# 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_spkb19634 # _entry.id spkb19634 # 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" "C5 H10 N2 O3" 146.144 GLN y GLUTAMINE C(CC(=O)N)[C@@H](C(=O)O)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" "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" "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 THR 2 1 n ALA 3 1 n THR 4 1 n LEU 5 1 n ILE 6 1 n LEU 7 1 n LEU 8 1 n LEU 9 1 n LEU 10 1 n ALA 11 1 n GLN 12 1 n VAL 13 1 n SER 14 1 n TRP 15 1 n ALA 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 @ 2025-07-07 02:22:07)" _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 95.29 _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 84.36 1 1 A THR 2 2 94.36 1 2 A ALA 3 2 97.62 1 3 A THR 4 2 96.81 1 4 A LEU 5 2 96.15 1 5 A ILE 6 2 97.25 1 6 A LEU 7 2 96.98 1 7 A LEU 8 2 96.79 1 8 A LEU 9 2 97.02 1 9 A LEU 10 2 97.34 1 10 A ALA 11 2 98.23 1 11 A GLN 12 2 94.91 1 12 A VAL 13 2 96.88 1 13 A SER 14 2 96.83 1 14 A TRP 15 2 92.85 1 15 A ALA 16 2 94.58 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 THR . 2 A 2 A 3 1 n ALA . 3 A 3 A 4 1 n THR . 4 A 4 A 5 1 n LEU . 5 A 5 A 6 1 n ILE . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n ALA . 11 A 11 A 12 1 n GLN . 12 A 12 A 13 1 n VAL . 13 A 13 A 14 1 n SER . 14 A 14 A 15 1 n TRP . 15 A 15 A 16 1 n ALA . 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 ? -14.141 -4.282 1.376 1.00 91.13 1 A 1 ATOM 2 C CA . MET A 1 1 ? -12.918 -3.756 2.005 1.00 90.38 1 A 1 ATOM 3 C C . MET A 1 1 ? -11.665 -4.120 1.214 1.00 91.63 1 A 1 ATOM 4 O O . MET A 1 1 ? -10.554 -3.844 1.651 1.00 90.87 1 A 1 ATOM 5 C CB . MET A 1 1 ? -12.799 -4.293 3.432 1.00 85.87 1 A 1 ATOM 6 C CG . MET A 1 1 ? -13.452 -3.367 4.435 1.00 80.51 1 A 1 ATOM 7 S SD . MET A 1 1 ? -13.067 -3.862 6.113 1.00 77.08 1 A 1 ATOM 8 C CE . MET A 1 1 ? -13.836 -2.524 7.007 1.00 67.45 1 A 1 ATOM 9 N N . THR A 1 2 ? -11.860 -4.723 0.073 1.00 96.13 2 A 1 ATOM 10 C CA . THR A 1 2 ? -10.725 -5.099 -0.775 1.00 96.68 2 A 1 ATOM 11 C C . THR A 1 2 ? -9.983 -3.866 -1.270 1.00 97.06 2 A 1 ATOM 12 O O . THR A 1 2 ? -8.754 -3.862 -1.351 1.00 96.25 2 A 1 ATOM 13 C CB . THR A 1 2 ? -11.213 -5.925 -1.964 1.00 95.25 2 A 1 ATOM 14 O OG1 . THR A 1 2 ? -12.222 -6.832 -1.529 1.00 90.13 2 A 1 ATOM 15 C CG2 . THR A 1 2 ? -10.077 -6.706 -2.579 1.00 89.00 2 A 1 ATOM 16 N N . ALA A 1 3 ? -10.729 -2.825 -1.595 1.00 97.21 3 A 1 ATOM 17 C CA . ALA A 1 3 ? -10.127 -1.581 -2.071 1.00 97.73 3 A 1 ATOM 18 C C . ALA A 1 3 ? -9.272 -0.940 -0.985 1.00 98.15 3 A 1 ATOM 19 O O . ALA A 1 3 ? -8.259 -0.309 -1.276 1.00 97.82 3 A 1 ATOM 20 C CB . ALA A 1 3 ? -11.215 -0.620 -2.518 1.00 97.17 3 A 1 ATOM 21 N N . THR A 1 4 ? -9.682 -1.117 0.259 1.00 97.97 4 A 1 ATOM 22 C CA . THR A 1 4 ? -8.944 -0.566 1.397 1.00 98.13 4 A 1 ATOM 23 C C . THR A 1 4 ? -7.584 -1.237 1.517 1.00 98.33 4 A 1 ATOM 24 O O . THR A 1 4 ? -6.587 -0.582 1.832 1.00 98.04 4 A 1 ATOM 25 C CB . THR A 1 4 ? -9.743 -0.765 2.688 1.00 97.73 4 A 1 ATOM 26 O OG1 . THR A 1 4 ? -11.086 -0.342 2.482 1.00 94.63 4 A 1 ATOM 27 C CG2 . THR A 1 4 ? -9.151 0.051 3.827 1.00 92.84 4 A 1 ATOM 28 N N . LEU A 1 5 ? -7.539 -2.534 1.252 1.00 97.93 5 A 1 ATOM 29 C CA . LEU A 1 5 ? -6.290 -3.285 1.309 1.00 98.04 5 A 1 ATOM 30 C C . LEU A 1 5 ? -5.333 -2.807 0.223 1.00 98.31 5 A 1 ATOM 31 O O . LEU A 1 5 ? -4.132 -2.675 0.460 1.00 98.25 5 A 1 ATOM 32 C CB . LEU A 1 5 ? -6.580 -4.777 1.138 1.00 97.89 5 A 1 ATOM 33 C CG . LEU A 1 5 ? -5.465 -5.667 1.674 1.00 94.78 5 A 1 ATOM 34 C CD1 . LEU A 1 5 ? -5.638 -5.895 3.172 1.00 91.72 5 A 1 ATOM 35 C CD2 . LEU A 1 5 ? -5.460 -6.992 0.943 1.00 92.24 5 A 1 ATOM 36 N N . ILE A 1 6 ? -5.872 -2.553 -0.949 1.00 98.19 6 A 1 ATOM 37 C CA . ILE A 1 6 ? -5.066 -2.070 -2.068 1.00 98.19 6 A 1 ATOM 38 C C . ILE A 1 6 ? -4.547 -0.669 -1.772 1.00 98.34 6 A 1 ATOM 39 O O . ILE A 1 6 ? -3.401 -0.339 -2.095 1.00 98.27 6 A 1 ATOM 40 C CB . ILE A 1 6 ? -5.890 -2.091 -3.370 1.00 98.10 6 A 1 ATOM 41 C CG1 . ILE A 1 6 ? -6.245 -3.534 -3.750 1.00 97.04 6 A 1 ATOM 42 C CG2 . ILE A 1 6 ? -5.100 -1.434 -4.511 1.00 96.54 6 A 1 ATOM 43 C CD1 . ILE A 1 6 ? -7.355 -3.622 -4.773 1.00 93.34 6 A 1 ATOM 44 N N . LEU A 1 7 ? -5.388 0.137 -1.157 1.00 98.22 7 A 1 ATOM 45 C CA . LEU A 1 7 ? -4.998 1.497 -0.794 1.00 98.16 7 A 1 ATOM 46 C C . LEU A 1 7 ? -3.858 1.471 0.214 1.00 98.28 7 A 1 ATOM 47 O O . LEU A 1 7 ? -2.910 2.251 0.109 1.00 98.23 7 A 1 ATOM 48 C CB . LEU A 1 7 ? -6.202 2.238 -0.209 1.00 98.03 7 A 1 ATOM 49 C CG . LEU A 1 7 ? -6.989 3.040 -1.243 1.00 95.83 7 A 1 ATOM 50 C CD1 . LEU A 1 7 ? -8.402 3.308 -0.744 1.00 94.45 7 A 1 ATOM 51 C CD2 . LEU A 1 7 ? -6.282 