# 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_spkb40780 # _entry.id spkb40780 # 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" "C3 H7 N O2 S" 121.158 CYS y CYSTEINE C([C@@H](C(=O)O)N)S ? "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 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" "C3 H7 N O3" 105.093 SER y SERINE C([C@@H](C(=O)O)N)O ? "L-PEPTIDE LINKING" "C4 H9 N O3" 119.119 THR y THREONINE C[C@H]([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 GLY 3 1 n ILE 4 1 n ILE 5 1 n LEU 6 1 n LEU 7 1 n SER 8 1 n PHE 9 1 n VAL 10 1 n LEU 11 1 n THR 12 1 n SER 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 @ 2025-07-08 01:36:58)" _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 94.14 _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 85.75 1 1 A ARG 2 2 86.17 1 2 A GLY 3 2 97.07 1 3 A ILE 4 2 95.53 1 4 A ILE 5 2 95.72 1 5 A LEU 6 2 95.78 1 6 A LEU 7 2 96.20 1 7 A SER 8 2 96.22 1 8 A PHE 9 2 95.58 1 9 A VAL 10 2 97.41 1 10 A LEU 11 2 95.90 1 11 A THR 12 2 97.02 1 12 A SER 13 2 96.92 1 13 A CYS 14 2 97.12 1 14 A LEU 15 2 94.05 1 15 A ALA 16 2 89.11 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 ARG . 2 A 2 A 3 1 n GLY . 3 A 3 A 4 1 n ILE . 4 A 4 A 5 1 n ILE . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n SER . 8 A 8 A 9 1 n PHE . 9 A 9 A 10 1 n VAL . 10 A 10 A 11 1 n LEU . 11 A 11 A 12 1 n THR . 12 A 12 A 13 1 n SER . 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 . MET A 1 1 ? 5.690 11.165 0.235 1.00 91.91 1 A 1 ATOM 2 C CA . MET A 1 1 ? 4.437 10.402 0.117 1.00 92.35 1 A 1 ATOM 3 C C . MET A 1 1 ? 4.724 8.910 -0.036 1.00 92.71 1 A 1 ATOM 4 O O . MET A 1 1 ? 4.856 8.409 -1.146 1.00 89.28 1 A 1 ATOM 5 C CB . MET A 1 1 ? 3.658 10.868 -1.107 1.00 88.56 1 A 1 ATOM 6 C CG . MET A 1 1 ? 3.194 12.304 -1.001 1.00 83.26 1 A 1 ATOM 7 S SD . MET A 1 1 ? 2.356 12.834 -2.498 1.00 79.76 1 A 1 ATOM 8 C CE . MET A 1 1 ? 2.933 14.510 -2.629 1.00 68.18 1 A 1 ATOM 9 N N . ARG A 1 2 ? 4.842 8.231 1.067 1.00 93.40 2 A 1 ATOM 10 C CA . ARG A 1 2 ? 5.108 6.793 1.055 1.00 94.89 2 A 1 ATOM 11 C C . ARG A 1 2 ? 3.992 6.017 1.748 1.00 96.07 2 A 1 ATOM 12 O O . ARG A 1 2 ? 3.836 4.821 1.530 1.00 94.14 2 A 1 ATOM 13 C CB . ARG A 1 2 ? 6.448 6.504 1.734 1.00 92.31 2 A 1 ATOM 14 C CG . ARG A 1 2 ? 