# 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_spkb35255 # _entry.id spkb35255 # 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" "C3 H7 N O2 S" 121.158 CYS y CYSTEINE C([C@@H](C(=O)O)N)S ? "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 H10 N3 O2" 156.162 HIS y HISTIDINE c1c([nH+]c[nH]1)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" "C9 H11 N O2" 165.189 PHE y PHENYLALANINE c1ccc(cc1)C[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" "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 HIS 1 1 n CYS 2 1 n LEU 3 1 n PRO 4 1 n LEU 5 1 n GLU 6 1 n SER 7 1 n ILE 8 1 n ALA 9 1 n LEU 10 1 n PHE 11 1 n LEU 12 1 n VAL 13 1 n CYS 14 1 n LEU 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 @ 2025-07-04 01:42:04)" _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 90.59 _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 HIS 1 2 75.63 1 1 A CYS 2 2 79.47 1 2 A LEU 3 2 85.38 1 3 A PRO 4 2 92.73 1 4 A LEU 5 2 89.98 1 5 A GLU 6 2 90.79 1 6 A SER 7 2 94.86 1 7 A ILE 8 2 92.97 1 8 A ALA 9 2 96.25 1 9 A LEU 10 2 93.48 1 10 A PHE 11 2 93.46 1 11 A LEU 12 2 93.92 1 12 A VAL 13 2 95.95 1 13 A CYS 14 2 94.15 1 14 A LEU 15 2 93.97 1 15 A ALA 16 2 91.51 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 HIS . 1 A 1 A 2 1 n CYS . 2 A 2 A 3 1 n LEU . 3 A 3 A 4 1 n PRO . 4 A 4 A 5 1 n LEU . 5 A 5 A 6 1 n GLU . 6 A 6 A 7 1 n SER . 7 A 7 A 8 1 n ILE . 8 A 8 A 9 1 n ALA . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n PHE . 11 A 11 A 12 1 n LEU . 12 A 12 A 13 1 n VAL . 13 A 13 A 14 1 n CYS . 14 A 14 A 15 1 n LEU . 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 . HIS A 1 1 ? -6.027 12.363 -6.016 1.00 79.90 1 A 1 ATOM 2 C CA . HIS A 1 1 ? -5.519 10.974 -5.994 1.00 82.83 1 A 1 ATOM 3 C C . HIS A 1 1 ? -5.872 10.313 -4.665 1.00 84.55 1 A 1 ATOM 4 O O . HIS A 1 1 ? -5.075 10.334 -3.730 1.00 79.07 1 A 1 ATOM 5 C CB . HIS A 1 1 ? -4.011 10.975 -6.180 1.00 80.34 1 A 1 ATOM 6 C CG . HIS A 1 1 ? -3.571 11.881 -7.288 1.00 73.17 1 A 1 ATOM 7 N ND1 . HIS A 1 1 ? -2.763 12.969 -7.092 1.00 69.01 1 A 1 ATOM 8 C CD2 . HIS A 1 1 ? -3.868 11.833 -8.604 1.00 67.56 1 A 1 ATOM 9 C CE1 . HIS A 1 1 ? -2.554 13.566 -8.248 1.00 69.75 1 A 1 ATOM 10 N NE2 . HIS A 1 1 ? -3.221 12.897 -9.214 1.00 70.10 1 A 1 ATOM 11 N N . CYS A 1 2 ? -7.065 9.733 -4.570 1.00 80.53 2 A 1 ATOM 12 C CA . CYS A 1 2 ? -7.516 