# 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_spkb34238 # _entry.id spkb34238 # 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" "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" "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 MET 1 1 n ARG 2 1 n ALA 3 1 n SER 4 1 n LEU 5 1 n SER 6 1 n ILE 7 1 n LEU 8 1 n VAL 9 1 n ALA 10 1 n PHE 11 1 n PRO 12 1 n ALA 13 1 n LEU 14 1 n ALA 15 1 n ALA 16 1 n ALA 17 # _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 @ 2025-07-11 16:53:33)" _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 95.40 _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 86.69 1 1 A ARG 2 2 89.14 1 2 A ALA 3 2 96.70 1 3 A SER 4 2 96.00 1 4 A LEU 5 2 96.27 1 5 A SER 6 2 97.50 1 6 A ILE 7 2 96.60 1 7 A LEU 8 2 97.05 1 8 A VAL 9 2 98.05 1 9 A ALA 10 2 98.56 1 10 A PHE 11 2 96.41 1 11 A PRO 12 2 98.10 1 12 A ALA 13 2 98.45 1 13 A LEU 14 2 96.62 1 14 A ALA 15 2 97.85 1 15 A ALA 16 2 97.43 1 16 A ALA 17 2 91.17 1 17 # _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 ARG . 2 A 2 A 3 1 n ALA . 3 A 3 A 4 1 n SER . 4 A 4 A 5 1 n LEU . 5 A 5 A 6 1 n SER . 6 A 6 A 7 1 n ILE . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n VAL . 9 A 9 A 10 1 n ALA . 10 A 10 A 11 1 n PHE . 11 A 11 A 12 1 n PRO . 12 A 12 A 13 1 n ALA . 13 A 13 A 14 1 n LEU . 14 A 14 A 15 1 n ALA . 15 A 15 A 16 1 n ALA . 16 A 16 A 17 1 n ALA . 17 A 17 # _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 ? -9.397 10.318 4.236 1.00 92.12 1 A 1 ATOM 2 C CA . MET A 1 1 ? -8.097 9.634 4.129 1.00 91.42 1 A 1 ATOM 3 C C . MET A 1 1 ? -8.286 8.122 4.126 1.00 92.73 1 A 1 ATOM 4 O O . MET A 1 1 ? -9.218 7.607 4.742 1.00 90.93 1 A 1 ATOM 5 C CB . MET A 1 1 ? -7.196 10.029 5.296 1.00 87.99 1 A 1 ATOM 6 C CG . MET A 1 1 ? -6.827 11.506 5.270 1.00 85.62 1 A 1 ATOM 7 S SD . MET A 1 1 ? -5.775 11.969 6.656 1.00 82.25 1 A 1 ATOM 8 C CE . MET A 1 1 ? -5.573 13.711 6.324 1.00 70.49 1 A 1 ATOM 9 N N . ARG A 1 2 ? -7.421 7.414 3.442 1.00 94.62 2 A 1 ATOM 10 C CA . ARG A 1 2 ? -7.506 5.958 3.345 1.00 96.60 2 A 1 ATOM 11 C C . ARG A 1 2 ? -6.428 5.304 4.203 1.00 97.52 2 A 1 ATOM 12 O O . ARG A 1 2 ? -5.241 5.498 3.960 1.00 96.80 2 A 1 ATOM 13 C CB . ARG A 1 2 ? -7.359 5.542 1.880 1.00 94.77 2 A 1 ATOM 14 C CG . ARG A 1 2 ? -7.972 