7.336 5.603 0.942 1.00 86.97 2 A 1 ATOM 15 C CD . ARG A 1 2 ? 8.521 6.387 0.402 1.00 85.52 2 A 1 ATOM 16 N NE . ARG A 1 2 ? 8.071 7.567 -0.330 1.00 80.35 2 A 1 ATOM 17 C CZ . ARG A 1 2 ? 8.844 8.609 -0.590 1.00 79.04 2 A 1 ATOM 18 N NH1 . ARG A 1 2 ? 10.106 8.626 -0.210 1.00 72.63 2 A 1 ATOM 19 N NH2 . ARG A 1 2 ? 8.344 9.653 -1.227 1.00 72.60 2 A 1 ATOM 20 N N . GLY A 1 3 ? 3.240 6.717 2.570 1.00 95.97 3 A 1 ATOM 21 C CA . GLY A 1 3 ? 2.140 6.084 3.288 1.00 97.16 3 A 1 ATOM 22 C C . GLY A 1 3 ? 1.146 5.430 2.350 1.00 97.87 3 A 1 ATOM 23 O O . GLY A 1 3 ? 0.646 4.339 2.614 1.00 97.27 3 A 1 ATOM 24 N N . ILE A 1 4 ? 0.867 6.102 1.241 1.00 97.02 4 A 1 ATOM 25 C CA . ILE A 1 4 ? -0.072 5.575 0.253 1.00 97.45 4 A 1 ATOM 26 C C . ILE A 1 4 ? 0.463 4.295 -0.386 1.00 97.98 4 A 1 ATOM 27 O O . ILE A 1 4 ? -0.299 3.401 -0.752 1.00 97.42 4 A 1 ATOM 28 C CB . ILE A 1 4 ? -0.369 6.626 -0.829 1.00 97.01 4 A 1 ATOM 29 C CG1 . ILE A 1 4 ? 0.931 7.178 -1.411 1.00 94.19 4 A 1 ATOM 30 C CG2 . ILE A 1 4 ? -1.233 7.736 -0.256 1.00 93.97 4 A 1 ATOM 31 C CD1 . ILE A 1 4 ? 1.238 6.579 -2.757 1.00 89.23 4 A 1 ATOM 32 N N . ILE A 1 5 ? 1.767 4.227 -0.529 1.00 96.99 5 A 1 ATOM 33 C CA . ILE A 1 5 ? 2.408 3.052 -1.106 1.00 97.08 5 A 1 ATOM 34 C C . ILE A 1 5 ? 2.202 1.845 -0.202 1.00 97.48 5 A 1 ATOM 35 O O . ILE A 1 5 ? 1.885 0.747 -0.662 1.00 97.23 5 A 1 ATOM 36 C CB . ILE A 1 5 ? 3.915 3.281 -1.311 1.00 97.01 5 A 1 ATOM 37 C CG1 . ILE A 1 5 ? 4.176 4.651 -1.934 1.00 94.83 5 A 1 ATOM 38 C CG2 . ILE A 1 5 ? 4.485 2.167 -2.186 1.00 94.93 5 A 1 ATOM 39 C CD1 . ILE A 1 5 ? 3.569 4.797 -3.311 1.00 90.19 5 A 1 ATOM 40 N N . LEU A 1 6 ? 2.405 2.072 1.074 1.00 97.41 6 A 1 ATOM 41 C CA . LEU A 1 6 ? 2.233 1.014 2.062 1.00 97.59 6 A 1 ATOM 42 C C . LEU A 1 6 ? 0.791 0.518 2.064 1.00 97.94 6 A 1 ATOM 43 O O . LEU A 1 6 ? 0.535 -0.684 2.134 1.00 97.80 6 A 1 ATOM 44 C CB . LEU A 1 6 ? 2.623 1.527 3.450 1.00 97.59 6 A 1 ATOM 45 C CG . LEU A 1 6 ? 4.080 1.271 3.830 1.00 93.77 6 A 1 ATOM 46 C CD1 . LEU A 1 6 ? 4.343 -0.218 3.914 1.00 91.85 6 A 1 ATOM 47 C CD2 . LEU A 1 6 ? 