# 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_spkb24725 # _entry.id spkb24725 # 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" "C4 H8 N2 O3" 132.118 ASN y ASPARAGINE C([C@@H](C(=O)O)N)C(=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" "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" "C5 H9 N O2" 115.130 PRO y PROLINE C1C[C@H](NC1)C(=O)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 GLN 2 1 n LEU 3 1 n LEU 4 1 n ASN 5 1 n PHE 6 1 n GLY 7 1 n LEU 8 1 n LEU 9 1 n LEU 10 1 n LEU 11 1 n PRO 12 1 n PHE 13 1 n VAL 14 1 n ALA 15 1 n GLY 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 @ 2025-07-05 02:34:27)" _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 93.58 _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 84.96 1 1 A GLN 2 2 88.34 1 2 A LEU 3 2 93.88 1 3 A LEU 4 2 93.84 1 4 A ASN 5 2 93.63 1 5 A PHE 6 2 93.28 1 6 A GLY 7 2 97.33 1 7 A LEU 8 2 95.71 1 8 A LEU 9 2 95.81 1 9 A LEU 10 2 96.10 1 10 A LEU 11 2 95.41 1 11 A PRO 12 2 97.18 1 12 A PHE 13 2 95.03 1 13 A VAL 14 2 95.60 1 14 A ALA 15 2 95.68 1 15 A GLY 16 2 86.46 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 LEU . 3 A 3 A 4 1 n LEU . 4 A 4 A 5 1 n ASN . 5 A 5 A 6 1 n PHE . 6 A 6 A 7 1 n GLY . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n LEU . 11 A 11 A 12 1 n PRO . 12 A 12 A 13 1 n PHE . 13 A 13 A 14 1 n VAL . 14 A 14 A 15 1 n ALA . 15 A 15 A 16 1 n GLY . 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 ? -5.453 11.626 1.899 1.00 91.22 1 A 1 ATOM 2 C CA . MET A 1 1 ? -4.016 11.808 2.196 1.00 91.98 1 A 1 ATOM 3 C C . MET A 1 1 ? -3.191 10.676 1.589 1.00 92.15 1 A 1 ATOM 4 O O . MET A 1 1 ? -3.742 9.667 1.157 1.00 90.52 1 A 1 ATOM 5 C CB . MET A 1 1 ? -3.800 11.844 3.706 1.00 87.19 1 A 1 ATOM 6 C CG . MET A 1 1 ? -3.961 13.243 4.285 1.00 81.55 1 A 1 ATOM 7 S SD . MET A 1 1 ? -3.613 13.268 6.048 1.00 77.26 1 A 1 ATOM 8 C CE . MET A 1 1 ? -3.962 14.988 6.408 1.00 67.81 1 A 1 ATOM 9 N N . GLN A 1 2 ? -1.890 10.870 1.571 1.00 92.06 2 A 1 ATOM 10 C CA . GLN A 1 2 ? -0.971 9.865 1.030 1.00 94.02 2 A 1 ATOM 11 C C . GLN A 1 2 ? -0.847 8.676 1.984 1.00 95.01 2 A 1 ATOM 12 O O . GLN A 1 2 ? -0.248 7.656 1.644 1.00 92.84 2 A 1 ATOM 13 C CB . GLN A 1 2 ? 0.403 10.508 0.811 1.00 91.93 2 A 1 ATOM 14 C CG . GLN A 1 2 ? 0.389 11.571 -0.285 1.00 86.61 2 A 1 ATOM 15 C CD . GLN A 1 2 ? 