# 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_spkb11499 # _entry.id spkb11499 # 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 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" "C5 H9 N O2" 115.130 PRO y PROLINE C1C[C@H](NC1)C(=O)O ? "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" "C11 H12 N2 O2" 204.225 TRP y TRYPTOPHAN c1ccc2c(c1)c(c[nH]2)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 GLY 2 1 n GLY 3 1 n ALA 4 1 n LEU 5 1 n GLY 6 1 n PRO 7 1 n ALA 8 1 n LEU 9 1 n LEU 10 1 n LEU 11 1 n THR 12 1 n SER 13 1 n LEU 14 1 n LEU 15 1 n GLY 16 1 n ALA 17 1 n TRP 18 1 n ALA 19 # _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 18:25:37)" _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 90.33 _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 71.16 1 1 A GLY 2 2 80.01 1 2 A GLY 3 2 85.61 1 3 A ALA 4 2 88.54 1 4 A LEU 5 2 86.86 1 5 A GLY 6 2 93.43 1 6 A PRO 7 2 93.48 1 7 A ALA 8 2 94.43 1 8 A LEU 9 2 93.65 1 9 A LEU 10 2 93.97 1 10 A LEU 11 2 93.66 1 11 A THR 12 2 93.68 1 12 A SER 13 2 95.50 1 13 A LEU 14 2 95.32 1 14 A LEU 15 2 94.52 1 15 A GLY 16 2 96.39 1 16 A ALA 17 2 96.37 1 17 A TRP 18 2 87.36 1 18 A ALA 19 2 85.64 1 19 # _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 GLY . 2 A 2 A 3 1 n GLY . 3 A 3 A 4 1 n ALA . 4 A 4 A 5 1 n LEU . 5 A 5 A 6 1 n GLY . 6 A 6 A 7 1 n PRO . 7 A 7 A 8 1 n ALA . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n LEU . 11 A 11 A 12 1 n THR . 12 A 12 A 13 1 n SER . 13 A 13 A 14 1 n LEU . 14 A 14 A 15 1 n LEU . 15 A 15 A 16 1 n GLY . 16 A 16 A 17 1 n ALA . 17 A 17 A 18 1 n TRP . 18 A 18 A 19 1 n ALA . 19 A 19 # _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 ? -0.129 16.727 7.568 1.00 75.52 1 A 1 ATOM 2 C CA . MET A 1 1 ? 0.348 15.469 8.180 1.00 76.37 1 A 1 ATOM 3 C C . MET A 1 1 ? -0.835 14.688 8.736 1.00 77.23 1 A 1 ATOM 4 O O . MET A 1 1 ? -1.779 15.277 9.234 1.00 72.15 1 A 1 ATOM 5 C CB . MET A 1 1 ? 1.317 15.783 9.317 1.00 71.88 1 A 1 ATOM 6 C CG . MET A 1 1 ? 2.539 16.522 8.810 1.00 69.85 1 A 1 ATOM 7 S SD . MET A 1 1 ? 3.617 17.021 10.157 1.00 67.10 1 A 1 ATOM 8 C CE . MET A 1 1 ? 