# 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_spkb33625 # _entry.id spkb33625 # 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 H10 N2 O3" 146.144 GLN y GLUTAMINE C(CC(=O)N)[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" "C3 H7 N O3" 105.093 SER y SERINE C([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" "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 GLN 2 1 n PHE 3 1 n LEU 4 1 n ALA 5 1 n SER 6 1 n LEU 7 1 n VAL 8 1 n SER 9 1 n PHE 10 1 n LEU 11 1 n LEU 12 1 n VAL 13 1 n VAL 14 1 n TRP 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 @ 2025-07-11 18:16:02)" _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 92.89 _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 87.34 1 1 A GLN 2 2 88.03 1 2 A PHE 3 2 91.30 1 3 A LEU 4 2 92.06 1 4 A ALA 5 2 95.14 1 5 A SER 6 2 95.38 1 6 A LEU 7 2 94.24 1 7 A VAL 8 2 96.23 1 8 A SER 9 2 95.82 1 9 A PHE 10 2 93.36 1 10 A LEU 11 2 94.73 1 11 A LEU 12 2 94.75 1 12 A VAL 13 2 97.23 1 13 A VAL 14 2 96.33 1 14 A TRP 15 2 91.51 1 15 A SER 16 2 87.89 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 GLN . 2 A 2 A 3 1 n PHE . 3 A 3 A 4 1 n LEU . 4 A 4 A 5 1 n ALA . 5 A 5 A 6 1 n SER . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n VAL . 8 A 8 A 9 1 n SER . 9 A 9 A 10 1 n PHE . 10 A 10 A 11 1 n LEU . 11 A 11 A 12 1 n LEU . 12 A 12 A 13 1 n VAL . 13 A 13 A 14 1 n VAL . 14 A 14 A 15 1 n TRP . 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 ? -11.595 1.808 7.076 1.00 92.76 1 A 1 ATOM 2 C CA . MET A 1 1 ? -10.193 2.163 7.343 1.00 93.66 1 A 1 ATOM 3 C C . MET A 1 1 ? -9.291 1.768 6.173 1.00 94.34 1 A 1 ATOM 4 O O . MET A 1 1 ? -8.143 1.380 6.356 1.00 93.38 1 A 1 ATOM 5 C CB . MET A 1 1 ? -9.719 1.459 8.614 1.00 90.92 1 A 1 ATOM 6 C CG . MET A 1 1 ? -10.402 1.992 9.852 1.00 85.49 1 A 1 ATOM 7 S SD . MET A 1 1 ? -9.936 1.047 11.309 1.00 78.76 1 A 1 ATOM 8 C CE . MET A 1 1 ? -10.688 2.036 12.573 1.00 69.44 1 A 1 ATOM 9 N N . GLN A 1 2 ? -9.832 1.871 4.981 1.00 93.75 2 A 1 ATOM 10 C CA . GLN A 1 2 ? -9.079 1.498 3.785 1.00 95.03 2 A 1 ATOM 11 C C . GLN A 1 2 ? -8.047 2.565 3.423 1.00 95.75 2 A 1 ATOM 12 O O . GLN A 1 2 ? -7.086 2.286 2.707 1.00 93.65 2 A 1 ATOM 13 C CB . GLN A 1 2 ? -10.048 1.276 2.620 1.00 93.18 2 A 1 ATOM 14 C CG . GLN A 1 2 ? -10.878 0.013 2.785 1.00 87.13 2 A 1 ATOM 15 C CD . GLN A 1 2 ? -11.908 -0.141 1.683 1.00 83.48 2 A 1 ATOM 16 O OE1 . GLN A 1 2 ? -12.399 0.842 1.143 1.00 77.70 2 A 1 ATOM 17 