0.820 11.018 -1.639 1.00 85.63 2 A 1 ATOM 16 O OE1 . GLN A 1 2 ? 0.575 9.862 -1.959 1.00 79.98 2 A 1 ATOM 17 N NE2 . GLN A 1 2 ? 1.482 11.835 -2.431 1.00 76.94 2 A 1 ATOM 18 N N . LEU A 1 3 ? -1.420 8.821 3.169 1.00 95.65 3 A 1 ATOM 19 C CA . LEU A 1 3 ? -1.386 7.753 4.173 1.00 96.24 3 A 1 ATOM 20 C C . LEU A 1 3 ? -2.006 6.481 3.612 1.00 96.76 3 A 1 ATOM 21 O O . LEU A 1 3 ? -1.598 5.374 3.959 1.00 95.92 3 A 1 ATOM 22 C CB . LEU A 1 3 ? -2.141 8.203 5.430 1.00 95.72 3 A 1 ATOM 23 C CG . LEU A 1 3 ? -1.234 8.818 6.496 1.00 92.64 3 A 1 ATOM 24 C CD1 . LEU A 1 3 ? -2.043 9.703 7.434 1.00 89.83 3 A 1 ATOM 25 C CD2 . LEU A 1 3 ? -0.550 7.709 7.287 1.00 88.32 3 A 1 ATOM 26 N N . LEU A 1 4 ? -2.999 6.655 2.735 1.00 96.04 4 A 1 ATOM 27 C CA . LEU A 1 4 ? -3.668 5.516 2.114 1.00 96.00 4 A 1 ATOM 28 C C . LEU A 1 4 ? -2.681 4.748 1.242 1.00 96.40 4 A 1 ATOM 29 O O . LEU A 1 4 ? -2.763 3.525 1.117 1.00 96.10 4 A 1 ATOM 30 C CB . LEU A 1 4 ? -4.864 5.999 1.279 1.00 95.58 4 A 1 ATOM 31 C CG . LEU A 1 4 ? -6.192 5.335 1.647 1.00 93.02 4 A 1 ATOM 32 C CD1 . LEU A 1 4 ? -6.123 3.832 1.426 1.00 89.52 4 A 1 ATOM 33 C CD2 . LEU A 1 4 ? -6.543 5.639 3.099 1.00 88.09 4 A 1 ATOM 34 N N . ASN A 1 5 ? -1.759 5.497 0.640 1.00 95.47 5 A 1 ATOM 35 C CA . ASN A 1 5 ? -0.733 4.897 -0.212 1.00 95.92 5 A 1 ATOM 36 C C . ASN A 1 5 ? 0.170 3.990 0.615 1.00 96.38 5 A 1 ATOM 37 O O . ASN A 1 5 ? 0.546 2.902 0.181 1.00 96.14 5 A 1 ATOM 38 C CB . ASN A 1 5 ? 0.106 5.994 -0.873 1.00 95.13 5 A 1 ATOM 39 C CG . ASN A 1 5 ? -0.562 6.521 -2.133 1.00 92.84 5 A 1 ATOM 40 O OD1 . ASN A 1 5 ? 0.103 6.966 -3.067 1.00 89.63 5 A 1 ATOM 41 N ND2 . ASN A 1 5 ? -1.881 6.491 -2.189 1.00 87.51 5 A 1 ATOM 42 N N . PHE A 1 6 ? 0.497 4.460 1.820 1.00 96.21 6 A 1 ATOM 43 C CA . PHE A 1 6 ? 1.346 3.683 2.720 1.00 96.06 6 A 1 ATOM 44 C C . PHE A 1 6 ? 0.619 2.426 3.167 1.00 96.78 6 A 1 ATOM 45 O O . PHE A 1 6 ? 1.220 1.363 3.301 1.00 96.10 6 A 1 ATOM 46 C CB . PHE A 1 6 ? 1.724 4.534 3.937 1.00 95.43 6 A 1 ATOM 47 C CG . PHE A 1 6 ? 3.197 4.854 3.978 1.00 93.76 6 A 1 ATOM 48 C CD1 . PHE A 1 6 ? 3.724 5.855 3.176 1.00 90.84 6 A 1 ATOM 49 C CD2 . PHE A 1 6 ? 4.040 4.145 4.817 1.00 91.05 6 A 1 ATOM 50 C CE1 . PHE A 1 6 ? 5.083 6.151 3.203 1.00 90.36 6 A 1 ATOM 51 C CE2 . PHE A 1 6 ? 5.402 4.433 4.856 1.00 89.41 6 A 1 ATOM 52 C CZ . PHE A 1 6 ? 