# 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_spkb34696 # _entry.id spkb34696 # 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 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" "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" "C4 H9 N O3" 119.119 THR y THREONINE C[C@H]([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 LYS 2 1 n PHE 3 1 n SER 4 1 n THR 5 1 n LEU 6 1 n SER 7 1 n THR 8 1 n VAL 9 1 n ALA 10 1 n ALA 11 1 n ILE 12 1 n ALA 13 1 n ALA 14 1 n PHE 15 1 n ALA 16 1 n SER 17 1 n ALA 18 # _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 @ 2025-07-12 16:14:41)" _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 92.85 _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 80.13 1 1 A LYS 2 2 82.18 1 2 A PHE 3 2 88.32 1 3 A SER 4 2 92.79 1 4 A THR 5 2 93.66 1 5 A LEU 6 2 94.56 1 6 A SER 7 2 94.80 1 7 A THR 8 2 95.96 1 8 A VAL 9 2 96.93 1 9 A ALA 10 2 97.21 1 10 A ALA 11 2 97.26 1 11 A ILE 12 2 96.09 1 12 A ALA 13 2 97.82 1 13 A ALA 14 2 97.93 1 14 A PHE 15 2 95.07 1 15 A ALA 16 2 97.68 1 16 A SER 17 2 94.33 1 17 A ALA 18 2 90.97 1 18 # _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 PHE . 3 A 3 A 4 1 n SER . 4 A 4 A 5 1 n THR . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n SER . 7 A 7 A 8 1 n THR . 8 A 8 A 9 1 n VAL . 9 A 9 A 10 1 n ALA . 10 A 10 A 11 1 n ALA . 11 A 11 A 12 1 n ILE . 12 A 12 A 13 1 n ALA . 13 A 13 A 14 1 n ALA . 14 A 14 A 15 1 n PHE . 15 A 15 A 16 1 n ALA . 16 A 16 A 17 1 n SER . 17 A 17 A 18 1 n ALA . 18 A 18 # _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 ? -14.734 -0.216 2.999 1.00 83.89 1 A 1 ATOM 2 C CA . MET A 1 1 ? -13.278 -0.082 2.867 1.00 86.15 1 A 1 ATOM 3 C C . MET A 1 1 ? -12.701 -1.107 1.899 1.00 87.38 1 A 1 ATOM 4 O O . MET A 1 1 ? -11.556 -0.992 1.487 1.00 83.88 1 A 1 ATOM 5 C CB . MET A 1 1 ? -12.603 -0.244 4.229 1.00 80.52 1 A 1 ATOM 6 C CG . MET A 1 1 ? -12.904 0.903 5.175 1.00 79.23 1 A 1 ATOM 7 S SD . MET A 1 1 ? -12.020 0.736 6.730 1.00 75.18 1 A 1 ATOM 8 C CE . MET A 1 1 ? -12.645 2.157 7.609 1.00 64.85 1 A 1 ATOM 9 N N . LYS A 1 2 ? -13.496 -2.079 1.572 1.00 87.02 2 A 1 ATOM 10 C CA . LYS A 1 2 ? -13.085 -3.138 0.649 1.00 89.06 2 A 1 ATOM 11 C C . LYS A 1 2 ? -11.901 -3.944 1.185 1.00 89.98 2 A 1 ATOM 12 O O . LYS A 1 2 ? -11.166 -3.484 2.055 1.00 89.38 2 A 1 ATOM 13 C CB . LYS A 1 2 ? -12.730 -2.544 -0.713 1.00 84.86 2 A 1 ATOM 14 C CG . LYS A 1 2 ? -13.927 -2.392 -1.624 1.00 80.45 2 A 1 ATOM 15 C CD . LYS A 1 2 ? -13.516 -1.779 -2.940 1.00 78.81 2 A 1 ATOM 16 C CE . LYS A 1 2 ? -14.666 -1.820 -3.928 1.00 72.69 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? -14.890 -3.196 -4.439 1.00 67.33 2 A 1 ATOM 18 N N . PHE A 1 3 ? -11.719 -5.146 0.648 1.00 90.47 3 A 1 ATOM 19 C CA . PHE A 1 3 ? -10.635 -6.018 1.078 1.00 92.73 3 A 1 ATOM 20 C C . PHE A 1 3 ? -9.409 -5.802 0.199 1.00 95.01 3 A 1 ATOM 21 O O . PHE A 1 3 ? -9.247 -6.444 -0.840 1.00 93.33 3 A 1 ATOM 22 C CB . PHE A 1 3 ? -11.080 -7.476 1.001 1.00 91.03 3 A 1 ATOM 23 C CG . PHE A 1 3 ? -12.231 -7.789 1.920 1.00 88.59 3 A 1 ATOM 24 C CD1 . PHE A 1 3 ? -12.004 -8.032 3.262 1.00 85.44 3 A 1 ATOM 25 C CD2 . PHE A 1 3 ? -13.525 -7.832 1.435 1.00 85.48 3 A 1 ATOM 26 C CE1 . PHE A 1 3 ? -13.058 -8.320 4.117 1.00 83.30 3 A 1 ATOM 27 C CE2 . PHE A 1 3 ? -14.588 -8.115 2.282 1.00 83.69 3 A 1 ATOM 28 C CZ . PHE A 1 3 ? -14.354 -8.362 3.626 1.00 82.47 3 A 1 ATOM 29 N N . SER A 1 4 ? -8.551 -4.885 0.622 1.00 94.50 4 A 1 ATOM 30 C CA . SER A 1 4 ? -7.350 -4.574 -0.145 1.00 94.95 4 A 1 ATOM 31 C C . SER A 1 4 ? -6.144 -4.403 0.772 1.00 96.23 4 A 1 ATOM 32 O O . SER A 1 4 ? -5.678 -3.292 0.996 1.00 95.15 4 A 1 ATOM 33 C CB . SER A 1 4 ? -7.575 -3.314 -0.962 1.00 92.58 4 A 1 ATOM 34 O OG . SER A 1 4 ? -8.118 -2.283 -0.171 1.00 83.30 4 A 1 ATOM 35 N N . THR A 1 5 ? -5.650 -5.513 1.303 1.00 93.88 5 A 1 ATOM 36 C CA . THR A 1 5 ? -4.496 -5.485 2.192 1.00 95.08 5 A 1 ATOM 37 C C . THR A 1 5 ? -3.220 -5.225 1.401 1.00 96.07 5 A 1 ATOM 38 O O . THR A 1 5 ? -2.403 -4.389 1.776 1.00 95.25 5 A 1 ATOM 39 C CB . THR A 1 5 ? -4.359 -6.806 2.959 1.00 94.25 5 A 1 ATOM 40 O OG1 . THR A 1 5 ? -5.604 -7.141 3.556 1.00 90.88 5 A 1 ATOM 41 C CG2 . THR A 1 5 ? -3.302 -6.691 4.045 1.00 90.20 5 A 1 ATOM 42 N N . LEU A 1 6 ? -3.057 -5.934 0.306 1.00 96.86 6 A 1 ATOM 43 C CA . LEU A 1 6 ? -1.889 -5.762 -0.550 1.00 96.93 6 A 1 ATOM 44 C C . LEU A 1 6 ? -1.946 -4.434 -1.288 1.00 97.38 6 A 1 ATOM 45 O O . LEU A 1 6 ? -0.920 -3.790 -1.495 1.00 96.96 6 A 1 ATOM 46 C CB . LEU A 1 6 ? -1.813 -6.913 -1.549 1.00 96.44 6 A 1 ATOM 47 C CG . LEU A 1 6 ? -1.198 -8.184 -0.979 1.00 92.95 6 A 1 ATOM 48 C CD1 . LEU A 1 6 ? -1.770 -9.410 -1.673 1.00 90.08 6 A 1 ATOM 49 C CD2 . LEU A 1 6 ? 