5.005 1.917 2.815 1.00 92.33 6 A 1 ATOM 48 N N . LEU A 1 7 ? -0.129 1.455 1.985 1.00 97.80 7 A 1 ATOM 49 C CA . LEU A 1 7 ? -1.550 1.119 1.964 1.00 97.98 7 A 1 ATOM 50 C C . LEU A 1 7 ? -1.883 0.291 0.726 1.00 98.30 7 A 1 ATOM 51 O O . LEU A 1 7 ? -2.629 -0.687 0.795 1.00 98.29 7 A 1 ATOM 52 C CB . LEU A 1 7 ? -2.393 2.397 1.990 1.00 97.98 7 A 1 ATOM 53 C CG . LEU A 1 7 ? -2.927 2.761 3.372 1.00 94.90 7 A 1 ATOM 54 C CD1 . LEU A 1 7 ? -3.849 1.676 3.880 1.00 91.45 7 A 1 ATOM 55 C CD2 . LEU A 1 7 ? -1.771 2.973 4.332 1.00 92.93 7 A 1 ATOM 56 N N . SER A 1 8 ? -1.324 0.698 -0.410 1.00 97.65 8 A 1 ATOM 57 C CA . SER A 1 8 ? -1.546 -0.005 -1.669 1.00 97.67 8 A 1 ATOM 58 C C . SER A 1 8 ? -0.934 -1.401 -1.620 1.00 97.96 8 A 1 ATOM 59 O O . SER A 1 8 ? -1.502 -2.361 -2.134 1.00 97.76 8 A 1 ATOM 60 C CB . SER A 1 8 ? -0.945 0.789 -2.823 1.00 97.26 8 A 1 ATOM 61 O OG . SER A 1 8 ? -1.386 0.278 -4.058 1.00 89.03 8 A 1 ATOM 62 N N . PHE A 1 9 ? 0.225 -1.487 -0.984 1.00 97.77 9 A 1 ATOM 63 C CA . PHE A 1 9 ? 0.921 -2.758 -0.843 1.00 97.75 9 A 1 ATOM 64 C C . PHE A 1 9 ? 0.105 -3.736 -0.003 1.00 98.10 9 A 1 ATOM 65 O O . PHE A 1 9 ? -0.053 -4.900 -0.363 1.00 97.73 9 A 1 ATOM 66 C CB . PHE A 1 9 ? 2.281 -2.521 -0.193 1.00 97.45 9 A 1 ATOM 67 C CG . PHE A 1 9 ? 2.910 -3.784 0.322 1.00 95.71 9 A 1 ATOM 68 C CD1 . PHE A 1 9 ? 3.388 -4.738 -0.556 1.00 93.75 9 A 1 ATOM 69 C CD2 . PHE A 1 9 ? 3.017 -4.008 1.682 1.00 94.14 9 A 1 ATOM 70 C CE1 . PHE A 1 9 ? 3.967 -5.903 -0.092 1.00 93.01 9 A 1 ATOM 71 C CE2 . PHE A 1 9 ? 3.594 -5.178 2.155 1.00 92.72 9 A 1 ATOM 72 C CZ . PHE A 1 9 ? 4.067 -6.125 1.270 1.00 93.26 9 A 1 ATOM 73 N N . VAL A 1 10 ? -0.393 -3.252 1.096 1.00 98.21 10 A 1 ATOM 74 C CA . VAL A 1 10 ? -1.201 -4.080 1.988 1.00 98.19 10 A 1 ATOM 75 C C . VAL A 1 10 ? -2.503 -4.482 1.309 1.00 98.35 10 A 1 ATOM 76 O O . VAL A 1 10 ? -2.984 -5.605 1.472 1.00 98.02 10 A 1 ATOM 77 C CB . VAL A 1 10 ? -1.509 -3.342 3.299 1.00 97.76 10 A 1 ATOM 78 C CG1 . VAL A 1 10 ? -2.260 -4.250 4.255 1.00 95.66 10 A 1 ATOM 79 C CG2 . VAL A 1 10 ? -0.231 -2.844 3.942 1.00 95.70 10 A 1 ATOM 80 N N . LEU A 1 11 ? -3.052 -3.557 0.551 1.00 98.05 11 A 1 ATOM 81 C CA . LEU A 1 11 ? -4.300 -3.810 -0.157 1.00 98.08 11 A 1 ATOM 82 C C . LEU A 1 11 ? -4.112 -4.871 -1.231 1.00 98.28 11 A 1 ATOM 83 O O . LEU A 1 11 ? -4.888 -5.816 -1.325 1.00 98.08 11 A 1 ATOM 84 C CB . LEU A 1 11 ? -4.810 -2.520 -0.794 1.00 97.88 11 A 1 ATOM 85 C CG . LEU A 1 11 ? -6.172 -2.085 -0.274 1.00 93.66 11 A 1 ATOM 86 C CD1 . LEU A 1 11 ? -6.028 -1.332 1.032 1.00 91.39 11 