N NE2 . GLN A 1 2 ? -12.252 -1.367 1.340 1.00 72.60 2 A 1 ATOM 18 N N . PHE A 1 3 ? -8.242 3.785 3.928 1.00 94.04 3 A 1 ATOM 19 C CA . PHE A 1 3 ? -7.300 4.870 3.664 1.00 94.59 3 A 1 ATOM 20 C C . PHE A 1 3 ? -5.941 4.569 4.293 1.00 96.15 3 A 1 ATOM 21 O O . PHE A 1 3 ? -4.892 4.839 3.699 1.00 95.44 3 A 1 ATOM 22 C CB . PHE A 1 3 ? -7.851 6.187 4.221 1.00 93.34 3 A 1 ATOM 23 C CG . PHE A 1 3 ? -9.023 6.715 3.425 1.00 91.85 3 A 1 ATOM 24 C CD1 . PHE A 1 3 ? -8.828 7.205 2.146 1.00 88.56 3 A 1 ATOM 25 C CD2 . PHE A 1 3 ? -10.295 6.712 3.963 1.00 88.71 3 A 1 ATOM 26 C CE1 . PHE A 1 3 ? -9.889 7.693 1.400 1.00 87.47 3 A 1 ATOM 27 C CE2 . PHE A 1 3 ? -11.369 7.200 3.220 1.00 87.30 3 A 1 ATOM 28 C CZ . PHE A 1 3 ? -11.162 7.689 1.944 1.00 86.85 3 A 1 ATOM 29 N N . LEU A 1 4 ? -5.957 4.004 5.487 1.00 94.85 4 A 1 ATOM 30 C CA . LEU A 1 4 ? -4.726 3.651 6.188 1.00 95.36 4 A 1 ATOM 31 C C . LEU A 1 4 ? -3.985 2.549 5.440 1.00 95.89 4 A 1 ATOM 32 O O . LEU A 1 4 ? -2.764 2.575 5.305 1.00 96.12 4 A 1 ATOM 33 C CB . LEU A 1 4 ? -5.047 3.206 7.622 1.00 95.05 4 A 1 ATOM 34 C CG . LEU A 1 4 ? -4.785 4.271 8.683 1.00 89.84 4 A 1 ATOM 35 C CD1 . LEU A 1 4 ? -3.299 4.579 8.754 1.00 84.51 4 A 1 ATOM 36 C CD2 . LEU A 1 4 ? -5.568 5.538 8.374 1.00 84.85 4 A 1 ATOM 37 N N . ALA A 1 5 ? -4.738 1.569 4.950 1.00 95.28 5 A 1 ATOM 38 C CA . ALA A 1 5 ? -4.157 0.453 4.204 1.00 95.39 5 A 1 ATOM 39 C C . ALA A 1 5 ? -3.522 0.943 2.904 1.00 95.78 5 A 1 ATOM 40 O O . ALA A 1 5 ? -2.488 0.430 2.477 1.00 94.94 5 A 1 ATOM 41 C CB . ALA A 1 5 ? -5.240 -0.577 3.911 1.00 94.32 5 A 1 ATOM 42 N N . SER A 1 6 ? -4.137 1.934 2.291 1.00 97.02 6 A 1 ATOM 43 C CA . SER A 1 6 ? -3.629 2.500 1.046 1.00 97.27 6 A 1 ATOM 44 C C . SER A 1 6 ? -2.289 3.198 1.272 1.00 97.51 6 A 1 ATOM 45 O O . SER A 1 6 ? -1.362 3.056 0.477 1.00 96.16 6 A 1 ATOM 46 C CB . SER A 1 6 ? -4.646 3.486 0.477 1.00 96.51 6 A 1 ATOM 47 O OG . SER A 1 6 ? -4.297 3.828 -0.840 1.00 87.80 6 A 1 ATOM 48 N N . LEU A 1 7 ? -2.191 3.926 2.373 1.00 96.67 7 A 1 ATOM 49 C CA . LEU A 1 7 ? -0.958 4.630 2.717 1.00 96.81 7 A 1 ATOM 50 C C . LEU A 1 7 ? 0.186 3.653 2.965 1.00 97.22 7 A 1 ATOM 51 O O . LEU A 1 7 ? 1.293 3.831 2.454 1.00 96.98 7 A 1 ATOM 52 C CB . LEU A 1 7 ? -1.194 5.491 3.960 1.00 96.65 7 A 1 ATOM 53 C CG . LEU A 1 7 ? -1.483 6.952 3.628 1.00 91.72 7 A 1 ATOM 54 C CD1 . LEU A 1 7 ? -2.242 7.627 4.755 1.00 88.59 7 A 1 ATOM 55 C CD2 . LEU A 1 7 ? -0.169 7.678 3.369 1.00 89.29 7 A 1 ATOM 56 N N . VAL A 1 8 ? -0.090 2.629 3.742 1.00 97.21 8 A 1 ATOM 57 C CA . VAL A 1 8 ? 