5.927 5.437 4.049 1.00 90.08 6 A 1 ATOM 53 N N . GLY A 1 7 ? -0.685 2.572 3.396 1.00 97.04 7 A 1 ATOM 54 C CA . GLY A 1 7 ? -1.496 1.432 3.805 1.00 97.21 7 A 1 ATOM 55 C C . GLY A 1 7 ? -1.582 0.403 2.697 1.00 97.71 7 A 1 ATOM 56 O O . GLY A 1 7 ? -1.588 -0.802 2.950 1.00 97.36 7 A 1 ATOM 57 N N . LEU A 1 8 ? -1.651 0.899 1.462 1.00 97.31 8 A 1 ATOM 58 C CA . LEU A 1 8 ? -1.714 0.032 0.287 1.00 97.30 8 A 1 ATOM 59 C C . LEU A 1 8 ? -0.426 -0.769 0.160 1.00 97.54 8 A 1 ATOM 60 O O . LEU A 1 8 ? -0.417 -1.864 -0.406 1.00 97.00 8 A 1 ATOM 61 C CB . LEU A 1 8 ? -1.929 0.887 -0.965 1.00 96.95 8 A 1 ATOM 62 C CG . LEU A 1 8 ? -3.199 0.531 -1.739 1.00 94.69 8 A 1 ATOM 63 C CD1 . LEU A 1 8 ? -3.676 1.727 -2.556 1.00 92.63 8 A 1 ATOM 64 C CD2 . LEU A 1 8 ? -2.942 -0.657 -2.652 1.00 92.26 8 A 1 ATOM 65 N N . LEU A 1 9 ? 0.650 -0.206 0.693 1.00 97.10 9 A 1 ATOM 66 C CA . LEU A 1 9 ? 1.953 -0.867 0.659 1.00 97.02 9 A 1 ATOM 67 C C . LEU A 1 9 ? 1.931 -2.119 1.532 1.00 97.43 9 A 1 ATOM 68 O O . LEU A 1 9 ? 2.675 -3.068 1.293 1.00 96.99 9 A 1 ATOM 69 C CB . LEU A 1 9 ? 3.028 0.102 1.161 1.00 96.62 9 A 1 ATOM 70 C CG . LEU A 1 9 ? 4.293 0.123 0.305 1.00 94.83 9 A 1 ATOM 71 C CD1 . LEU A 1 9 ? 4.094 1.032 -0.911 1.00 93.35 9 A 1 ATOM 72 C CD2 . LEU A 1 9 ? 5.473 0.602 1.130 1.00 93.17 9 A 1 ATOM 73 N N . LEU A 1 10 ? 1.065 -2.100 2.542 1.00 97.11 10 A 1 ATOM 74 C CA . LEU A 1 10 ? 0.950 -3.220 3.469 1.00 97.19 10 A 1 ATOM 75 C C . LEU A 1 10 ? -0.059 -4.243 2.964 1.00 97.59 10 A 1 ATOM 76 O O . LEU A 1 10 ? -0.080 -5.383 3.425 1.00 97.27 10 A 1 ATOM 77 C CB . LEU A 1 10 ? 0.534 -2.707 4.848 1.00 96.83 10 A 1 ATOM 78 C CG . LEU A 1 10 ? 1.701 -2.431 5.796 1.00 95.22 10 A 1 ATOM 79 C CD1 . LEU A 1 10 ? 2.473 -1.189 5.365 1.00 93.98 10 A 1 ATOM 80 C CD2 . LEU A 1 10 ? 1.179 -2.252 7.219 1.00 93.61 10 A 1 ATOM 81 N N . LEU A 1 11 ? -0.889 -3.816 2.019 1.00 97.08 11 A 1 ATOM 82 C CA . LEU A 1 11 ? -1.911 -4.693 1.452 1.00 96.89 11 A 1 ATOM 83 C C . LEU A 1 11 ? -1.289 -5.962 0.866 1.00 97.20 11 A 1 ATOM 84 O O . LEU A 1 11 ? -1.760 -7.068 1.151 1.00 96.80 11 A 1 ATOM 85 C CB . LEU A 1 11 ? -2.705 -3.938 0.384 1.00 96.32 11 A 1 ATOM 86 C CG . LEU A 1 11 ? -4.070 -4.547 0.086 1.00 94.12 11 A 1 ATOM 87 C CD1 . LEU A 1 11 ? -5.081 -3.443 -0.190 1.00 92.63 11 A 1 ATOM 88 C CD2 . LEU A 1 11 ? -3.980 -5.481 -1.113 1.00 92.27 11 A 1 ATOM 89 N N . PRO A 1 12 ? -0.237 -5.813 0.040 1.00 97.59 12 A 1 ATOM 90 C CA . PRO A 1 12 ? 