# 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_spkb19834 # _entry.id spkb19834 # 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 H9 N O4" 147.129 GLU y "GLUTAMIC ACID" C(CC(=O)O)[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" "C6 H15 N2 O2" 147.195 LYS y LYSINE C(CC[NH3+])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" # _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 LYS 2 1 n TRP 3 1 n THR 4 1 n ILE 5 1 n LEU 6 1 n THR 7 1 n ALA 8 1 n LEU 9 1 n LEU 10 1 n ILE 11 1 n ILE 12 1 n SER 13 1 n ALA 14 1 n GLU 15 1 n SER 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 @ 2025-07-09 16:51:23)" _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 95.67 _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 92.53 1 1 A LYS 2 2 92.62 1 2 A TRP 3 2 95.18 1 3 A THR 4 2 97.54 1 4 A ILE 5 2 97.50 1 5 A LEU 6 2 96.46 1 6 A THR 7 2 97.00 1 7 A ALA 8 2 98.62 1 8 A LEU 9 2 96.94 1 9 A LEU 10 2 97.22 1 10 A ILE 11 2 97.84 1 11 A ILE 12 2 97.60 1 12 A SER 13 2 96.57 1 13 A ALA 14 2 98.53 1 14 A GLU 15 2 91.63 1 15 A SER 16 2 90.34 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 LYS . 2 A 2 A 3 1 n TRP . 3 A 3 A 4 1 n THR . 4 A 4 A 5 1 n ILE . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n THR . 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 ILE . 11 A 11 A 12 1 n ILE . 12 A 12 A 13 1 n SER . 13 A 13 A 14 1 n ALA . 14 A 14 A 15 1 n GLU . 15 A 15 A 16 1 n SER . 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 ? 1.125 11.870 -0.635 1.00 96.90 1 A 1 ATOM 2 C CA . MET A 1 1 ? 0.059 10.856 -0.470 1.00 97.41 1 A 1 ATOM 3 C C . MET A 1 1 ? 0.339 9.965 0.738 1.00 97.89 1 A 1 ATOM 4 O O . MET A 1 1 ? 1.417 9.402 0.854 1.00 96.83 1 A 1 ATOM 5 C CB . MET A 1 1 ? -0.027 9.996 -1.731 1.00 95.27 1 A 1 ATOM 6 C CG . MET A 1 1 ? -0.589 10.786 -2.904 1.00 90.54 1 A 1 ATOM 7 S SD . MET A 1 1 ? 0.241 10.358 -4.437 1.00 87.45 1 A 1 ATOM 8 C CE . MET A 1 1 ? 0.041 11.861 -5.358 1.00 77.95 1 A 1 ATOM 9 N N . LYS A 1 2 ? -0.619 9.870 1.622 1.00 97.86 2 A 1 ATOM 10 C CA . LYS A 1 2 ? -0.458 9.090 2.854 1.00 98.12 2 A 1 ATOM 11 C C . LYS A 1 2 ? -1.038 7.680 2.726 1.00 98.30 2 A 1 ATOM 12 O O . LYS A 1 2 ? -0.467 6.721 3.240 1.00 98.04 2 A 1 ATOM 13 C CB . LYS A 1 2 ? -1.144 9.845 3.996 1.00 97.50 2 A 1 ATOM 14 C CG . LYS A 1 2 ? -0.953 9.176 5.339 1.00 93.33 2 A 1 ATOM 15 C CD . LYS A 1 2 ? 