4.183 1.596 1.00 90.09 2 A 1 ATOM 15 C CD . ARG A 1 2 ? -7.909 3.884 0.111 1.00 88.35 2 A 1 ATOM 16 N NE . ARG A 1 2 ? -8.456 2.562 -0.193 1.00 84.40 2 A 1 ATOM 17 C CZ . ARG A 1 2 ? -8.445 2.027 -1.405 1.00 83.58 2 A 1 ATOM 18 N NH1 . ARG A 1 2 ? -7.934 2.680 -2.427 1.00 76.93 2 A 1 ATOM 19 N NH2 . ARG A 1 2 ? -8.955 0.820 -1.586 1.00 76.90 2 A 1 ATOM 20 N N . ALA A 1 3 ? -6.844 4.528 5.203 1.00 96.21 3 A 1 ATOM 21 C CA . ALA A 1 3 ? -5.902 3.853 6.101 1.00 96.84 3 A 1 ATOM 22 C C . ALA A 1 3 ? -5.019 2.866 5.340 1.00 97.52 3 A 1 ATOM 23 O O . ALA A 1 3 ? -3.850 2.684 5.674 1.00 96.94 3 A 1 ATOM 24 C CB . ALA A 1 3 ? -6.668 3.133 7.202 1.00 96.00 3 A 1 ATOM 25 N N . SER A 1 4 ? -5.591 2.230 4.315 1.00 97.42 4 A 1 ATOM 26 C CA . SER A 1 4 ? -4.856 1.257 3.509 1.00 97.38 4 A 1 ATOM 27 C C . SER A 1 4 ? -3.677 1.897 2.792 1.00 97.75 4 A 1 ATOM 28 O O . SER A 1 4 ? -2.643 1.261 2.596 1.00 97.39 4 A 1 ATOM 29 C CB . SER A 1 4 ? -5.786 0.613 2.493 1.00 96.46 4 A 1 ATOM 30 O OG . SER A 1 4 ? -6.828 -0.075 3.152 1.00 89.62 4 A 1 ATOM 31 N N . LEU A 1 5 ? -3.817 3.166 2.416 1.00 97.47 5 A 1 ATOM 32 C CA . LEU A 1 5 ? -2.747 3.878 1.723 1.00 97.75 5 A 1 ATOM 33 C C . LEU A 1 5 ? -1.485 3.935 2.573 1.00 98.09 5 A 1 ATOM 34 O O . LEU A 1 5 ? -0.379 3.723 2.074 1.00 97.87 5 A 1 ATOM 35 C CB . LEU A 1 5 ? -3.201 5.296 1.374 1.00 97.57 5 A 1 ATOM 36 C CG . LEU A 1 5 ? -3.909 5.403 0.025 1.00 95.27 5 A 1 ATOM 37 C CD1 . LEU A 1 5 ? -4.480 6.798 -0.161 1.00 93.15 5 A 1 ATOM 38 C CD2 . LEU A 1 5 ? -2.935 5.083 -1.103 1.00 93.02 5 A 1 ATOM 39 N N . SER A 1 6 ? -1.648 4.223 3.863 1.00 98.23 6 A 1 ATOM 40 C CA . SER A 1 6 ? -0.509 4.301 4.776 1.00 98.30 6 A 1 ATOM 41 C C . SER A 1 6 ? 0.201 2.957 4.871 1.00 98.43 6 A 1 ATOM 42 O O . SER A 1 6 ? 1.427 2.894 4.971 1.00 98.16 6 A 1 ATOM 43 C CB . SER A 1 6 ? -0.968 4.744 6.163 1.00 97.84 6 A 1 ATOM 44 O OG . SER A 1 6 ? -1.461 6.069 6.128 1.00 94.07 6 A 1 ATOM 45 N N . ILE A 1 7 ? -0.573 1.877 4.825 1.00 98.20 7 A 1 ATOM 46 C CA . ILE A 1 7 ? -0.008 0.533 4.909 1.00 98.17 7 A 1 ATOM 47 C C . ILE A 1 7 ? 0.839 0.239 3.674 1.00 98.45 7 A 1 ATOM 48 O O . ILE A 1 7 ? 