A 1 ATOM 87 C CD2 . LEU A 1 11 ? -6.881 -1.239 -1.312 1.00 91.80 11 A 1 ATOM 88 N N . THR A 1 12 ? -3.081 -4.701 -2.043 1.00 98.49 12 A 1 ATOM 89 C CA . THR A 1 12 ? -2.802 -5.645 -3.120 1.00 98.37 12 A 1 ATOM 90 C C . THR A 1 12 ? -2.473 -7.027 -2.565 1.00 98.47 12 A 1 ATOM 91 O O . THR A 1 12 ? -2.798 -8.045 -3.168 1.00 98.01 12 A 1 ATOM 92 C CB . THR A 1 12 ? -1.648 -5.130 -3.993 1.00 97.82 12 A 1 ATOM 93 O OG1 . THR A 1 12 ? -1.708 -5.770 -5.271 1.00 94.39 12 A 1 ATOM 94 C CG2 . THR A 1 12 ? -0.300 -5.409 -3.366 1.00 93.62 12 A 1 ATOM 95 N N . SER A 1 13 ? -1.828 -7.042 -1.420 1.00 98.42 13 A 1 ATOM 96 C CA . SER A 1 13 ? -1.462 -8.289 -0.762 1.00 98.31 13 A 1 ATOM 97 C C . SER A 1 13 ? -2.701 -9.019 -0.260 1.00 98.41 13 A 1 ATOM 98 O O . SER A 1 13 ? -2.778 -10.248 -0.315 1.00 97.67 13 A 1 ATOM 99 C CB . SER A 1 13 ? -0.514 -8.016 0.398 1.00 97.59 13 A 1 ATOM 100 O OG . SER A 1 13 ? -0.209 -9.194 1.079 1.00 91.14 13 A 1 ATOM 101 N N . CYS A 1 14 ? -3.666 -8.263 0.217 1.00 98.07 14 A 1 ATOM 102 C CA . CYS A 1 14 ? -4.904 -8.832 0.735 1.00 98.07 14 A 1 ATOM 103 C C . CYS A 1 14 ? -5.904 -9.095 -0.387 1.00 98.23 14 A 1 ATOM 104 O O . CYS A 1 14 ? -6.738 -9.994 -0.289 1.00 97.31 14 A 1 ATOM 105 C CB . CYS A 1 14 ? -5.513 -7.890 1.771 1.00 97.33 14 A 1 ATOM 106 S SG . CYS A 1 14 ? -6.459 -8.763 3.028 1.00 93.74 14 A 1 ATOM 107 N N . LEU A 1 15 ? -5.820 -8.285 -1.421 1.00 96.88 15 A 1 ATOM 108 C CA . LEU A 1 15 ? -6.716 -8.406 -2.567 1.00 96.83 15 A 1 ATOM 109 C C . LEU A 1 15 ? -6.403 -9.642 -3.394 1.00 97.36 15 A 1 ATOM 110 O O . LEU A 1 15 ? -7.309 -10.314 -3.892 1.00 96.47 15 A 1 ATOM 111 C CB . LEU A 1 15 ? -6.619 -7.147 -3.435 1.00 95.73 15 A 1 ATOM 112 C CG . LEU A 1 15 ? -7.213 -7.274 -4.828 1.00 92.91 15 A 1 ATOM 113 C CD1 . LEU A 1 15 ? -7.851 -5.966 -5.255 1.00 89.24 15 A 1 ATOM 114 C CD2 . LEU A 1 15 ? -6.136 -7.683 -5.832 1.00 86.95 15 A 1 ATOM 115 N N . ALA A 1 16 ? -5.122 -9.938 -3.557 1.00 95.06 16 A 1 ATOM 116 C CA . ALA A 1 16 ? -4.668 -11.080 -4.350 1.00 93.15 16 A 1 ATOM 117 C C . ALA A 1 16 ? -5.447 -12.340 -3.976 1.00 91.73 16 A 1 ATOM 118 O O . ALA A 1 16 ? -5.822 -13.102 -4.883 1.00 87.42 16 A 1 ATOM 119 C CB . ALA A 1 16 ? -3.171 -11.293 -4.147 1.00 88.44 16 A 1 ATOM 120 O OXT . ALA A 1 16 ? -5.685 -12.571 -2.806 1.00 78.83 16 A 1 #