# 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_spkb12011 # _entry.id spkb12011 # 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 H15 N4 O2" 175.209 ARG y ARGININE C(C[C@@H](C(=O)O)N)CNC(=[NH2+])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" "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" "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 PHE 2 1 n ARG 3 1 n LEU 4 1 n VAL 5 1 n GLY 6 1 n LEU 7 1 n PHE 8 1 n PHE 9 1 n LEU 10 1 n VAL 11 1 n LEU 12 1 n GLY 13 1 n ALA 14 1 n SER 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 18:48:35)" _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 88.36 _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 79.04 1 1 A PHE 2 2 81.90 1 2 A ARG 3 2 84.62 1 3 A LEU 4 2 90.90 1 4 A VAL 5 2 93.64 1 5 A GLY 6 2 94.91 1 6 A LEU 7 2 90.98 1 7 A PHE 8 2 89.35 1 8 A PHE 9 2 89.37 1 9 A LEU 10 2 91.50 1 10 A VAL 11 2 93.26 1 11 A LEU 12 2 90.42 1 12 A GLY 13 2 93.77 1 13 A ALA 14 2 92.91 1 14 A SER 15 2 87.39 1 15 A ALA 16 2 79.41 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 PHE . 2 A 2 A 3 1 n ARG . 3 A 3 A 4 1 n LEU . 4 A 4 A 5 1 n VAL . 5 A 5 A 6 1 n GLY . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n PHE . 8 A 8 A 9 1 n PHE . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n VAL . 11 A 11 A 12 1 n LEU . 12 A 12 A 13 1 n GLY . 13 A 13 A 14 1 n ALA . 14 A 14 A 15 1 n SER . 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 ? -9.519 5.098 8.624 1.00 83.25 1 A 1 ATOM 2 C CA . MET A 1 1 ? -8.251 4.425 8.295 1.00 86.20 1 A 1 ATOM 3 C C . MET A 1 1 ? -7.715 4.878 6.938 1.00 87.67 1 A 1 ATOM 4 O O . MET A 1 1 ? -7.932 4.224 5.920 1.00 84.63 1 A 1 ATOM 5 C CB . MET A 1 1 ? -8.463 2.913 8.271 1.00 79.05 1 A 1 ATOM 6 C CG . MET A 1 1 ? -8.272 2.273 9.628 1.00 74.30 1 A 1 ATOM 7 S SD . MET A 1 1 ? -8.401 0.488 9.529 1.00 72.21 1 A 1 ATOM 8 C CE . MET A 1 1 ? -7.946 0.054 11.205 1.00 64.99 1 A 1 ATOM 9 N N . PHE A 1 2 ? -7.035 6.009 6.930 1.00 83.02 2 A 1 ATOM 10 C CA . PHE A 1 2 ? -6.471 6.555 5.699 1.00 87.74 2 A 1 ATOM 11 C C . PHE A 1 2 ? -4.947 6.493 5.712 1.00 91.67 2 A 1 ATOM 12 O O . PHE A 1 2 ? -4.313 6.416 4.660 1.00 88.65 2 A 1 ATOM 13 C CB . PHE A 1 2 ? -6.936 8.001 5.531 1.00 84.05 2 A 1 ATOM 14 C CG . PHE A 1 2 ? -6.851 8.471 4.106 1.00 81.34 2 A 1 ATOM 15 C CD1 . PHE A 1 2 ? -7.762 