1.920 -0.348 3.774 1.00 98.16 7 A 1 ATOM 49 C CB . ILE A 1 7 ? -1.125 -0.517 5.054 1.00 97.83 7 A 1 ATOM 50 C CG1 . ILE A 1 7 ? -1.918 -0.278 6.345 1.00 95.80 7 A 1 ATOM 51 C CG2 . ILE A 1 7 ? -0.518 -1.924 5.069 1.00 95.22 7 A 1 ATOM 52 C CD1 . ILE A 1 7 ? -3.156 -1.150 6.447 1.00 90.97 7 A 1 ATOM 53 N N . LEU A 1 8 ? 0.355 0.659 2.508 1.00 98.09 8 A 1 ATOM 54 C CA . LEU A 1 8 ? 1.078 0.434 1.261 1.00 98.11 8 A 1 ATOM 55 C C . LEU A 1 8 ? 2.399 1.194 1.255 1.00 98.31 8 A 1 ATOM 56 O O . LEU A 1 8 ? 3.404 0.707 0.737 1.00 98.18 8 A 1 ATOM 57 C CB . LEU A 1 8 ? 0.217 0.867 0.065 1.00 98.00 8 A 1 ATOM 58 C CG . LEU A 1 8 ? -0.621 -0.255 -0.540 1.00 96.42 8 A 1 ATOM 59 C CD1 . LEU A 1 8 ? 0.286 -1.310 -1.153 1.00 94.86 8 A 1 ATOM 60 C CD2 . LEU A 1 8 ? -1.514 -0.897 0.509 1.00 94.46 8 A 1 ATOM 61 N N . VAL A 1 9 ? 2.396 2.392 1.835 1.00 98.48 9 A 1 ATOM 62 C CA . VAL A 1 9 ? 3.606 3.206 1.903 1.00 98.48 9 A 1 ATOM 63 C C . VAL A 1 9 ? 4.638 2.560 2.820 1.00 98.60 9 A 1 ATOM 64 O O . VAL A 1 9 ? 5.833 2.527 2.509 1.00 98.47 9 A 1 ATOM 65 C CB . VAL A 1 9 ? 3.283 4.627 2.396 1.00 98.22 9 A 1 ATOM 66 C CG1 . VAL A 1 9 ? 4.557 5.441 2.592 1.00 97.04 9 A 1 ATOM 67 C CG2 . VAL A 1 9 ? 2.373 5.332 1.398 1.00 97.04 9 A 1 ATOM 68 N N . ALA A 1 10 ? 4.172 2.055 3.966 1.00 98.64 10 A 1 ATOM 69 C CA . ALA A 1 10 ? 5.066 1.420 4.934 1.00 98.63 10 A 1 ATOM 70 C C . ALA A 1 10 ? 5.430 -0.001 4.516 1.00 98.71 10 A 1 ATOM 71 O O . ALA A 1 10 ? 6.546 -0.463 4.769 1.00 98.48 10 A 1 ATOM 72 C CB . ALA A 1 10 ? 4.416 1.411 6.312 1.00 98.34 10 A 1 ATOM 73 N N . PHE A 1 11 ? 4.487 -0.697 3.884 1.00 98.30 11 A 1 ATOM 74 C CA . PHE A 1 11 ? 4.689 -2.078 3.452 1.00 98.29 11 A 1 ATOM 75 C C . PHE A 1 11 ? 4.374 -2.226 1.965 1.00 98.50 11 A 1 ATOM 76 O O . PHE A 1 11 ? 3.286 -2.673 1.591 1.00 98.26 11 A 1 ATOM 77 C CB . PHE A 1 11 ? 3.807 -3.020 4.275 1.00 97.85 11 A 1 ATOM 78 C CG . PHE A 1 11 ? 4.393 -3.379 5.614 1.00 96.68 11 A 1 ATOM 79 C CD1 . PHE A 1 11 ? 4.421 -2.458 6.644 1.00 95.10 11 A 1 ATOM 80 C CD2 . PHE A 1 11 ? 4.918 -4.642 5.831 1.00 95.54 11 A 1 ATOM 81 C CE1 . PHE A 1 11 ? 4.964 -2.782 7.880 1.00 94.27 11 A 1 ATOM 82 C CE2 . PHE A 1 11 ? 5.462 -4.983 7.061 1.00 93.82 11 A 1 ATOM 83 C CZ . PHE A 1 11 ? 5.485 -4.050 8.091 1.00 93.86 11 A 1 ATOM 84 N N . PRO A 1 12 ? 5.328 -1.870 1.102 1.00 98.51 12 A 1 ATOM 85 C CA . PRO A 1 12 ? 