4.361 -1.524 1.00 94.67 7 A 1 ATOM 52 N N . LEU A 1 8 ? -3.949 0.559 1.177 1.00 98.20 8 A 1 ATOM 53 C CA . LEU A 1 8 ? -2.906 0.410 2.189 1.00 98.04 8 A 1 ATOM 54 C C . LEU A 1 8 ? -1.619 -0.083 1.545 1.00 98.22 8 A 1 ATOM 55 O O . LEU A 1 8 ? -0.530 0.380 1.890 1.00 98.18 8 A 1 ATOM 56 C CB . LEU A 1 8 ? -3.371 -0.569 3.267 1.00 97.91 8 A 1 ATOM 57 C CG . LEU A 1 8 ? -3.852 0.107 4.550 1.00 95.19 8 A 1 ATOM 58 C CD1 . LEU A 1 8 ? -4.800 -0.805 5.318 1.00 93.96 8 A 1 ATOM 59 C CD2 . LEU A 1 8 ? -2.661 0.470 5.425 1.00 94.65 8 A 1 ATOM 60 N N . LEU A 1 9 ? -1.748 -1.000 0.611 1.00 98.06 9 A 1 ATOM 61 C CA . LEU A 1 9 ? -0.591 -1.543 -0.096 1.00 98.02 9 A 1 ATOM 62 C C . LEU A 1 9 ? 0.072 -0.461 -0.936 1.00 98.24 9 A 1 ATOM 63 O O . LEU A 1 9 ? 1.300 -0.406 -1.028 1.00 98.21 9 A 1 ATOM 64 C CB . LEU A 1 9 ? -1.035 -2.711 -0.978 1.00 98.02 9 A 1 ATOM 65 C CG . LEU A 1 9 ? 0.122 -3.510 -1.564 1.00 96.05 9 A 1 ATOM 66 C CD1 . LEU A 1 9 ? 0.027 -4.974 -1.160 1.00 94.53 9 A 1 ATOM 67 C CD2 . LEU A 1 9 ? 0.140 -3.392 -3.073 1.00 95.04 9 A 1 ATOM 68 N N . LEU A 1 10 ? -0.734 0.389 -1.537 1.00 98.38 10 A 1 ATOM 69 C CA . LEU A 1 10 ? -0.220 1.486 -2.354 1.00 98.28 10 A 1 ATOM 70 C C . LEU A 1 10 ? 0.576 2.462 -1.496 1.00 98.26 10 A 1 ATOM 71 O O . LEU A 1 10 ? 1.642 2.928 -1.898 1.00 97.92 10 A 1 ATOM 72 C CB . LEU A 1 10 ? -1.386 2.201 -3.037 1.00 98.13 10 A 1 ATOM 73 C CG . LEU A 1 10 ? -1.303 2.177 -4.564 1.00 96.91 10 A 1 ATOM 74 C CD1 . LEU A 1 10 ? -2.697 2.218 -5.176 1.00 95.41 10 A 1 ATOM 75 C CD2 . LEU A 1 10 ? -0.476 3.335 -5.075 1.00 95.40 10 A 1 ATOM 76 N N . ALA A 1 11 ? 0.058 2.750 -0.317 1.00 98.47 11 A 1 ATOM 77 C CA . ALA A 1 11 ? 0.742 3.659 0.601 1.00 98.35 11 A 1 ATOM 78 C C . ALA A 1 11 ? 1.999 3.007 1.171 1.00 98.36 11 A 1 ATOM 79 O O . ALA A 1 11 ? 3.005 3.678 1.399 1.00 97.85 11 A 1 ATOM 80 C CB . ALA A 1 11 ? -0.208 4.064 1.721 1.00 98.11 11 A 1 ATOM 81 N N . GLN A 1 12 ? 1.945 1.691 1.380 1.00 98.36 12 A 1 ATOM 82 C CA . GLN A 1 12 ? 3.081 0.953 1.924 1.00 98.27 12 A 1 ATOM 83 C C . GLN A 1 12 ? 4.182 0.806 0.881 1.00 98.39 12 A 1 ATOM 84 O O . GLN A 1 12 ? 5.356 1.008 1.180 1.00 97.68 12 A 1 ATOM 85 C CB . GLN A 1 12 ? 2.616 -0.418 2.404 1.00 97.79 12 A 1 ATOM 86 C CG . GLN A 1 12 ? 3.229 -0.777 3.737 1.00 95.33 12 A 1 ATOM 87 C CD . GLN A 1 12 ? 