0.110 9.894 6.152 1.00 89.85 2 A 1 ATOM 16 C CE . LYS A 1 2 ? 0.089 9.414 7.588 1.00 83.63 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? 1.034 10.196 8.421 1.00 76.96 2 A 1 ATOM 18 N N . TRP A 1 3 ? -2.164 7.546 2.050 1.00 98.12 3 A 1 ATOM 19 C CA . TRP A 1 3 ? -2.819 6.249 1.898 1.00 98.47 3 A 1 ATOM 20 C C . TRP A 1 3 ? -2.234 5.440 0.747 1.00 98.60 3 A 1 ATOM 21 O O . TRP A 1 3 ? -2.291 4.217 0.746 1.00 98.35 3 A 1 ATOM 22 C CB . TRP A 1 3 ? -4.320 6.452 1.686 1.00 98.14 3 A 1 ATOM 23 C CG . TRP A 1 3 ? -5.123 6.045 2.879 1.00 96.72 3 A 1 ATOM 24 C CD1 . TRP A 1 3 ? -5.317 6.760 4.010 1.00 94.67 3 A 1 ATOM 25 C CD2 . TRP A 1 3 ? -5.843 4.802 3.062 1.00 95.78 3 A 1 ATOM 26 N NE1 . TRP A 1 3 ? -6.110 6.051 4.890 1.00 93.33 3 A 1 ATOM 27 C CE2 . TRP A 1 3 ? -6.447 4.843 4.330 1.00 95.26 3 A 1 ATOM 28 C CE3 . TRP A 1 3 ? -6.026 3.674 2.261 1.00 92.99 3 A 1 ATOM 29 C CZ2 . TRP A 1 3 ? -7.223 3.785 4.809 1.00 91.59 3 A 1 ATOM 30 C CZ3 . TRP A 1 3 ? -6.799 2.623 2.740 1.00 91.11 3 A 1 ATOM 31 C CH2 . TRP A 1 3 ? -7.387 2.683 4.004 1.00 89.44 3 A 1 ATOM 32 N N . THR A 1 4 ? -1.655 6.115 -0.228 1.00 98.62 4 A 1 ATOM 33 C CA . THR A 1 4 ? -1.063 5.443 -1.384 1.00 98.70 4 A 1 ATOM 34 C C . THR A 1 4 ? 0.014 4.451 -0.962 1.00 98.75 4 A 1 ATOM 35 O O . THR A 1 4 ? 0.110 3.355 -1.508 1.00 98.56 4 A 1 ATOM 36 C CB . THR A 1 4 ? -0.450 6.469 -2.346 1.00 98.52 4 A 1 ATOM 37 O OG1 . THR A 1 4 ? 0.266 7.446 -1.609 1.00 95.13 4 A 1 ATOM 38 C CG2 . THR A 1 4 ? -1.518 7.140 -3.182 1.00 94.52 4 A 1 ATOM 39 N N . ILE A 1 5 ? 0.818 4.830 -0.006 1.00 98.62 5 A 1 ATOM 40 C CA . ILE A 1 5 ? 1.893 3.965 0.477 1.00 98.55 5 A 1 ATOM 41 C C . ILE A 1 5 ? 1.337 2.729 1.183 1.00 98.55 5 A 1 ATOM 42 O O . ILE A 1 5 ? 1.906 1.643 1.095 1.00 98.38 5 A 1 ATOM 43 C CB . ILE A 1 5 ? 2.827 4.749 1.422 1.00 98.41 5 A 1 ATOM 44 C CG1 . ILE A 1 5 ? 2.035 5.458 2.513 1.00 97.23 5 A 1 ATOM 45 C CG2 . ILE A 1 5 ? 3.648 5.763 0.626 1.00 96.79 5 A 1 ATOM 46 C CD1 . ILE A 1 5 ? 2.046 4.709 3.829 1.00 93.49 5 A 1 ATOM 47 N N . LEU A 1 6 ? 0.250 2.905 1.865 1.00 98.73 6 A 1 ATOM 48 C CA . LEU A 1 6 ? -0.385 1.802 2.583 1.00 98.72 6 A 1 ATOM 49 C C . LEU A 1 6 ? -1.045 0.831 1.611 1.00 98.76 6 A 1 ATOM 50 O O . LEU A 1 6 ? -0.993 -0.383 1.799 1.00 98.68 6 A 1 ATOM 51 C CB . LEU A 1 6 ? -1.426 2.352 3.561 1.00 98.56 6 A 1 ATOM 52 C CG . LEU A 1 6 ? -1.628 1.458 4.781 1.00 94.92 6 A 1 ATOM 53 C CD1 . LEU A 1 6 ? -0.567 