# 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_spkb41855 # _entry.id spkb41855 # 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" "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 ALA 2 1 n CYS 3 1 n ARG 4 1 n SER 5 1 n TRP 6 1 n VAL 7 1 n LEU 8 1 n GLY 9 1 n ILE 10 1 n LEU 11 1 n LEU 12 1 n VAL 13 1 n LEU 14 1 n VAL 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 @ 2025-07-03 13:54:10)" _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 94.36 _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 84.59 1 1 A ALA 2 2 92.98 1 2 A CYS 3 2 93.08 1 3 A ARG 4 2 87.48 1 4 A SER 5 2 94.96 1 5 A TRP 6 2 94.80 1 6 A VAL 7 2 97.53 1 7 A LEU 8 2 96.13 1 8 A GLY 9 2 97.93 1 9 A ILE 10 2 96.55 1 10 A LEU 11 2 96.73 1 11 A LEU 12 2 96.77 1 12 A VAL 13 2 97.86 1 13 A LEU 14 2 97.63 1 14 A VAL 15 2 96.11 1 15 A GLY 16 2 92.31 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 ALA . 2 A 2 A 3 1 n CYS . 3 A 3 A 4 1 n ARG . 4 A 4 A 5 1 n SER . 5 A 5 A 6 1 n TRP . 6 A 6 A 7 1 n VAL . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n GLY . 9 A 9 A 10 1 n ILE . 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 LEU . 14 A 14 A 15 1 n VAL . 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 ? -6.548 10.329 10.794 1.00 90.17 1 A 1 ATOM 2 C CA . MET A 1 1 ? -5.288 9.694 10.367 1.00 90.95 1 A 1 ATOM 3 C C . MET A 1 1 ? -5.155 8.294 10.971 1.00 91.87 1 A 1 ATOM 4 O O . MET A 1 1 ? -4.376 8.077 11.891 1.00 88.96 1 A 1 ATOM 5 C CB . MET A 1 1 ? -4.111 10.559 10.794 1.00 87.75 1 A 1 ATOM 6 C CG . MET A 1 1 ? -4.133 10.889 12.278 1.00 82.45 1 A 1 ATOM 7 S SD . MET A 1 1 ? -2.726 11.902 12.767 1.00 77.98 1 A 1 ATOM 8 C CE . MET A 1 1 ? -3.381 13.514 12.411 1.00 66.62 1 A 1 ATOM 9 N N . ALA A 1 2 ? -5.926 7.376 10.461 1.00 91.97 2 A 1 ATOM 10 C CA . ALA A 1 2 ? -5.886 6.006 10.967 1.00 93.90 2 A 1 ATOM 11 C C . ALA A 1 2 ? -6.269 5.023 9.865 1.00 95.04 2 A 1 ATOM 12 O O . ALA A 1 2 ? -7.445 4.851 9.563 1.00 92.63 2 A 1 ATOM 13 C CB . ALA A 1 2 ? -6.826 5.875 12.157 1.00 91.36 2 A 1 ATOM 14 N N . CYS A 1 3 ? -5.290 4.397 9.272 1.00 95.21 3 A 1 ATOM 15 C CA . CYS A 1 3 ? -5.539 3.426 8.209 1.00 95.76 3 A 1 ATOM 16 C C . CYS A 1 3 ? -4.718 2.163 8.447 1.00 96.05 3 A 1 ATOM 17 O O . CYS A 1 3 ? -3.571 2.236 8.863 1.00 93.60 3 A 1 ATOM 18 C CB . CYS A 1 3 ? -5.167 4.041 6.868 1.00 92.79 3 A 1 ATOM 