2.780 -2.139 4.218 1.00 92.69 12 A 1 ATOM 88 O OE1 . GLN A 1 12 ? 3.587 -3.040 4.385 1.00 88.29 12 A 1 ATOM 89 N NE2 . GLN A 1 12 ? 1.500 -2.317 4.445 1.00 87.41 12 A 1 ATOM 90 N N . VAL A 1 13 ? 3.801 0.482 -0.339 1.00 98.26 13 A 1 ATOM 91 C CA . VAL A 1 13 ? 4.775 0.308 -1.420 1.00 98.12 13 A 1 ATOM 92 C C . VAL A 1 13 ? 5.504 1.617 -1.702 1.00 98.23 13 A 1 ATOM 93 O O . VAL A 1 13 ? 6.636 1.617 -2.188 1.00 97.47 13 A 1 ATOM 94 C CB . VAL A 1 13 ? 4.080 -0.225 -2.691 1.00 97.42 13 A 1 ATOM 95 C CG1 . VAL A 1 13 ? 3.435 0.905 -3.489 1.00 94.51 13 A 1 ATOM 96 C CG2 . VAL A 1 13 ? 5.061 -0.987 -3.558 1.00 94.15 13 A 1 ATOM 97 N N . SER A 1 14 ? 4.867 2.719 -1.394 1.00 98.06 14 A 1 ATOM 98 C CA . SER A 1 14 ? 5.470 4.042 -1.577 1.00 98.01 14 A 1 ATOM 99 C C . SER A 1 14 ? 6.581 4.275 -0.556 1.00 98.03 14 A 1 ATOM 100 O O . SER A 1 14 ? 7.484 5.087 -0.783 1.00 97.27 14 A 1 ATOM 101 C CB . SER A 1 14 ? 4.399 5.119 -1.452 1.00 97.31 14 A 1 ATOM 102 O OG . SER A 1 14 ? 4.966 6.401 -1.554 1.00 92.27 14 A 1 ATOM 103 N N . TRP A 1 15 ? 6.515 3.564 0.565 1.00 96.87 15 A 1 ATOM 104 C CA . TRP A 1 15 ? 7.514 3.674 1.627 1.00 96.74 15 A 1 ATOM 105 C C . TRP A 1 15 ? 8.386 2.423 1.733 1.00 96.79 15 A 1 ATOM 106 O O . TRP A 1 15 ? 9.228 2.334 2.616 1.00 95.73 15 A 1 ATOM 107 C CB . TRP A 1 15 ? 6.825 3.959 2.961 1.00 95.46 15 A 1 ATOM 108 C CG . TRP A 1 15 ? 6.940 5.388 3.384 1.00 93.35 15 A 1 ATOM 109 C CD1 . TRP A 1 15 ? 6.033 6.372 3.180 1.00 92.15 15 A 1 ATOM 110 C CD2 . TRP A 1 15 ? 8.034 6.002 4.103 1.00 93.65 15 A 1 ATOM 111 N NE1 . TRP A 1 15 ? 6.484 7.559 3.716 1.00 91.36 15 A 1 ATOM 112 C CE2 . TRP A 1 15 ? 7.710 7.365 4.290 1.00 92.24 15 A 1 ATOM 113 C CE3 . TRP A 1 15 ? 9.247 5.520 4.600 1.00 90.78 15 A 1 ATOM 114 C CZ2 . TRP A 1 15 ? 8.569 8.245 4.955 1.00 90.57 15 A 1 ATOM 115 C CZ3 . TRP A 1 15 ? 10.101 6.394 5.263 1.00 87.47 15 A 1 ATOM 116 C CH2 . TRP A 1 15 ? 9.761 7.740 5.434 1.00 86.75 15 A 1 ATOM 117 N N . ALA A 1 16 ? 8.176 1.477 0.830 1.00 97.39 16 A 1 ATOM 118 C CA . ALA A 1 16 ? 8.913 0.208 0.850 1.00 96.53 16 A 1 ATOM 119 C C . ALA A 1 16 ? 9.598 -0.028 -0.488 1.00 95.62 16 A 1 ATOM 120 O O . ALA A 1 16 ? 9.062 -0.763 -1.325 1.00 93.61 16 A 1 ATOM 121 C CB . ALA A 1 16 ? 7.974 -0.927 1.199 1.00 95.01 16 A 1 ATOM 122 O OXT . ALA A 1 16 ? 10.690 0.545 -0.697 1.00 89.33 16 A 1 #