0.421 -6.985 -0.545 1.00 97.45 12 A 1 ATOM 91 C C . PRO A 1 12 ? 1.099 -7.844 0.508 1.00 97.67 12 A 1 ATOM 92 O O . PRO A 1 12 ? 1.337 -9.032 0.293 1.00 97.01 12 A 1 ATOM 93 C CB . PRO A 1 12 ? 1.464 -6.375 -1.494 1.00 96.77 12 A 1 ATOM 94 C CG . PRO A 1 12 ? 1.716 -5.011 -0.954 1.00 96.21 12 A 1 ATOM 95 C CD . PRO A 1 12 ? 0.394 -4.558 -0.375 1.00 97.53 12 A 1 ATOM 96 N N . PHE A 1 13 ? 1.397 -7.247 1.639 1.00 97.26 13 A 1 ATOM 97 C CA . PHE A 1 13 ? 2.044 -7.954 2.738 1.00 97.01 13 A 1 ATOM 98 C C . PHE A 1 13 ? 1.048 -8.876 3.435 1.00 97.26 13 A 1 ATOM 99 O O . PHE A 1 13 ? 1.413 -9.964 3.880 1.00 96.38 13 A 1 ATOM 100 C CB . PHE A 1 13 ? 2.609 -6.935 3.734 1.00 96.47 13 A 1 ATOM 101 C CG . PHE A 1 13 ? 3.582 -7.548 4.704 1.00 95.46 13 A 1 ATOM 102 C CD1 . PHE A 1 13 ? 4.846 -7.931 4.285 1.00 93.14 13 A 1 ATOM 103 C CD2 . PHE A 1 13 ? 3.225 -7.733 6.032 1.00 93.44 13 A 1 ATOM 104 C CE1 . PHE A 1 13 ? 5.749 -8.496 5.176 1.00 93.05 13 A 1 ATOM 105 C CE2 . PHE A 1 13 ? 4.125 -8.301 6.933 1.00 92.59 13 A 1 ATOM 106 C CZ . PHE A 1 13 ? 5.389 -8.682 6.504 1.00 93.32 13 A 1 ATOM 107 N N . VAL A 1 14 ? -0.193 -8.417 3.523 1.00 97.20 14 A 1 ATOM 108 C CA . VAL A 1 14 ? -1.239 -9.213 4.166 1.00 96.79 14 A 1 ATOM 109 C C . VAL A 1 14 ? -1.986 -10.069 3.150 1.00 96.84 14 A 1 ATOM 110 O O . VAL A 1 14 ? -2.456 -11.162 3.474 1.00 96.08 14 A 1 ATOM 111 C CB . VAL A 1 14 ? -2.231 -8.293 4.916 1.00 95.83 14 A 1 ATOM 112 C CG1 . VAL A 1 14 ? -2.988 -7.406 3.932 1.00 93.15 14 A 1 ATOM 113 C CG2 . VAL A 1 14 ? -3.219 -9.121 5.724 1.00 93.33 14 A 1 ATOM 114 N N . ALA A 1 15 ? -2.099 -9.569 1.930 1.00 96.54 15 A 1 ATOM 115 C CA . ALA A 1 15 ? -2.792 -10.290 0.859 1.00 96.01 15 A 1 ATOM 116 C C . ALA A 1 15 ? -1.982 -11.501 0.406 1.00 96.12 15 A 1 ATOM 117 O O . ALA A 1 15 ? -2.534 -12.578 0.180 1.00 95.06 15 A 1 ATOM 118 C CB . ALA A 1 15 ? -3.056 -9.353 -0.314 1.00 94.67 15 A 1 ATOM 119 N N . GLY A 1 16 ? -0.667 -11.313 0.299 1.00 92.67 16 A 1 ATOM 120 C CA . GLY A 1 16 ? 0.221 -12.398 -0.146 1.00 89.19 16 A 1 ATOM 121 C C . GLY A 1 16 ? 0.387 -12.385 -1.646 1.00 85.62 16 A 1 ATOM 122 O O . GLY A 1 16 ? 1.376 -11.821 -2.130 1.00 80.46 16 A 1 ATOM 123 O OXT . GLY A 1 16 ? -0.470 -12.916 -2.319 1.00 84.35 16 A 1 #