8.023 3.163 1.00 79.70 2 A 1 ATOM 16 C CD2 . PHE A 1 2 ? -5.866 9.360 3.714 1.00 77.66 2 A 1 ATOM 17 C CE1 . PHE A 1 2 ? -7.690 8.450 1.848 1.00 76.90 2 A 1 ATOM 18 C CE2 . PHE A 1 2 ? -5.784 9.793 2.398 1.00 74.90 2 A 1 ATOM 19 C CZ . PHE A 1 2 ? -6.701 9.335 1.465 1.00 75.27 2 A 1 ATOM 20 N N . ARG A 1 3 ? -4.377 6.522 6.898 1.00 92.58 3 A 1 ATOM 21 C CA . ARG A 1 3 ? -2.920 6.471 7.042 1.00 94.48 3 A 1 ATOM 22 C C . ARG A 1 3 ? -2.377 5.093 6.659 1.00 95.48 3 A 1 ATOM 23 O O . ARG A 1 3 ? -1.298 4.987 6.076 1.00 93.59 3 A 1 ATOM 24 C CB . ARG A 1 3 ? -2.531 6.808 8.481 1.00 93.06 3 A 1 ATOM 25 C CG . ARG A 1 3 ? -1.065 7.172 8.627 1.00 86.11 3 A 1 ATOM 26 C CD . ARG A 1 3 ? -0.778 8.538 8.028 1.00 84.63 3 A 1 ATOM 27 N NE . ARG A 1 3 ? 0.627 8.914 8.156 1.00 78.10 3 A 1 ATOM 28 C CZ . ARG A 1 3 ? 1.169 9.378 9.279 1.00 75.44 3 A 1 ATOM 29 N NH1 . ARG A 1 3 ? 0.445 9.498 10.379 1.00 68.24 3 A 1 ATOM 30 N NH2 . ARG A 1 3 ? 2.450 9.712 9.306 1.00 69.07 3 A 1 ATOM 31 N N . LEU A 1 4 ? -3.124 4.049 6.994 1.00 92.46 4 A 1 ATOM 32 C CA . LEU A 1 4 ? -2.718 2.680 6.686 1.00 94.05 4 A 1 ATOM 33 C C . LEU A 1 4 ? -2.657 2.452 5.180 1.00 94.90 4 A 1 ATOM 34 O O . LEU A 1 4 ? -1.730 1.826 4.670 1.00 93.81 4 A 1 ATOM 35 C CB . LEU A 1 4 ? -3.689 1.683 7.333 1.00 93.55 4 A 1 ATOM 36 C CG . LEU A 1 4 ? -3.179 1.028 8.614 1.00 89.23 4 A 1 ATOM 37 C CD1 . LEU A 1 4 ? -1.951 0.182 8.329 1.00 85.23 4 A 1 ATOM 38 C CD2 . LEU A 1 4 ? -2.878 2.062 9.678 1.00 83.96 4 A 1 ATOM 39 N N . VAL A 1 5 ? -3.655 2.957 4.477 1.00 95.49 5 A 1 ATOM 40 C CA . VAL A 1 5 ? -3.726 2.807 3.024 1.00 95.48 5 A 1 ATOM 41 C C . VAL A 1 5 ? -2.570 3.540 2.347 1.00 95.58 5 A 1 ATOM 42 O O . VAL A 1 5 ? -1.957 3.025 1.410 1.00 94.32 5 A 1 ATOM 43 C CB . VAL A 1 5 ? -5.065 3.333 2.485 1.00 94.44 5 A 1 ATOM 44 C CG1 . VAL A 1 5 ? -5.175 3.084 0.992 1.00 89.92 5 A 1 ATOM 45 C CG2 . VAL A 1 5 ? -6.228 2.686 3.217 1.00 90.24 5 A 1 ATOM 46 N N . GLY A 1 6 ? -2.285 4.739 2.824 1.00 94.75 6 A 1 ATOM 47 C CA . GLY A 1 6 ? -1.201 5.536 2.254 1.00 94.75 6 A 1 ATOM 48 C C . GLY A 1 6 ? 0.160 4.897 2.478 1.00 95.64 6 A 1 ATOM 49 O O . GLY A 1 6 ? 1.004 4.872 1.583 1.00 94.51 6 A 1 ATOM 50 N N . LEU A 1 7 ? 0.362 4.376 3.679 1.00 93.92 7 A 1 ATOM 51 C CA . LEU A 1 7 ? 1.620 3.717 4.029 1.00 94.29 7 A 1 ATOM 52 C C . LEU A 1 7 ? 