1.753 5.839 1.00 91.16 6 A 1 ATOM 54 C CD2 . LEU A 1 6 ? -3.016 1.670 5.372 1.00 92.13 6 A 1 ATOM 55 N N . THR A 1 7 ? -1.650 1.368 0.577 1.00 98.65 7 A 1 ATOM 56 C CA . THR A 1 7 ? -2.330 0.554 -0.431 1.00 98.64 7 A 1 ATOM 57 C C . THR A 1 7 ? -1.324 -0.299 -1.201 1.00 98.73 7 A 1 ATOM 58 O O . THR A 1 7 ? -1.580 -1.462 -1.507 1.00 98.59 7 A 1 ATOM 59 C CB . THR A 1 7 ? -3.093 1.456 -1.408 1.00 98.34 7 A 1 ATOM 60 O OG1 . THR A 1 7 ? -3.902 2.375 -0.680 1.00 93.28 7 A 1 ATOM 61 C CG2 . THR A 1 7 ? -3.990 0.625 -2.311 1.00 92.80 7 A 1 ATOM 62 N N . ALA A 1 8 ? -0.189 0.280 -1.514 1.00 98.64 8 A 1 ATOM 63 C CA . ALA A 1 8 ? 0.855 -0.425 -2.255 1.00 98.65 8 A 1 ATOM 64 C C . ALA A 1 8 ? 1.386 -1.616 -1.460 1.00 98.73 8 A 1 ATOM 65 O O . ALA A 1 8 ? 1.703 -2.659 -2.022 1.00 98.57 8 A 1 ATOM 66 C CB . ALA A 1 8 ? 1.986 0.541 -2.570 1.00 98.49 8 A 1 ATOM 67 N N . LEU A 1 9 ? 1.486 -1.454 -0.172 1.00 98.73 9 A 1 ATOM 68 C CA . LEU A 1 9 ? 1.975 -2.514 0.706 1.00 98.69 9 A 1 ATOM 69 C C . LEU A 1 9 ? 0.990 -3.680 0.752 1.00 98.76 9 A 1 ATOM 70 O O . LEU A 1 9 ? 1.397 -4.839 0.809 1.00 98.62 9 A 1 ATOM 71 C CB . LEU A 1 9 ? 2.185 -1.953 2.114 1.00 98.46 9 A 1 ATOM 72 C CG . LEU A 1 9 ? 3.035 -2.850 3.009 1.00 95.43 9 A 1 ATOM 73 C CD1 . LEU A 1 9 ? 4.515 -2.575 2.783 1.00 92.93 9 A 1 ATOM 74 C CD2 . LEU A 1 9 ? 2.687 -2.627 4.473 1.00 93.94 9 A 1 ATOM 75 N N . LEU A 1 10 ? -0.274 -3.371 0.737 1.00 98.80 10 A 1 ATOM 76 C CA . LEU A 1 10 ? -1.324 -4.387 0.785 1.00 98.79 10 A 1 ATOM 77 C C . LEU A 1 10 ? -1.372 -5.183 -0.514 1.00 98.84 10 A 1 ATOM 78 O O . LEU A 1 10 ? -1.590 -6.395 -0.502 1.00 98.69 10 A 1 ATOM 79 C CB . LEU A 1 10 ? -2.671 -3.710 1.058 1.00 98.62 10 A 1 ATOM 80 C CG . LEU A 1 10 ? -3.753 -4.664 1.553 1.00 96.30 10 A 1 ATOM 81 C CD1 . LEU A 1 10 ? -4.672 -3.959 2.539 1.00 93.53 10 A 1 ATOM 82 C CD2 . LEU A 1 10 ? -4.569 -5.198 0.384 1.00 94.22 10 A 1 ATOM 83 N N . ILE A 1 11 ? -1.159 -4.508 -1.626 1.00 98.82 11 A 1 ATOM 84 C CA . ILE A 1 11 ? -1.196 -5.146 -2.938 1.00 98.80 11 A 1 ATOM 85 C C . ILE A 1 11 ? 0.009 -6.063 -3.133 1.00 98.83 11 A 1 ATOM 86 O O . ILE A 1 11 ? -0.128 -7.201 -3.580 1.00 98.70 11 A 1 ATOM 87 C CB . ILE A 1 11 ? -1.234 -4.081 -4.050 1.00 98.66 11 A 1 ATOM 88 C CG1 . ILE A 1 11 ? -2.531 -3.275 -3.984 1.00 97.52 11 A 1 ATOM 89 C CG2 . ILE A 1 11 ? -1.109 -4.751 -5.420 1.00 97.23 11 A 1 ATOM 90 C CD1 . ILE A 1 11 ? -2.464 -1.980 -4.769 1.00 94.12 11 A 1 ATOM 91 N N . ILE A 1 12 ? 