2 . LEU A 1 3 ? -1.527 6.781 9.332 1.00 83.72 3 A 1 ATOM 25 N N . ARG A 1 4 ? -2.401 3.629 5.729 1.00 96.65 4 A 1 ATOM 26 C CA . ARG A 1 4 ? -2.583 2.209 5.437 1.00 96.83 4 A 1 ATOM 27 C C . ARG A 1 4 ? -2.811 1.984 3.955 1.00 96.99 4 A 1 ATOM 28 O O . ARG A 1 4 ? -2.334 0.998 3.385 1.00 96.00 4 A 1 ATOM 29 C CB . ARG A 1 4 ? -3.740 1.624 6.250 1.00 95.93 4 A 1 ATOM 30 C CG . ARG A 1 4 ? -4.573 2.653 6.993 1.00 87.95 4 A 1 ATOM 31 C CD . ARG A 1 4 ? -5.609 3.273 6.078 1.00 86.70 4 A 1 ATOM 32 N NE . ARG A 1 4 ? -6.563 2.259 5.592 1.00 81.12 4 A 1 ATOM 33 C CZ . ARG A 1 4 ? -7.719 2.550 5.021 1.00 77.41 4 A 1 ATOM 34 N NH1 . ARG A 1 4 ? -8.080 3.813 4.836 1.00 69.92 4 A 1 ATOM 35 N NH2 . ARG A 1 4 ? -8.515 1.577 4.613 1.00 72.88 4 A 1 ATOM 36 N N . ILE A 1 5 ? -3.494 2.892 3.337 1.00 96.50 5 A 1 ATOM 37 C CA . ILE A 1 5 ? -3.755 2.818 1.904 1.00 95.91 5 A 1 ATOM 38 C C . ILE A 1 5 ? -2.455 3.004 1.128 1.00 96.14 5 A 1 ATOM 39 O O . ILE A 1 5 ? -2.216 2.336 0.122 1.00 95.34 5 A 1 ATOM 40 C CB . ILE A 1 5 ? -4.781 3.875 1.463 1.00 95.49 5 A 1 ATOM 41 C CG1 . ILE A 1 5 ? -6.062 3.777 2.288 1.00 91.23 5 A 1 ATOM 42 C CG2 . ILE A 1 5 ? -5.098 3.701 -0.022 1.00 90.57 5 A 1 ATOM 43 C CD1 . ILE A 1 5 ? -7.011 4.936 2.061 1.00 83.95 5 A 1 ATOM 44 N N . SER A 1 6 ? -1.634 3.900 1.613 1.00 95.89 6 A 1 ATOM 45 C CA . SER A 1 6 ? -0.348 4.178 0.981 1.00 95.55 6 A 1 ATOM 46 C C . SER A 1 6 ? 0.540 2.937 0.978 1.00 96.00 6 A 1 ATOM 47 O O . SER A 1 6 ? 1.172 2.620 -0.025 1.00 95.69 6 A 1 ATOM 48 C CB . SER A 1 6 ? 0.358 5.320 1.705 1.00 95.08 6 A 1 ATOM 49 O OG . SER A 1 6 ? -0.331 6.537 1.527 1.00 82.35 6 A 1 ATOM 50 N N . VAL A 1 7 ? 0.574 2.240 2.096 1.00 97.14 7 A 1 ATOM 51 C CA . VAL A 1 7 ? 1.377 1.022 2.224 1.00 96.95 7 A 1 ATOM 52 C C . VAL A 1 7 ? 0.859 -0.056 1.276 1.00 97.10 7 A 1 ATOM 53 O O . VAL A 1 7 ? 1.637 -0.726 0.597 1.00 96.56 7 A 1 ATOM 54 C CB . VAL A 1 7 ? 1.366 0.500 3.674 1.00 96.60 7 A 1 ATOM 55 C CG1 . VAL A 1 7 ? 2.175 -0.784 3.803 1.00 93.98 7 A 1 ATOM 56 C CG2 . VAL A 1 7 ? 