0.311 -8.147 -1.137 1.00 88.90 6 A 1 ATOM 50 N N . SER A 1 7 ? -3.139 -4.042 -1.675 1.00 96.57 7 A 1 ATOM 51 C CA . SER A 1 7 ? -3.340 -2.782 -2.386 1.00 96.55 7 A 1 ATOM 52 C C . SER A 1 7 ? -3.038 -1.591 -1.486 1.00 97.21 7 A 1 ATOM 53 O O . SER A 1 7 ? -2.396 -0.632 -1.909 1.00 96.90 7 A 1 ATOM 54 C CB . SER A 1 7 ? -4.770 -2.699 -2.901 1.00 95.37 7 A 1 ATOM 55 O OG . SER A 1 7 ? -4.951 -1.545 -3.672 1.00 86.18 7 A 1 ATOM 56 N N . THR A 1 8 ? -3.485 -1.670 -0.242 1.00 96.41 8 A 1 ATOM 57 C CA . THR A 1 8 ? -3.265 -0.596 0.722 1.00 96.86 8 A 1 ATOM 58 C C . THR A 1 8 ? -1.792 -0.497 1.089 1.00 97.60 8 A 1 ATOM 59 O O . THR A 1 8 ? -1.220 0.591 1.110 1.00 97.43 8 A 1 ATOM 60 C CB . THR A 1 8 ? -4.094 -0.832 1.991 1.00 96.52 8 A 1 ATOM 61 O OG1 . THR A 1 8 ? -5.464 -0.994 1.637 1.00 94.22 8 A 1 ATOM 62 C CG2 . THR A 1 8 ? -3.972 0.344 2.947 1.00 92.70 8 A 1 ATOM 63 N N . VAL A 1 9 ? -1.179 -1.625 1.374 1.00 97.24 9 A 1 ATOM 64 C CA . VAL A 1 9 ? 0.234 -1.664 1.743 1.00 97.52 9 A 1 ATOM 65 C C . VAL A 1 9 ? 1.102 -1.243 0.564 1.00 97.90 9 A 1 ATOM 66 O O . VAL A 1 9 ? 2.145 -0.611 0.745 1.00 97.75 9 A 1 ATOM 67 C CB . VAL A 1 9 ? 0.643 -3.069 2.220 1.00 97.09 9 A 1 ATOM 68 C CG1 . VAL A 1 9 ? 2.122 -3.115 2.569 1.00 95.64 9 A 1 ATOM 69 C CG2 . VAL A 1 9 ? -0.187 -3.480 3.424 1.00 95.39 9 A 1 ATOM 70 N N . ALA A 1 10 ? 0.677 -1.591 -0.629 1.00 97.30 10 A 1 ATOM 71 C CA . ALA A 1 10 ? 1.415 -1.240 -1.836 1.00 97.13 10 A 1 ATOM 72 C C . ALA A 1 10 ? 1.488 0.272 -2.001 1.00 97.69 10 A 1 ATOM 73 O O . ALA A 1 10 ? 2.529 0.814 -2.369 1.00 97.45 10 A 1 ATOM 74 C CB . ALA A 1 10 ? 0.750 -1.867 -3.054 1.00 96.46 10 A 1 ATOM 75 N N . ALA A 1 11 ? 0.390 0.943 -1.723 1.00 97.28 11 A 1 ATOM 76 C CA . ALA A 1 11 ? 0.335 2.396 -1.824 1.00 97.26 11 A 1 ATOM 77 C C . ALA A 1 11 ? 1.202 3.050 -0.756 1.00 97.85 11 A 1 ATOM 78 O O . ALA A 1 11 ? 1.888 4.035 -1.019 1.00 97.44 11 A 1 ATOM 79 C CB . ALA A 1 11 ? -1.108 2.866 -1.696 1.00 96.46 11 A 1 ATOM 80 N N . ILE A 1 12 ? 1.175 2.484 0.446 1.00 97.18 12 A 1 ATOM 81 C CA . ILE A 1 12 ? 1.970 2.998 1.555 1.00 97.29 12 A 1 ATOM 82 C C . ILE A 1 12 ? 3.454 2.765 1.297 1.00 97.81 12 A 1 ATOM 83 O O . ILE A 1 12 ? 4.292 3.622 1.589 1.00 97.62 12 A 1 ATOM 84 C CB . ILE A 1 12 ? 1.551 2.334 2.880 1.00 96.96 12 A 1 ATOM 85 C CG1 . ILE A 1 12 ? 0.093 2.664 3.209 1.00 95.30 12 A 1 ATOM 86 C CG2 . ILE A 1 12 ? 2.461 2.805 4.022 1.00 94.98 12 A 1 ATOM 87 C CD1 . ILE A 1 12 ? -0.522 1.716 4.221 1.00 91.56 12 A 1 ATOM 88 N N . ALA A 1 13 ? 3.770 1.599 0.754 1.00 97.96 13 A 1 ATOM 89 C CA . ALA A 1 13 ? 