1.177 -5.565 -2.807 1.00 98.73 12 A 1 ATOM 92 C CA . ILE A 1 12 ? 2.404 -6.339 -2.964 1.00 98.66 12 A 1 ATOM 93 C C . ILE A 1 12 ? 2.411 -7.562 -2.049 1.00 98.71 12 A 1 ATOM 94 O O . ILE A 1 12 ? 2.944 -8.615 -2.407 1.00 98.51 12 A 1 ATOM 95 C CB . ILE A 1 12 ? 3.639 -5.458 -2.686 1.00 98.41 12 A 1 ATOM 96 C CG1 . ILE A 1 12 ? 4.927 -6.227 -3.000 1.00 96.95 12 A 1 ATOM 97 C CG2 . ILE A 1 12 ? 3.645 -4.991 -1.230 1.00 96.82 12 A 1 ATOM 98 C CD1 . ILE A 1 12 ? 6.141 -5.336 -3.100 1.00 94.01 12 A 1 ATOM 99 N N . SER A 1 13 ? 1.828 -7.423 -0.892 1.00 98.73 13 A 1 ATOM 100 C CA . SER A 1 13 ? 1.757 -8.510 0.083 1.00 98.67 13 A 1 ATOM 101 C C . SER A 1 13 ? 0.797 -9.601 -0.380 1.00 98.67 13 A 1 ATOM 102 O O . SER A 1 13 ? 1.060 -10.791 -0.199 1.00 98.13 13 A 1 ATOM 103 C CB . SER A 1 13 ? 1.313 -7.968 1.442 1.00 98.23 13 A 1 ATOM 104 O OG . SER A 1 13 ? 1.465 -8.945 2.445 1.00 86.98 13 A 1 ATOM 105 N N . ALA A 1 14 ? -0.304 -9.201 -0.961 1.00 98.75 14 A 1 ATOM 106 C CA . ALA A 1 14 ? -1.314 -10.143 -1.448 1.00 98.69 14 A 1 ATOM 107 C C . ALA A 1 14 ? -0.972 -10.664 -2.839 1.00 98.67 14 A 1 ATOM 108 O O . ALA A 1 14 ? -1.373 -11.763 -3.217 1.00 98.15 14 A 1 ATOM 109 C CB . ALA A 1 14 ? -2.679 -9.467 -1.463 1.00 98.38 14 A 1 ATOM 110 N N . GLU A 1 15 ? -0.241 -9.876 -3.593 1.00 98.43 15 A 1 ATOM 111 C CA . GLU A 1 15 ? 0.142 -10.243 -4.955 1.00 98.12 15 A 1 ATOM 112 C C . GLU A 1 15 ? 1.172 -11.364 -4.957 1.00 97.56 15 A 1 ATOM 113 O O . GLU A 1 15 ? 1.321 -12.077 -5.944 1.00 94.73 15 A 1 ATOM 114 C CB . GLU A 1 15 ? 0.717 -9.021 -5.677 1.00 97.26 15 A 1 ATOM 115 C CG . GLU A 1 15 ? 0.925 -9.256 -7.155 1.00 90.85 15 A 1 ATOM 116 C CD . GLU A 1 15 ? 2.132 -8.512 -7.680 1.00 86.99 15 A 1 ATOM 117 O OE1 . GLU A 1 15 ? 3.253 -8.832 -7.261 1.00 80.01 15 A 1 ATOM 118 O OE2 . GLU A 1 15 ? 1.959 -7.614 -8.521 1.00 80.69 15 A 1 ATOM 119 N N . SER A 1 16 ? 1.881 -11.531 -3.860 1.00 96.44 16 A 1 ATOM 120 C CA . SER A 1 16 ? 2.929 -12.549 -3.726 1.00 95.12 16 A 1 ATOM 121 C C . SER A 1 16 ? 2.527 -13.869 -4.396 1.00 91.70 16 A 1 ATOM 122 O O . SER A 1 16 ? 3.348 -14.447 -5.118 1.00 86.86 16 A 1 ATOM 123 C CB . SER A 1 16 ? 3.233 -12.776 -2.243 1.00 92.54 16 A 1 ATOM 124 O OG . SER A 1 16 ? 3.856 -11.646 -1.678 1.00 85.49 16 A 1 ATOM 125 O OXT . SER A 1 16 ? 1.418 -14.322 -4.213 1.00 84.20 16 A 1 #