4.825 17.950 9.230 1.00 59.14 1 A 1 ATOM 9 N N . GLY A 1 2 ? -0.774 13.409 8.639 1.00 77.86 2 A 1 ATOM 10 C CA . GLY A 1 2 ? -1.846 12.568 9.138 1.00 79.98 2 A 1 ATOM 11 C C . GLY A 1 2 ? -2.023 11.344 8.260 1.00 83.19 2 A 1 ATOM 12 O O . GLY A 1 2 ? -1.473 11.262 7.162 1.00 79.00 2 A 1 ATOM 13 N N . GLY A 1 3 ? -2.803 10.400 8.738 1.00 81.54 3 A 1 ATOM 14 C CA . GLY A 1 3 ? -3.036 9.177 7.978 1.00 85.27 3 A 1 ATOM 15 C C . GLY A 1 3 ? -1.786 8.321 7.889 1.00 88.88 3 A 1 ATOM 16 O O . GLY A 1 3 ? -1.308 8.025 6.800 1.00 86.73 3 A 1 ATOM 17 N N . ALA A 1 4 ? -1.259 7.930 9.012 1.00 85.05 4 A 1 ATOM 18 C CA . ALA A 1 4 ? -0.074 7.085 9.070 1.00 89.21 4 A 1 ATOM 19 C C . ALA A 1 4 ? -0.470 5.690 9.544 1.00 92.21 4 A 1 ATOM 20 O O . ALA A 1 4 ? -1.540 5.497 10.114 1.00 90.45 4 A 1 ATOM 21 C CB . ALA A 1 4 ? 0.957 7.699 10.010 1.00 85.79 4 A 1 ATOM 22 N N . LEU A 1 5 ? 0.412 4.746 9.301 1.00 88.76 5 A 1 ATOM 23 C CA . LEU A 1 5 ? 0.164 3.358 9.716 1.00 89.74 5 A 1 ATOM 24 C C . LEU A 1 5 ? -0.985 2.743 8.929 1.00 91.95 5 A 1 ATOM 25 O O . LEU A 1 5 ? -0.814 1.726 8.268 1.00 90.08 5 A 1 ATOM 26 C CB . LEU A 1 5 ? -0.141 3.318 11.220 1.00 87.61 5 A 1 ATOM 27 C CG . LEU A 1 5 ? 1.024 3.812 12.076 1.00 85.35 5 A 1 ATOM 28 C CD1 . LEU A 1 5 ? 0.521 4.370 13.398 1.00 82.39 5 A 1 ATOM 29 C CD2 . LEU A 1 5 ? 1.997 2.673 12.316 1.00 78.98 5 A 1 ATOM 30 N N . GLY A 1 6 ? -2.148 3.371 9.004 1.00 91.78 6 A 1 ATOM 31 C CA . GLY A 1 6 ? -3.320 2.884 8.284 1.00 92.54 6 A 1 ATOM 32 C C . GLY A 1 6 ? -3.085 2.803 6.787 1.00 94.69 6 A 1 ATOM 33 O O . GLY A 1 6 ? -3.045 1.708 6.212 1.00 94.72 6 A 1 ATOM 34 N N . PRO A 1 7 ? -2.925 3.967 6.131 1.00 93.62 7 A 1 ATOM 35 C CA . PRO A 1 7 ? -2.672 3.989 4.684 1.00 94.62 7 A 1 ATOM 36 C C . PRO A 1 7 ? -1.424 3.204 4.319 1.00 95.65 7 A 1 ATOM 37 O O . PRO A 1 7 ? -1.380 2.559 3.271 1.00 94.69 7 A 1 ATOM 38 C CB . PRO A 1 7 ? -2.485 5.482 4.376 1.00 92.50 7 A 1 ATOM 39 C CG . PRO A 1 7 ? -3.191 6.183 5.489 1.00 90.51 7 A 1 ATOM 40 C CD . PRO A 1 7 ? -3.044 5.287 6.701 1.00 92.75 7 A 1 ATOM 41 N N . ALA A 1 8 ? -0.414 3.253 5.163 1.00 93.89 8 A 1 ATOM 42 C CA . ALA A 1 8 ? 0.826 2.524 4.914 1.00 94.55 8 A 1 ATOM 43 C C . ALA A 1 8 ? 0.546 1.029 4.809 1.00 95.76 8 A 1 ATOM 44 O O . ALA A 1 8 ? 1.074 0.345 3.930 1.00 94.63 8 A 1 ATOM 45 C CB . ALA A 1 8 ? 1.817 2.807 6.034 1.00 93.34 8 A 1 ATOM 46 N N . LEU A 1 9 ? -0.290 0.537 5.691 1.00 95.29 9 A 1 ATOM 47 C CA . LEU A 1 9 ? -0.653 -0.881 5.691 1.00 95.35 9 A 1 ATOM 48 C C . LEU A 1 9 ? -1.455 -1.219 4.439 1.00 96.24 9 A 1 ATOM 49 O O . LEU A 1 9 ? -1.261 -2.271 3.832 1.00 95.82 9 A 1 ATOM 50 C CB . LEU A 1 9 ? -1.473 -1.190 6.941 1.00 94.97 9 A 1 ATOM 51 C CG . LEU A 1 9 ? -0.628 -1.135 8.215 1.00 92.31 9 A 1 ATOM 52 C CD1 . LEU A 1 9 ? -1.526 -1.053 9.438 1.00 89.94 9 A 1 ATOM 53 C CD2 . LEU A 1 9 ? 