5.124 -1.971 -0.348 1.00 98.38 12 A 1 ATOM 86 C C . PRO A 1 12 ? 4.889 -3.408 -0.803 1.00 98.51 12 A 1 ATOM 87 O O . PRO A 1 12 ? 4.298 -3.639 -1.861 1.00 98.18 12 A 1 ATOM 88 C CB . PRO A 1 12 ? 6.426 -1.406 -0.941 1.00 97.89 12 A 1 ATOM 89 C CG . PRO A 1 12 ? 7.438 -1.532 0.151 1.00 97.01 12 A 1 ATOM 90 C CD . PRO A 1 12 ? 6.667 -1.372 1.437 1.00 98.20 12 A 1 ATOM 91 N N . ALA A 1 13 ? 5.347 -4.380 -0.008 1.00 98.57 13 A 1 ATOM 92 C CA . ALA A 1 13 ? 5.164 -5.794 -0.334 1.00 98.55 13 A 1 ATOM 93 C C . ALA A 1 13 ? 3.680 -6.153 -0.419 1.00 98.63 13 A 1 ATOM 94 O O . ALA A 1 13 ? 3.292 -7.052 -1.167 1.00 98.24 13 A 1 ATOM 95 C CB . ALA A 1 13 ? 5.862 -6.656 0.711 1.00 98.26 13 A 1 ATOM 96 N N . LEU A 1 14 ? 2.845 -5.442 0.329 1.00 98.31 14 A 1 ATOM 97 C CA . LEU A 1 14 ? 1.408 -5.690 0.333 1.00 98.05 14 A 1 ATOM 98 C C . LEU A 1 14 ? 0.793 -5.379 -1.023 1.00 98.12 14 A 1 ATOM 99 O O . LEU A 1 14 ? -0.220 -5.967 -1.399 1.00 97.55 14 A 1 ATOM 100 C CB . LEU A 1 14 ? 0.738 -4.851 1.423 1.00 97.57 14 A 1 ATOM 101 C CG . LEU A 1 14 ? 0.677 -5.539 2.783 1.00 95.51 14 A 1 ATOM 102 C CD1 . LEU A 1 14 ? 0.125 -4.584 3.827 1.00 94.18 14 A 1 ATOM 103 C CD2 . LEU A 1 14 ? -0.198 -6.783 2.702 1.00 93.69 14 A 1 ATOM 104 N N . ALA A 1 15 ? 1.416 -4.476 -1.760 1.00 98.20 15 A 1 ATOM 105 C CA . ALA A 1 15 ? 0.926 -4.107 -3.088 1.00 97.96 15 A 1 ATOM 106 C C . ALA A 1 15 ? 0.987 -5.298 -4.041 1.00 98.12 15 A 1 ATOM 107 O O . ALA A 1 15 ? 0.175 -5.411 -4.959 1.00 97.61 15 A 1 ATOM 108 C CB . ALA A 1 15 ? 1.756 -2.951 -3.635 1.00 97.34 15 A 1 ATOM 109 N N . ALA A 1 16 ? 1.961 -6.179 -3.827 1.00 97.85 16 A 1 ATOM 110 C CA . ALA A 1 16 ? 2.126 -7.364 -4.662 1.00 97.59 16 A 1 ATOM 111 C C . ALA A 1 16 ? 1.138 -8.457 -4.275 1.00 97.85 16 A 1 ATOM 112 O O . ALA A 1 16 ? 0.838 -9.342 -5.079 1.00 97.09 16 A 1 ATOM 113 C CB . ALA A 1 16 ? 3.558 -7.886 -4.544 1.00 96.79 16 A 1 ATOM 114 N N . ALA A 1 17 ? 0.652 -8.389 -3.041 1.00 96.08 17 A 1 ATOM 115 C CA . ALA A 1 17 ? -0.291 -9.381 -2.535 1.00 94.31 17 A 1 ATOM 116 C C . ALA A 1 17 ? -1.700 -9.032 -2.983 1.00 92.59 17 A 1 ATOM 117 O O . ALA A 1 17 ? -2.453 -9.942 -3.370 1.00 89.47 17 A 1 ATOM 118 C CB . ALA A 1 17 ? -0.208 -9.454 -1.012 1.00 91.35 17 A 1 ATOM 119 O OXT . ALA A 1 17 ? -2.043 -7.847 -2.950 1.00 83.19 17 A 1 #