9.088 -3.337 1.00 81.72 2 A 1 ATOM 13 C C . CYS A 1 2 ? -7.567 7.577 -3.529 1.00 82.52 2 A 1 ATOM 14 O O . CYS A 1 2 ? -8.315 7.080 -4.370 1.00 77.90 2 A 1 ATOM 15 C CB . CYS A 1 2 ? -8.895 9.611 -2.944 1.00 79.49 2 A 1 ATOM 16 S SG . CYS A 1 2 ? -8.820 11.336 -2.412 1.00 74.67 2 A 1 ATOM 17 N N . LEU A 1 3 ? -6.768 6.848 -2.743 1.00 86.52 3 A 1 ATOM 18 C CA . LEU A 1 3 ? -6.744 5.391 -2.805 1.00 87.65 3 A 1 ATOM 19 C C . LEU A 1 3 ? -7.392 4.784 -1.568 1.00 89.50 3 A 1 ATOM 20 O O . LEU A 1 3 ? -7.349 5.385 -0.497 1.00 89.52 3 A 1 ATOM 21 C CB . LEU A 1 3 ? -5.304 4.901 -2.918 1.00 86.48 3 A 1 ATOM 22 C CG . LEU A 1 3 ? -4.653 5.203 -4.257 1.00 82.90 3 A 1 ATOM 23 C CD1 . LEU A 1 3 ? -3.150 4.999 -4.166 1.00 80.70 3 A 1 ATOM 24 C CD2 . LEU A 1 3 ? -5.233 4.307 -5.344 1.00 79.73 3 A 1 ATOM 25 N N . PRO A 1 4 ? -7.974 3.588 -1.704 1.00 93.02 4 A 1 ATOM 26 C CA . PRO A 1 4 ? -8.595 2.913 -0.565 1.00 94.32 4 A 1 ATOM 27 C C . PRO A 1 4 ? -7.548 2.379 0.410 1.00 94.53 4 A 1 ATOM 28 O O . PRO A 1 4 ? -6.410 2.118 0.024 1.00 93.22 4 A 1 ATOM 29 C CB . PRO A 1 4 ? -9.370 1.762 -1.212 1.00 91.85 4 A 1 ATOM 30 C CG . PRO A 1 4 ? -8.641 1.490 -2.487 1.00 89.75 4 A 1 ATOM 31 C CD . PRO A 1 4 ? -8.098 2.821 -2.944 1.00 92.43 4 A 1 ATOM 32 N N . LEU A 1 5 ? -7.938 2.210 1.664 1.00 92.01 5 A 1 ATOM 33 C CA . LEU A 1 5 ? -7.027 1.711 2.695 1.00 92.69 5 A 1 ATOM 34 C C . LEU A 1 5 ? -6.561 0.291 2.384 1.00 93.65 5 A 1 ATOM 35 O O . LEU A 1 5 ? -5.500 -0.138 2.827 1.00 93.63 5 A 1 ATOM 36 C CB . LEU A 1 5 ? -7.718 1.759 4.063 1.00 92.46 5 A 1 ATOM 37 C CG . LEU A 1 5 ? -7.372 2.986 4.899 1.00 87.30 5 A 1 ATOM 38 C CD1 . LEU A 1 5 ? -5.906 2.962 5.308 1.00 84.05 5 A 1 ATOM 39 C CD2 . LEU A 1 5 ? -7.686 4.271 4.138 1.00 84.03 5 A 1 ATOM 40 N N . GLU A 1 6 ? -7.358 -0.440 1.638 1.00 94.78 6 A 1 ATOM 41 C CA . GLU A 1 6 ? -7.012 -1.818 1.279 1.00 95.04 6 A 1 ATOM 42 C C . GLU A 1 6 ? -5.695 -1.872 0.511 1.00 95.52 6 A 1 ATOM 43 O O . GLU A 1 6 ? -4.817 -2.681 0.817 1.00 94.95 6 A 1 ATOM 44 C CB . GLU A 1 6 ? -8.131 -2.430 0.431 1.00 94.38 6 A 1 ATOM 45 C CG . GLU A 1 6 ? -8.161 -3.938 0.520 1.00 89.67 6 A 1 ATOM 46 C CD . GLU A 1 6 ? -8.647 -4.585 -0.761 1.00 85.98 6 A 1 ATOM 47 O OE1 . GLU A 1 6 ? -7.840 -4.722 -1.694 1.00 82.51 6 A 1 ATOM 48 O OE2 . GLU A 1 6 ? -9.829 -4.949 -0.836 1.00 84.30 6 A 1 ATOM 49 N N . SER A 1 7 ? -5.542 -1.017 -0.477 1.00 95.17 7 A 1 ATOM 50 C CA . SER A 1 7 ? -4.317 -0.976 -1.275 1.00 95.97 7 A 1 ATOM 51 C C . SER A 1 7 ? -3.134 -0.503 -0.443 1.00 96.30 7 A 1 ATOM 52 O O . SER A 1 7 ? -2.025 -1.023 -0.574 1.00 95.51 7 A 1 ATOM 53 C CB . SER A 1 7 ? -4.506 -0.059 -2.480 1.00 95.33 7 A 1 ATOM 54 O OG . SER A 1 7 ? -5.314 -0.688 -3.453 1.00 90.91 7 A 1 ATOM 55 N N . ILE A 1 8 ? -3.363 0.476 0.408 1.00 94.34 8 A 1 ATOM 56 C CA . ILE A 1 8 ? -2.307 0.998 1.276 1.00 94.19 8 A 1 ATOM 57 C C . ILE A 1 8 ? -1.807 -0.087 2.222 1.00 94.53 8 A 1 ATOM 58 O O . ILE A 1 8 ? -0.603 -0.247 2.429 1.00 94.76 8 A 1 ATOM 59 C CB . ILE A 1 8 ? -2.820 2.211 2.071 1.00 94.82 8 A 1 ATOM 60 C CG1 . ILE A 1 8 ? -3.249 3.332 1.110 1.00 91.92 8 A 1 ATOM 61 C CG2 . ILE A 1 8 ? -1.738 2.722 3.025 1.00 91.52 8 A 1 ATOM 62 C CD1 . ILE A 1 8 ? -2.092 3.879 0.289 1.00 87.71 8 A 1 ATOM 63 N N . ALA A 1 9 ? -2.734 -0.821 2.809 1.00 96.23 9 A 1 ATOM 64 C CA . ALA A 1 9 ? -2.375 -1.886 3.745 1.00 96.40 9 A 1 ATOM 65 C C . ALA A 1 9 ? -1.579 -2.981 3.039 1.00 96.62 9 A 1 ATOM 66 O O . ALA A 1 9 ? -0.582 -3.471 3.567 1.00 95.67 9 A 1 ATOM 67 C CB . ALA A 1 9 ? -3.635 -2.471 4.373 1.00 96.31 9 A 1 ATOM 68 N N . LEU A 1 10 ? -2.006 -3.360 1.855 1.00 95.52 10 A 1 ATOM 69 C CA . LEU A 1 10 ? -1.309 -4.393 1.090 1.00 95.33 10 A 1 ATOM 70 C C . LEU A 1 10 ? 0.109 -3.954 0.747 1.00 95.87 10 A 1 ATOM 71 O O . LEU A 1 10 ? 1.051 -4.744 0.830 1.00 95.03 10 A 1 ATOM 72 C CB . LEU A 1 10 ? -2.085 -4.697 -0.192 1.00 94.98 10 A 1 ATOM 73 C CG . LEU A 1 10 ? -3.221 -5.690 0.000 1.00 91.30 10 A 1 ATOM 74 C CD1 . LEU A 1 10 ? -4.183 -5.631 -1.180 1.00 89.61 10 A 1 ATOM 75 C CD2 . LEU A 1 10 ? -2.665 -7.105 0.147 1.00 90.18 10 A 1 ATOM 76 N N . PHE A 1 11 ? 0.262 -2.711 0.378 1.00 94.58 11 A 1 ATOM 77 C CA . PHE A 1 11 ? 1.577 -2.176 0.039 1.00 94.45 11 A 1 ATOM 78 C C . PHE A 1 11 ? 2.512 -2.233 1.244 1.00 95.44 11 A 1 ATOM 79 O O . PHE A 1 11 ? 3.669 -2.638 1.128 1.00 94.58 11 A 1 ATOM 80 C CB . PHE A 1 11 ? 1.435 -0.735 -0.446 1.00 94.83 11 A 1 ATOM 81 C CG . PHE A 1 11 ? 2.693 -0.219 -1.098 1.00 94.03 11 A 1 ATOM 82 C CD1 . PHE A 1 11 ? 2.960 -0.496 -2.432 1.00 91.70 11 A 1 ATOM 83 C CD2 . PHE A 1 11 ? 3.598 0.534 -0.372 1.00 92.35 11 A 1 ATOM 84 C CE1 . PHE A 1 11 ? 4.117 -0.027 -3.033 1.00 91.96 11 A 1 ATOM 85 C CE2 . PHE A 1 11 ? 4.767 1.002 -0.972 1.00 91.54 11 A 1 ATOM 86 C CZ . PHE A 1 11 ? 