0.263 -2.372 8.306 1.00 89.29 9 A 1 ATOM 54 N N . LEU A 1 10 ? -2.338 -0.315 4.054 1.00 95.28 10 A 1 ATOM 55 C CA . LEU A 1 10 ? -3.149 -0.530 2.855 1.00 95.15 10 A 1 ATOM 56 C C . LEU A 1 10 ? -2.262 -0.552 1.615 1.00 95.98 10 A 1 ATOM 57 O O . LEU A 1 10 ? -2.432 -1.398 0.735 1.00 95.97 10 A 1 ATOM 58 C CB . LEU A 1 10 ? -4.184 0.586 2.746 1.00 95.04 10 A 1 ATOM 59 C CG . LEU A 1 10 ? -5.222 0.527 3.868 1.00 92.82 10 A 1 ATOM 60 C CD1 . LEU A 1 10 ? -6.029 1.815 3.905 1.00 90.93 10 A 1 ATOM 61 C CD2 . LEU A 1 10 ? -6.154 -0.666 3.660 1.00 90.59 10 A 1 ATOM 62 N N . LEU A 1 11 ? -1.316 0.369 1.556 1.00 95.28 11 A 1 ATOM 63 C CA . LEU A 1 11 ? -0.400 0.441 0.420 1.00 95.01 11 A 1 ATOM 64 C C . LEU A 1 11 ? 0.440 -0.823 0.338 1.00 95.81 11 A 1 ATOM 65 O O . LEU A 1 11 ? 0.587 -1.412 -0.735 1.00 95.73 11 A 1 ATOM 66 C CB . LEU A 1 11 ? 0.498 1.668 0.577 1.00 94.55 11 A 1 ATOM 67 C CG . LEU A 1 11 ? -0.246 2.974 0.306 1.00 92.29 11 A 1 ATOM 68 C CD1 . LEU A 1 11 ? 0.565 4.157 0.816 1.00 90.55 11 A 1 ATOM 69 C CD2 . LEU A 1 11 ? -0.500 3.124 -1.192 1.00 90.05 11 A 1 ATOM 70 N N . THR A 1 12 ? 0.980 -1.235 1.452 1.00 95.91 12 A 1 ATOM 71 C CA . THR A 1 12 ? 1.805 -2.439 1.477 1.00 95.33 12 A 1 ATOM 72 C C . THR A 1 12 ? 0.960 -3.657 1.125 1.00 96.08 12 A 1 ATOM 73 O O . THR A 1 12 ? 1.449 -4.605 0.511 1.00 95.08 12 A 1 ATOM 74 C CB . THR A 1 12 ? 2.474 -2.604 2.849 1.00 93.93 12 A 1 ATOM 75 O OG1 . THR A 1 12 ? 3.447 -3.645 2.764 1.00 90.27 12 A 1 ATOM 76 C CG2 . THR A 1 12 ? 1.471 -2.980 3.921 1.00 89.18 12 A 1 ATOM 77 N N . SER A 1 13 ? -0.302 -3.606 1.480 1.00 96.66 13 A 1 ATOM 78 C CA . SER A 1 13 ? -1.225 -4.693 1.174 1.00 96.60 13 A 1 ATOM 79 C C . SER A 1 13 ? -1.385 -4.823 -0.334 1.00 97.20 13 A 1 ATOM 80 O O . SER A 1 13 ? -1.356 -5.930 -0.880 1.00 96.32 13 A 1 ATOM 81 C CB . SER A 1 13 ? -2.583 -4.427 1.822 1.00 95.84 13 A 1 ATOM 82 O OG . SER A 1 13 ? -3.391 -5.568 1.714 1.00 90.36 13 A 1 ATOM 83 N N . LEU A 1 14 ? -1.537 -3.683 -0.997 1.00 96.66 14 A 1 ATOM 84 C CA . LEU A 1 14 ? -1.672 -3.672 -2.454 1.00 96.46 14 A 1 ATOM 85 C C . LEU A 1 14 ? -0.392 -4.190 -3.097 1.00 96.97 14 A 1 ATOM 86 O O . LEU A 1 14 ? -0.437 -5.006 -4.020 1.00 96.61 14 A 1 ATOM 87 C CB . LEU A 1 14 ? -1.962 -2.247 -2.921 1.00 96.16 14 A 1 ATOM 88 C CG . LEU A 1 14 ? -3.354 -1.768 -2.501 1.00 94.81 14 A 1 ATOM 89 C CD1 . LEU A 1 14 ? -3.469 -0.264 -2.657 1.00 92.62 14 A 1 ATOM 90 C CD2 . LEU A 1 14 ? -4.421 -2.464 -3.343 1.00 92.26 14 A 1 ATOM 91 N N . LEU A 1 15 ? 