0.926 1.624 4.068 1.00 97.06 8 A 1 ATOM 58 C C . VAL A 1 8 ? 1.325 0.836 2.828 1.00 97.30 8 A 1 ATOM 59 O O . VAL A 1 8 ? 2.507 0.575 2.597 1.00 97.10 8 A 1 ATOM 60 C CB . VAL A 1 8 ? 0.412 0.665 5.152 1.00 96.59 8 A 1 ATOM 61 C CG1 . VAL A 1 8 ? 1.453 -0.404 5.452 1.00 94.41 8 A 1 ATOM 62 C CG2 . VAL A 1 8 ? 0.074 1.437 6.416 1.00 93.93 8 A 1 ATOM 63 N N . SER A 1 9 ? 0.339 0.452 2.031 1.00 97.14 9 A 1 ATOM 64 C CA . SER A 1 9 ? 0.589 -0.321 0.817 1.00 97.21 9 A 1 ATOM 65 C C . SER A 1 9 ? 1.405 0.488 -0.184 1.00 97.46 9 A 1 ATOM 66 O O . SER A 1 9 ? 2.340 -0.024 -0.801 1.00 96.66 9 A 1 ATOM 67 C CB . SER A 1 9 ? -0.732 -0.751 0.189 1.00 96.35 9 A 1 ATOM 68 O OG . SER A 1 9 ? -0.503 -1.688 -0.840 1.00 90.10 9 A 1 ATOM 69 N N . PHE A 1 10 ? 1.057 1.755 -0.330 1.00 95.80 10 A 1 ATOM 70 C CA . PHE A 1 10 ? 1.763 2.643 -1.254 1.00 96.09 10 A 1 ATOM 71 C C . PHE A 1 10 ? 3.215 2.822 -0.819 1.00 97.09 10 A 1 ATOM 72 O O . PHE A 1 10 ? 4.129 2.788 -1.645 1.00 96.64 10 A 1 ATOM 73 C CB . PHE A 1 10 ? 1.060 4.000 -1.302 1.00 95.65 10 A 1 ATOM 74 C CG . PHE A 1 10 ? 1.367 4.762 -2.568 1.00 93.92 10 A 1 ATOM 75 C CD1 . PHE A 1 10 ? 2.475 5.594 -2.642 1.00 90.61 10 A 1 ATOM 76 C CD2 . PHE A 1 10 ? 0.547 4.627 -3.677 1.00 91.51 10 A 1 ATOM 77 C CE1 . PHE A 1 10 ? 2.768 6.285 -3.809 1.00 89.56 10 A 1 ATOM 78 C CE2 . PHE A 1 10 ? 0.837 5.321 -4.848 1.00 89.51 10 A 1 ATOM 79 C CZ . PHE A 1 10 ? 1.947 6.146 -4.913 1.00 90.53 10 A 1 ATOM 80 N N . LEU A 1 11 ? 3.407 2.998 0.472 1.00 96.29 11 A 1 ATOM 81 C CA . LEU A 1 11 ? 4.752 3.172 1.012 1.00 96.44 11 A 1 ATOM 82 C C . LEU A 1 11 ? 5.591 1.918 0.793 1.00 96.96 11 A 1 ATOM 83 O O . LEU A 1 11 ? 6.779 2.000 0.492 1.00 96.63 11 A 1 ATOM 84 C CB . LEU A 1 11 ? 4.672 3.487 2.506 1.00 96.27 11 A 1 ATOM 85 C CG . LEU A 1 11 ? 5.856 4.312 2.995 1.00 93.71 11 A 1 ATOM 86 C CD1 . LEU A 1 11 ? 5.649 5.787 2.654 1.00 90.62 11 A 1 ATOM 87 C CD2 . LEU A 1 11 ? 6.032 4.142 4.492 1.00 90.93 11 A 1 ATOM 88 N N . LEU A 1 12 ? 4.973 0.758 0.943 1.00 97.09 12 A 1 ATOM 89 C CA . LEU A 1 12 ? 5.661 -0.520 0.768 1.00 97.01 12 A 1 ATOM 90 C C . LEU A 1 12 ? 6.104 -0.706 -0.679 1.00 97.32 12 A 1 ATOM 91 O O . LEU A 1 12 ? 7.219 -1.158 -0.944 1.00 96.71 12 A 1 ATOM 92 C CB . LEU A 1 12 ? 4.731 -1.659 1.197 1.00 96.71 12 A 1 ATOM 93 C CG . LEU A 1 12 ? 5.420 -2.723 2.044 1.00 93.02 12 A 1 ATOM 94 C CD1 . LEU A 1 12 ? 