5.023 0.721 -2.301 1.00 92.63 11 A 1 ATOM 87 N N . LEU A 1 12 ? 2.007 -1.821 2.399 1.00 94.87 12 A 1 ATOM 88 C CA . LEU A 1 12 ? 2.811 -1.825 3.620 1.00 95.01 12 A 1 ATOM 89 C C . LEU A 1 12 ? 3.134 -3.246 4.067 1.00 95.71 12 A 1 ATOM 90 O O . LEU A 1 12 ? 4.254 -3.534 4.487 1.00 94.81 12 A 1 ATOM 91 C CB . LEU A 1 12 ? 2.067 -1.085 4.733 1.00 94.79 12 A 1 ATOM 92 C CG . LEU A 1 12 ? 3.000 -0.272 5.619 1.00 92.78 12 A 1 ATOM 93 C CD1 . LEU A 1 12 ? 3.209 1.119 5.030 1.00 91.51 12 A 1 ATOM 94 C CD2 . LEU A 1 12 ? 2.441 -0.171 7.027 1.00 91.86 12 A 1 ATOM 95 N N . VAL A 1 13 ? 2.160 -4.138 3.988 1.00 96.73 13 A 1 ATOM 96 C CA . VAL A 1 13 ? 2.352 -5.528 4.403 1.00 96.56 13 A 1 ATOM 97 C C . VAL A 1 13 ? 3.362 -6.226 3.496 1.00 96.86 13 A 1 ATOM 98 O O . VAL A 1 13 ? 4.177 -7.025 3.961 1.00 95.91 13 A 1 ATOM 99 C CB . VAL A 1 13 ? 1.010 -6.282 4.393 1.00 96.12 13 A 1 ATOM 100 C CG1 . VAL A 1 13 ? 1.223 -7.777 4.585 1.00 94.76 13 A 1 ATOM 101 C CG2 . VAL A 1 13 ? 0.099 -5.747 5.491 1.00 94.70 13 A 1 ATOM 102 N N . CYS A 1 14 ? 3.319 -5.949 2.209 1.00 94.94 14 A 1 ATOM 103 C CA . CYS A 1 14 ? 4.261 -6.553 1.266 1.00 94.81 14 A 1 ATOM 104 C C . CYS A 1 14 ? 5.689 -6.103 1.552 1.00 95.01 14 A 1 ATOM 105 O O . CYS A 1 14 ? 6.637 -6.857 1.346 1.00 93.12 14 A 1 ATOM 106 C CB . CYS A 1 14 ? 3.871 -6.182 -0.169 1.00 94.07 14 A 1 ATOM 107 S SG . CYS A 1 14 ? 2.612 -7.287 -0.853 1.00 92.95 14 A 1 ATOM 108 N N . LEU A 1 15 ? 5.848 -4.870 2.013 1.00 94.75 15 A 1 ATOM 109 C CA . LEU A 1 15 ? 7.169 -4.342 2.343 1.00 95.06 15 A 1 ATOM 110 C C . LEU A 1 15 ? 7.691 -4.900 3.662 1.00 95.83 15 A 1 ATOM 111 O O . LEU A 1 15 ? 8.900 -5.027 3.853 1.00 95.13 15 A 1 ATOM 112 C CB . LEU A 1 15 ? 7.108 -2.816 2.414 1.00 94.56 15 A 1 ATOM 113 C CG . LEU A 1 15 ? 8.143 -2.132 1.526 1.00 93.50 15 A 1 ATOM 114 C CD1 . LEU A 1 15 ? 7.754 -2.228 0.057 1.00 91.98 15 A 1 ATOM 115 C CD2 . LEU A 1 15 ? 8.305 -0.674 1.936 1.00 90.97 15 A 1 ATOM 116 N N . ALA A 1 16 ? 6.782 -5.218 4.573 1.00 94.31 16 A 1 ATOM 117 C CA . ALA A 1 16 ? 7.150 -5.719 5.891 1.00 93.77 16 A 1 ATOM 118 C C . ALA A 1 16 ? 7.143 -7.244 5.936 1.00 92.86 16 A 1 ATOM 119 O O . ALA A 1 16 ? 6.228 -7.858 5.366 1.00 91.22 16 A 1 ATOM 120 C CB . ALA A 1 16 ? 6.209 -5.153 6.952 1.00 91.61 16 A 1 ATOM 121 O OXT . ALA A 1 16 ? 8.035 -7.822 6.551 1.00 85.28 16 A 1 #