1.907 1.551 4.625 1.00 93.54 7 A 1 ATOM 57 N N . LEU A 1 8 ? -0.450 -0.202 1.238 1.00 94.99 8 A 1 ATOM 58 C CA . LEU A 1 8 ? -1.080 -1.184 0.365 1.00 94.70 8 A 1 ATOM 59 C C . LEU A 1 8 ? -0.844 -0.833 -1.099 1.00 95.56 8 A 1 ATOM 60 O O . LEU A 1 8 ? -0.605 -1.709 -1.928 1.00 95.72 8 A 1 ATOM 61 C CB . LEU A 1 8 ? -2.581 -1.252 0.648 1.00 94.80 8 A 1 ATOM 62 C CG . LEU A 1 8 ? -3.184 -2.639 0.487 1.00 90.19 8 A 1 ATOM 63 C CD1 . LEU A 1 8 ? -2.945 -3.467 1.745 1.00 85.91 8 A 1 ATOM 64 C CD2 . LEU A 1 8 ? -4.673 -2.546 0.201 1.00 87.13 8 A 1 ATOM 65 N N . PHE A 1 9 ? -0.919 0.445 -1.397 1.00 95.66 9 A 1 ATOM 66 C CA . PHE A 1 9 ? -0.700 0.943 -2.751 1.00 95.62 9 A 1 ATOM 67 C C . PHE A 1 9 ? 0.727 0.675 -3.203 1.00 96.49 9 A 1 ATOM 68 O O . PHE A 1 9 ? 0.966 0.306 -4.352 1.00 96.32 9 A 1 ATOM 69 C CB . PHE A 1 9 ? -0.997 2.441 -2.803 1.00 95.31 9 A 1 ATOM 70 C CG . PHE A 1 9 ? -1.120 2.982 -4.201 1.00 93.20 9 A 1 ATOM 71 C CD1 . PHE A 1 9 ? -2.276 2.784 -4.937 1.00 90.28 9 A 1 ATOM 72 C CD2 . PHE A 1 9 ? -0.076 3.692 -4.769 1.00 90.64 9 A 1 ATOM 73 C CE1 . PHE A 1 9 ? -2.390 3.284 -6.224 1.00 89.58 9 A 1 ATOM 74 C CE2 . PHE A 1 9 ? -0.183 4.194 -6.060 1.00 88.73 9 A 1 ATOM 75 C CZ . PHE A 1 9 ? -1.341 3.990 -6.787 1.00 89.93 9 A 1 ATOM 76 N N . LEU A 1 10 ? 1.667 0.858 -2.292 1.00 96.74 10 A 1 ATOM 77 C CA . LEU A 1 10 ? 3.076 0.625 -2.587 1.00 96.93 10 A 1 ATOM 78 C C . LEU A 1 10 ? 3.334 -0.850 -2.871 1.00 97.51 10 A 1 ATOM 79 O O . LEU A 1 10 ? 4.085 -1.188 -3.790 1.00 97.24 10 A 1 ATOM 80 C CB . LEU A 1 10 ? 3.937 1.091 -1.410 1.00 96.75 10 A 1 ATOM 81 C CG . LEU A 1 10 ? 4.134 2.602 -1.324 1.00 92.22 10 A 1 ATOM 82 C CD1 . LEU A 1 10 ? 4.603 2.999 0.065 1.00 89.19 10 A 1 ATOM 83 C CD2 . LEU A 1 10 ? 5.136 3.065 -2.372 1.00 90.26 10 A 1 ATOM 84 N N . LEU A 1 11 ? 2.715 -1.716 -2.088 1.00 97.36 11 A 1 ATOM 85 C CA . LEU A 1 11 ? 2.873 -3.155 -2.257 1.00 97.11 11 A 1 ATOM 86 C C . LEU A 1 11 ? 2.297 -3.616 -3.590 1.00 97.38 11 A 1 ATOM 87 O O . LEU A 1 11 ? 2.912 -4.418 -4.294 1.00 97.02 11 A 1 ATOM 88 C CB . LEU A 1 11 ? 2.183 -3.891 -1.107 1.00 96.89 11 A 1 ATOM 89 C CG . LEU A 1 11 ? 2.920 -3.823 0.230 1.00 94.02 11 A 1 ATOM 90 C CD1 . LEU A 1 11 ? 1.985 -4.203 1.367 1.00 91.08 11 A 1 ATOM 91 C CD2 . LEU A 1 11 ? 4.129 -4.749 0.212 1.00 91.82 11 A 1 ATOM 92 N N . LEU A 1 12 ? 1.130 -3.095 -3.936 1.00 96.66 12 A 1 ATOM 93 C CA . LEU A 1 12 ? 