4.394 -3.482 2.874 1.00 89.94 12 A 1 ATOM 95 C CD2 . LEU A 1 12 ? 6.199 -3.685 1.173 1.00 90.16 12 A 1 ATOM 96 N N . VAL A 1 13 ? 5.238 -0.354 -1.620 1.00 98.11 13 A 1 ATOM 97 C CA . VAL A 1 13 ? 5.548 -0.486 -3.043 1.00 98.02 13 A 1 ATOM 98 C C . VAL A 1 13 ? 6.664 0.474 -3.450 1.00 98.18 13 A 1 ATOM 99 O O . VAL A 1 13 ? 7.563 0.108 -4.212 1.00 97.57 13 A 1 ATOM 100 C CB . VAL A 1 13 ? 4.296 -0.227 -3.899 1.00 97.44 13 A 1 ATOM 101 C CG1 . VAL A 1 13 ? 4.639 -0.284 -5.383 1.00 95.62 13 A 1 ATOM 102 C CG2 . VAL A 1 13 ? 3.216 -1.248 -3.582 1.00 95.70 13 A 1 ATOM 103 N N . VAL A 1 14 ? 6.606 1.681 -2.939 1.00 97.89 14 A 1 ATOM 104 C CA . VAL A 1 14 ? 7.614 2.698 -3.256 1.00 97.76 14 A 1 ATOM 105 C C . VAL A 1 14 ? 8.952 2.373 -2.599 1.00 97.76 14 A 1 ATOM 106 O O . VAL A 1 14 ? 10.013 2.572 -3.194 1.00 96.92 14 A 1 ATOM 107 C CB . VAL A 1 14 ? 7.136 4.091 -2.808 1.00 97.06 14 A 1 ATOM 108 C CG1 . VAL A 1 14 ? 8.223 5.131 -3.045 1.00 93.42 14 A 1 ATOM 109 C CG2 . VAL A 1 14 ? 5.880 4.483 -3.569 1.00 93.52 14 A 1 ATOM 110 N N . TRP A 1 15 ? 8.891 1.872 -1.368 1.00 96.29 15 A 1 ATOM 111 C CA . TRP A 1 15 ? 10.098 1.541 -0.623 1.00 95.56 15 A 1 ATOM 112 C C . TRP A 1 15 ? 10.636 0.162 -1.002 1.00 95.52 15 A 1 ATOM 113 O O . TRP A 1 15 ? 11.778 -0.164 -0.724 1.00 94.65 15 A 1 ATOM 114 C CB . TRP A 1 15 ? 9.813 1.597 0.887 1.00 94.79 15 A 1 ATOM 115 C CG . TRP A 1 15 ? 10.710 2.564 1.600 1.00 91.84 15 A 1 ATOM 116 C CD1 . TRP A 1 15 ? 10.375 3.796 2.058 1.00 89.78 15 A 1 ATOM 117 C CD2 . TRP A 1 15 ? 12.093 2.385 1.937 1.00 91.69 15 A 1 ATOM 118 N NE1 . TRP A 1 15 ? 11.459 4.397 2.659 1.00 89.33 15 A 1 ATOM 119 C CE2 . TRP A 1 15 ? 12.532 3.556 2.602 1.00 90.76 15 A 1 ATOM 120 C CE3 . TRP A 1 15 ? 13.014 1.351 1.742 1.00 89.12 15 A 1 ATOM 121 C CZ2 . TRP A 1 15 ? 13.842 3.699 3.067 1.00 88.82 15 A 1 ATOM 122 C CZ3 . TRP A 1 15 ? 14.315 1.498 2.205 1.00 86.28 15 A 1 ATOM 123 C CH2 . TRP A 1 15 ? 14.720 2.657 2.858 1.00 86.66 15 A 1 ATOM 124 N N . SER A 1 16 ? 9.807 -0.637 -1.640 1.00 94.78 16 A 1 ATOM 125 C CA . SER A 1 16 ? 10.187 -2.000 -2.018 1.00 92.91 16 A 1 ATOM 126 C C . SER A 1 16 ? 11.303 -1.972 -3.060 1.00 89.30 16 A 1 ATOM 127 O O . SER A 1 16 ? 12.381 -2.538 -2.791 1.00 85.19 16 A 1 ATOM 128 C CB . SER A 1 16 ? 8.980 -2.762 -2.558 1.00 88.58 16 A 1 ATOM 129 O OG . SER A 1 16 ? 9.346 -4.088 -2.858 1.00 81.23 16 A 1 ATOM 130 O OXT . SER A 1 16 ? 11.083 -1.385 -4.114 1.00 83.22 16 A 1 #