1.813 2.436 3.228 1.00 95.26 7 A 1 ATOM 53 O O . LEU A 1 7 ? 2.897 2.172 2.711 1.00 94.79 7 A 1 ATOM 54 C CB . LEU A 1 7 ? 1.641 3.399 5.524 1.00 94.00 7 A 1 ATOM 55 C CG . LEU A 1 7 ? 3.036 3.425 6.132 1.00 87.51 7 A 1 ATOM 56 C CD1 . LEU A 1 7 ? 3.352 4.802 6.697 1.00 83.96 7 A 1 ATOM 57 C CD2 . LEU A 1 7 ? 3.159 2.371 7.216 1.00 84.13 7 A 1 ATOM 58 N N . PHE A 1 8 ? 0.756 1.645 3.133 1.00 93.67 8 A 1 ATOM 59 C CA . PHE A 1 8 ? 0.799 0.387 2.391 1.00 93.42 8 A 1 ATOM 60 C C . PHE A 1 8 ? 1.069 0.630 0.914 1.00 94.30 8 A 1 ATOM 61 O O . PHE A 1 8 ? 1.841 -0.095 0.284 1.00 93.81 8 A 1 ATOM 62 C CB . PHE A 1 8 ? -0.525 -0.349 2.561 1.00 93.18 8 A 1 ATOM 63 C CG . PHE A 1 8 ? -0.349 -1.738 3.115 1.00 89.87 8 A 1 ATOM 64 C CD1 . PHE A 1 8 ? 0.109 -1.926 4.405 1.00 86.05 8 A 1 ATOM 65 C CD2 . PHE A 1 8 ? -0.643 -2.844 2.331 1.00 86.16 8 A 1 ATOM 66 C CE1 . PHE A 1 8 ? 0.274 -3.202 4.911 1.00 83.90 8 A 1 ATOM 67 C CE2 . PHE A 1 8 ? -0.481 -4.123 2.836 1.00 83.65 8 A 1 ATOM 68 C CZ . PHE A 1 8 ? -0.021 -4.306 4.129 1.00 84.79 8 A 1 ATOM 69 N N . PHE A 1 9 ? 0.433 1.653 0.372 1.00 93.63 9 A 1 ATOM 70 C CA . PHE A 1 9 ? 0.596 1.997 -1.040 1.00 93.80 9 A 1 ATOM 71 C C . PHE A 1 9 ? 2.037 2.411 -1.330 1.00 94.72 9 A 1 ATOM 72 O O . PHE A 1 9 ? 2.597 2.064 -2.370 1.00 93.89 9 A 1 ATOM 73 C CB . PHE A 1 9 ? -0.352 3.134 -1.401 1.00 93.25 9 A 1 ATOM 74 C CG . PHE A 1 9 ? -0.997 2.946 -2.747 1.00 89.32 9 A 1 ATOM 75 C CD1 . PHE A 1 9 ? -0.284 3.160 -3.912 1.00 86.13 9 A 1 ATOM 76 C CD2 . PHE A 1 9 ? -2.327 2.556 -2.836 1.00 85.91 9 A 1 ATOM 77 C CE1 . PHE A 1 9 ? -0.877 2.983 -5.149 1.00 84.23 9 A 1 ATOM 78 C CE2 . PHE A 1 9 ? -2.928 2.381 -4.070 1.00 83.41 9 A 1 ATOM 79 C CZ . PHE A 1 9 ? -2.203 2.593 -5.232 1.00 84.79 9 A 1 ATOM 80 N N . LEU A 1 10 ? 2.628 3.144 -0.406 1.00 94.61 10 A 1 ATOM 81 C CA . LEU A 1 10 ? 4.009 3.597 -0.553 1.00 94.44 10 A 1 ATOM 82 C C . LEU A 1 10 ? 4.972 2.416 -0.577 1.00 95.18 10 A 1 ATOM 83 O O . LEU A 1 10 ? 5.874 2.356 -1.413 1.00 94.10 10 A 1 ATOM 84 C CB . LEU A 1 10 ? 4.376 4.534 0.597 1.00 94.02 10 A 1 ATOM 85 C CG . LEU A 1 10 ? 5.538 5.460 0.284 1.00 88.67 10 A 1 ATOM 86 C CD1 . LEU A 1 10 ? 5.046 6.879 0.047 1.00 85.71 10 A 1 ATOM 87 C CD2 . LEU A 1 10 ? 6.555 5.435 1.406 1.00 85.25 10 A 1 ATOM 88 N N . VAL A 1 11 ? 