5.153 1.250 0.451 1.00 97.85 13 A 1 ATOM 90 C C . ALA A 1 13 ? 5.731 2.192 -0.597 1.00 98.12 13 A 1 ATOM 91 O O . ALA A 1 13 ? 6.883 2.615 -0.501 1.00 97.74 13 A 1 ATOM 92 C CB . ALA A 1 13 ? 5.227 -0.192 -0.043 1.00 97.41 13 A 1 ATOM 93 N N . ALA A 1 14 ? 4.934 2.514 -1.597 1.00 98.11 14 A 1 ATOM 94 C CA . ALA A 1 14 ? 5.359 3.425 -2.653 1.00 97.97 14 A 1 ATOM 95 C C . ALA A 1 14 ? 5.559 4.835 -2.107 1.00 98.28 14 A 1 ATOM 96 O O . ALA A 1 14 ? 6.483 5.543 -2.510 1.00 97.87 14 A 1 ATOM 97 C CB . ALA A 1 14 ? 4.329 3.433 -3.774 1.00 97.41 14 A 1 ATOM 98 N N . PHE A 1 15 ? 4.698 5.231 -1.187 1.00 97.67 15 A 1 ATOM 99 C CA . PHE A 1 15 ? 4.785 6.551 -0.567 1.00 97.57 15 A 1 ATOM 100 C C . PHE A 1 15 ? 5.967 6.627 0.397 1.00 97.96 15 A 1 ATOM 101 O O . PHE A 1 15 ? 6.602 7.676 0.533 1.00 97.31 15 A 1 ATOM 102 C CB . PHE A 1 15 ? 3.486 6.858 0.178 1.00 96.96 15 A 1 ATOM 103 C CG . PHE A 1 15 ? 3.379 8.298 0.597 1.00 94.67 15 A 1 ATOM 104 C CD1 . PHE A 1 15 ? 2.996 9.265 -0.323 1.00 92.92 15 A 1 ATOM 105 C CD2 . PHE A 1 15 ? 3.654 8.683 1.897 1.00 93.56 15 A 1 ATOM 106 C CE1 . PHE A 1 15 ? 2.894 10.598 0.050 1.00 92.62 15 A 1 ATOM 107 C CE2 . PHE A 1 15 ? 3.557 10.018 2.283 1.00 92.38 15 A 1 ATOM 108 C CZ . PHE A 1 15 ? 3.175 10.974 1.354 1.00 92.10 15 A 1 ATOM 109 N N . ALA A 1 16 ? 6.254 5.511 1.049 1.00 97.97 16 A 1 ATOM 110 C CA . ALA A 1 16 ? 7.359 5.441 2.002 1.00 97.81 16 A 1 ATOM 111 C C . ALA A 1 16 ? 8.711 5.394 1.296 1.00 98.06 16 A 1 ATOM 112 O O . ALA A 1 16 ? 9.756 5.530 1.931 1.00 97.49 16 A 1 ATOM 113 C CB . ALA A 1 16 ? 7.196 4.212 2.895 1.00 97.09 16 A 1 ATOM 114 N N . SER A 1 17 ? 8.690 5.193 -0.006 1.00 97.06 17 A 1 ATOM 115 C CA . SER A 1 17 ? 9.911 5.121 -0.807 1.00 96.95 17 A 1 ATOM 116 C C . SER A 1 17 ? 10.365 6.507 -1.263 1.00 96.97 17 A 1 ATOM 117 O O . SER A 1 17 ? 11.316 6.636 -2.038 1.00 95.11 17 A 1 ATOM 118 C CB . SER A 1 17 ? 9.692 4.221 -2.024 1.00 95.28 17 A 1 ATOM 119 O OG . SER A 1 17 ? 10.920 3.884 -2.637 1.00 84.59 17 A 1 ATOM 120 N N . ALA A 1 18 ? 9.695 7.541 -0.771 1.00 95.60 18 A 1 ATOM 121 C CA . ALA A 1 18 ? 10.017 8.916 -1.147 1.00 93.91 18 A 1 ATOM 122 C C . ALA A 1 18 ? 11.221 9.422 -0.356 1.00 92.67 18 A 1 ATOM 123 O O . ALA A 1 18 ? 12.350 9.371 -0.871 1.00 88.78 18 A 1 ATOM 124 C CB . ALA A 1 18 ? 8.807 9.811 -0.924 1.00 91.01 18 A 1 ATOM 125 O OXT . ALA A 1 18 ? 11.033 9.851 0.773 1.00 83.86 18 A 1 #