0.472 -3.446 -5.189 1.00 96.18 12 A 1 ATOM 94 C C . LEU A 1 12 ? 1.238 -2.904 -6.387 1.00 96.30 12 A 1 ATOM 95 O O . LEU A 1 12 ? 1.356 -3.578 -7.413 1.00 94.79 12 A 1 ATOM 96 C CB . LEU A 1 12 ? -0.955 -2.905 -5.190 1.00 95.36 12 A 1 ATOM 97 C CG . LEU A 1 12 ? -1.913 -3.626 -4.248 1.00 92.08 12 A 1 ATOM 98 C CD1 . LEU A 1 12 ? -3.160 -2.790 -4.022 1.00 87.86 12 A 1 ATOM 99 C CD2 . LEU A 1 12 ? -2.280 -4.988 -4.820 1.00 86.81 12 A 1 ATOM 100 N N . GLY A 1 13 ? 1.755 -1.709 -6.251 1.00 95.94 13 A 1 ATOM 101 C CA . GLY A 1 13 ? 2.519 -1.087 -7.325 1.00 95.32 13 A 1 ATOM 102 C C . GLY A 1 13 ? 3.889 -1.704 -7.517 1.00 95.71 13 A 1 ATOM 103 O O . GLY A 1 13 ? 4.449 -1.672 -8.613 1.00 94.16 13 A 1 ATOM 104 N N . SER A 1 14 ? 4.436 -2.268 -6.449 1.00 96.07 14 A 1 ATOM 105 C CA . SER A 1 14 ? 5.754 -2.893 -6.492 1.00 96.04 14 A 1 ATOM 106 C C . SER A 1 14 ? 5.672 -4.366 -6.870 1.00 95.90 14 A 1 ATOM 107 O O . SER A 1 14 ? 6.560 -4.889 -7.547 1.00 92.35 14 A 1 ATOM 108 C CB . SER A 1 14 ? 6.458 -2.747 -5.142 1.00 94.35 14 A 1 ATOM 109 O OG . SER A 1 14 ? 7.817 -3.079 -5.252 1.00 83.62 14 A 1 ATOM 110 N N . CYS A 1 15 ? 4.610 -5.031 -6.438 1.00 93.34 15 A 1 ATOM 111 C CA . CYS A 1 15 ? 4.424 -6.454 -6.710 1.00 93.01 15 A 1 ATOM 112 C C . CYS A 1 15 ? 3.092 -6.728 -7.408 1.00 93.84 15 A 1 ATOM 113 O O . CYS A 1 15 ? 2.431 -7.736 -7.145 1.00 90.71 15 A 1 ATOM 114 C CB . CYS A 1 15 ? 4.509 -7.250 -5.400 1.00 89.35 15 A 1 ATOM 115 S SG . CYS A 1 15 ? 4.821 -9.003 -5.666 1.00 81.19 15 A 1 ATOM 116 N N . GLY A 1 16 ? 2.710 -5.838 -8.304 1.00 88.48 16 A 1 ATOM 117 C CA . GLY A 1 16 ? 1.456 -5.978 -9.023 1.00 85.41 16 A 1 ATOM 118 C C . GLY A 1 16 ? 1.479 -5.239 -10.343 1.00 85.28 16 A 1 ATOM 119 O O . GLY A 1 16 ? 2.321 -4.373 -10.571 1.00 81.01 16 A 1 ATOM 120 N N . ALA A 1 17 ? 0.538 -5.598 -11.221 1.00 88.21 17 A 1 ATOM 121 C CA . ALA A 1 17 ? 0.464 -4.963 -12.531 1.00 85.35 17 A 1 ATOM 122 C C . ALA A 1 17 ? -0.942 -4.400 -12.748 1.00 82.99 17 A 1 ATOM 123 O O . ALA A 1 17 ? -1.234 -3.307 -12.248 1.00 75.51 17 A 1 ATOM 124 C CB . ALA A 1 17 ? 0.837 -5.968 -13.623 1.00 78.31 17 A 1 ATOM 125 O OXT . ALA A 1 17 ? -1.772 -5.045 -13.387 1.00 68.89 17 A 1 #