4.771 1.485 0.336 1.00 95.19 11 A 1 ATOM 89 C CA . VAL A 1 11 ? 5.618 0.295 0.423 1.00 94.75 11 A 1 ATOM 90 C C . VAL A 1 11 ? 5.462 -0.570 -0.817 1.00 94.82 11 A 1 ATOM 91 O O . VAL A 1 11 ? 6.430 -1.161 -1.300 1.00 93.64 11 A 1 ATOM 92 C CB . VAL A 1 11 ? 5.277 -0.525 1.678 1.00 93.88 11 A 1 ATOM 93 C CG1 . VAL A 1 11 ? 6.171 -1.751 1.776 1.00 90.11 11 A 1 ATOM 94 C CG2 . VAL A 1 11 ? 5.427 0.324 2.927 1.00 90.46 11 A 1 ATOM 95 N N . LEU A 1 12 ? 4.245 -0.643 -1.324 1.00 94.28 12 A 1 ATOM 96 C CA . LEU A 1 12 ? 3.960 -1.442 -2.514 1.00 93.70 12 A 1 ATOM 97 C C . LEU A 1 12 ? 4.739 -0.920 -3.715 1.00 94.11 12 A 1 ATOM 98 O O . LEU A 1 12 ? 5.298 -1.695 -4.491 1.00 92.31 12 A 1 ATOM 99 C CB . LEU A 1 12 ? 2.460 -1.414 -2.809 1.00 92.39 12 A 1 ATOM 100 C CG . LEU A 1 12 ? 1.956 -2.650 -3.543 1.00 88.28 12 A 1 ATOM 101 C CD1 . LEU A 1 12 ? 1.586 -3.743 -2.554 1.00 85.25 12 A 1 ATOM 102 C CD2 . LEU A 1 12 ? 0.774 -2.300 -4.421 1.00 83.07 12 A 1 ATOM 103 N N . GLY A 1 13 ? 4.781 0.386 -3.861 1.00 94.28 13 A 1 ATOM 104 C CA . GLY A 1 13 ? 5.503 1.004 -4.968 1.00 93.65 13 A 1 ATOM 105 C C . GLY A 1 13 ? 7.001 0.784 -4.870 1.00 94.25 13 A 1 ATOM 106 O O . GLY A 1 13 ? 7.679 0.570 -5.873 1.00 92.89 13 A 1 ATOM 107 N N . ALA A 1 14 ? 7.526 0.833 -3.657 1.00 94.24 14 A 1 ATOM 108 C CA . ALA A 1 14 ? 8.953 0.620 -3.422 1.00 93.48 14 A 1 ATOM 109 C C . ALA A 1 14 ? 9.345 -0.835 -3.648 1.00 93.98 14 A 1 ATOM 110 O O . ALA A 1 14 ? 10.473 -1.127 -4.039 1.00 91.30 14 A 1 ATOM 111 C CB . ALA A 1 14 ? 9.309 1.043 -2.001 1.00 91.54 14 A 1 ATOM 112 N N . SER A 1 15 ? 8.410 -1.743 -3.392 1.00 92.26 15 A 1 ATOM 113 C CA . SER A 1 15 ? 8.648 -3.175 -3.571 1.00 91.40 15 A 1 ATOM 114 C C . SER A 1 15 ? 8.712 -3.549 -5.046 1.00 90.74 15 A 1 ATOM 115 O O . SER A 1 15 ? 9.364 -4.521 -5.425 1.00 85.59 15 A 1 ATOM 116 C CB . SER A 1 15 ? 7.550 -3.984 -2.887 1.00 87.77 15 A 1 ATOM 117 O OG . SER A 1 15 ? 8.095 -5.093 -2.215 1.00 76.59 15 A 1 ATOM 118 N N . ALA A 1 16 ? 8.030 -2.784 -5.887 1.00 87.49 16 A 1 ATOM 119 C CA . ALA A 1 16 ? 7.980 -3.033 -7.319 1.00 84.41 16 A 1 ATOM 120 C C . ALA A 1 16 ? 9.314 -2.707 -8.000 1.00 81.53 16 A 1 ATOM 121 O O . ALA A 1 16 ? 10.197 -2.115 -7.359 1.00 75.02 16 A 1 ATOM 122 C CB . ALA A 1 16 ? 6.850 -2.224 -7.944 1.00 77.46 16 A 1 ATOM 123 O OXT . ALA A 1 16 ? 9.480 -3.039 -9.187 1.00 70.55 16 A 1 #