0.736 -3.714 -2.609 1.00 96.64 15 A 1 ATOM 92 C CA . LEU A 1 15 ? 2.027 -4.155 -3.132 1.00 96.19 15 A 1 ATOM 93 C C . LEU A 1 15 ? 2.183 -5.657 -2.944 1.00 96.55 15 A 1 ATOM 94 O O . LEU A 1 15 ? 2.641 -6.359 -3.847 1.00 95.90 15 A 1 ATOM 95 C CB . LEU A 1 15 ? 3.140 -3.404 -2.406 1.00 95.53 15 A 1 ATOM 96 C CG . LEU A 1 15 ? 3.273 -1.959 -2.884 1.00 93.72 15 A 1 ATOM 97 C CD1 . LEU A 1 15 ? 4.063 -1.133 -1.877 1.00 91.09 15 A 1 ATOM 98 C CD2 . LEU A 1 15 ? 3.956 -1.926 -4.245 1.00 90.50 15 A 1 ATOM 99 N N . GLY A 1 16 ? 1.790 -6.142 -1.794 1.00 96.68 16 A 1 ATOM 100 C CA . GLY A 1 16 ? 1.870 -7.570 -1.514 1.00 96.14 16 A 1 ATOM 101 C C . GLY A 1 16 ? 0.980 -8.363 -2.444 1.00 96.81 16 A 1 ATOM 102 O O . GLY A 1 16 ? 1.333 -9.462 -2.877 1.00 95.93 16 A 1 ATOM 103 N N . ALA A 1 17 ? -0.170 -7.795 -2.768 1.00 96.67 17 A 1 ATOM 104 C CA . ALA A 1 17 ? -1.110 -8.445 -3.680 1.00 96.61 17 A 1 ATOM 105 C C . ALA A 1 17 ? -0.487 -8.597 -5.066 1.00 97.17 17 A 1 ATOM 106 O O . ALA A 1 17 ? -0.674 -9.617 -5.732 1.00 95.86 17 A 1 ATOM 107 C CB . ALA A 1 17 ? -2.397 -7.628 -3.756 1.00 95.53 17 A 1 ATOM 108 N N . TRP A 1 18 ? 0.236 -7.555 -5.496 1.00 93.49 18 A 1 ATOM 109 C CA . TRP A 1 18 ? 0.901 -7.591 -6.805 1.00 92.04 18 A 1 ATOM 110 C C . TRP A 1 18 ? 2.210 -8.363 -6.718 1.00 92.57 18 A 1 ATOM 111 O O . TRP A 1 18 ? 2.642 -8.960 -7.701 1.00 91.38 18 A 1 ATOM 112 C CB . TRP A 1 18 ? 1.167 -6.163 -7.298 1.00 89.79 18 A 1 ATOM 113 C CG . TRP A 1 18 ? -0.011 -5.252 -7.098 1.00 87.84 18 A 1 ATOM 114 C CD1 . TRP A 1 18 ? -0.001 -4.020 -6.524 1.00 86.06 18 A 1 ATOM 115 C CD2 . TRP A 1 18 ? -1.383 -5.495 -7.468 1.00 87.86 18 A 1 ATOM 116 N NE1 . TRP A 1 18 ? -1.262 -3.485 -6.511 1.00 84.28 18 A 1 ATOM 117 C CE2 . TRP A 1 18 ? -2.142 -4.371 -7.081 1.00 86.01 18 A 1 ATOM 118 C CE3 . TRP A 1 18 ? -2.044 -6.566 -8.092 1.00 84.67 18 A 1 ATOM 119 C CZ2 . TRP A 1 18 ? -3.517 -4.290 -7.292 1.00 84.52 18 A 1 ATOM 120 C CZ3 . TRP A 1 18 ? -3.411 -6.483 -8.301 1.00 80.96 18 A 1 ATOM 121 C CH2 . TRP A 1 18 ? -4.139 -5.358 -7.905 1.00 81.57 18 A 1 ATOM 122 N N . ALA A 1 19 ? 2.830 -8.335 -5.575 1.00 92.92 19 A 1 ATOM 123 C CA . ALA A 1 19 ? 4.116 -8.993 -5.362 1.00 90.30 19 A 1 ATOM 124 C C . ALA A 1 19 ? 3.963 -10.517 -5.346 1.00 87.25 19 A 1 ATOM 125 O O . ALA A 1 19 ? 2.882 -11.040 -5.651 1.00 82.51 19 A 1 ATOM 126 C CB . ALA A 1 19 ? 4.727 -8.499 -4.058 1.00 84.65 19 A 1 ATOM 127 O OXT . ALA A 1 19 ? 4.941 -11.216 -5.036 1.00 76.23 19 A 1 #