19 S SG . CYS A 1 3 ? -6.307 5.366 6.399 1.00 85.10 3 A 1 ATOM 20 N N . ARG A 1 4 ? -5.340 1.047 8.187 1.00 95.58 4 A 1 ATOM 21 C CA . ARG A 1 4 ? -4.657 -0.242 8.370 1.00 96.09 4 A 1 ATOM 22 C C . ARG A 1 4 ? -4.447 -0.942 7.037 1.00 96.51 4 A 1 ATOM 23 O O . ARG A 1 4 ? -3.694 -1.903 6.947 1.00 95.47 4 A 1 ATOM 24 C CB . ARG A 1 4 ? -5.489 -1.124 9.298 1.00 94.84 4 A 1 ATOM 25 C CG . ARG A 1 4 ? -4.772 -1.398 10.604 1.00 89.01 4 A 1 ATOM 26 C CD . ARG A 1 4 ? -4.639 -2.898 10.828 1.00 86.53 4 A 1 ATOM 27 N NE . ARG A 1 4 ? -4.768 -3.242 12.250 1.00 80.98 4 A 1 ATOM 28 C CZ . ARG A 1 4 ? -5.098 -4.450 12.684 1.00 79.96 4 A 1 ATOM 29 N NH1 . ARG A 1 4 ? -5.312 -5.439 11.841 1.00 73.35 4 A 1 ATOM 30 N NH2 . ARG A 1 4 ? -5.228 -4.685 13.972 1.00 73.93 4 A 1 ATOM 31 N N . SER A 1 5 ? -5.104 -0.462 5.998 1.00 96.96 5 A 1 ATOM 32 C CA . SER A 1 5 ? -4.982 -1.045 4.660 1.00 97.30 5 A 1 ATOM 33 C C . SER A 1 5 ? -4.098 -0.191 3.766 1.00 97.73 5 A 1 ATOM 34 O O . SER A 1 5 ? -3.801 -0.560 2.639 1.00 97.00 5 A 1 ATOM 35 C CB . SER A 1 5 ? -6.369 -1.181 4.045 1.00 96.02 5 A 1 ATOM 36 O OG . SER A 1 5 ? -7.016 -2.321 4.563 1.00 84.76 5 A 1 ATOM 37 N N . TRP A 1 6 ? -3.683 0.944 4.290 1.00 97.04 6 A 1 ATOM 38 C CA . TRP A 1 6 ? -2.821 1.842 3.519 1.00 97.27 6 A 1 ATOM 39 C C . TRP A 1 6 ? -1.483 1.166 3.219 1.00 97.71 6 A 1 ATOM 40 O O . TRP A 1 6 ? -0.911 1.347 2.153 1.00 97.17 6 A 1 ATOM 41 C CB . TRP A 1 6 ? -2.608 3.134 4.306 1.00 96.92 6 A 1 ATOM 42 C CG . TRP A 1 6 ? -1.308 3.194 5.040 1.00 95.88 6 A 1 ATOM 43 C CD1 . TRP A 1 6 ? -0.924 2.429 6.087 1.00 93.41 6 A 1 ATOM 44 C CD2 . TRP A 1 6 ? -0.191 4.065 4.737 1.00 94.81 6 A 1 ATOM 45 N NE1 . TRP A 1 6 ? 0.364 2.768 6.460 1.00 92.57 6 A 1 ATOM 46 C CE2 . TRP A 1 6 ? 0.832 3.774 5.649 1.00 94.50 6 A 1 ATOM 47 C CE3 . TRP A 1 6 ? 0.021 5.062 3.784 1.00 93.38 6 A 1 ATOM 48 C CZ2 . TRP A 1 6 ? 2.059 4.445 5.630 1.00 93.69 6 A 1 ATOM 49 C CZ3 . TRP A 1 6 ? 1.238 5.741 3.769 1.00 91.47 6 A 1 ATOM 50 C CH2 . TRP A 1 6 ? 2.246 5.420 4.683 1.00 91.42 6 A 1 ATOM 51 N N . VAL A 1 7 ? -1.009 0.389 4.168 1.00 97.94 7 A 1 ATOM 52 C CA . VAL A 1 7 ? 0.260 -0.320 3.991 1.00 98.06 7 A 1 ATOM 53 C C . VAL A 1 7 ? 0.150 -1.297 2.823 1.00 98.12 7 A 1 ATOM 54 O O . VAL A 1 7 ? 1.093 -1.475 2.054 1.00 97.91 7 A 1 ATOM 55 C CB . VAL A 1 7 ? 0.631 -1.075 5.277 1.00 97.86 7 A 1 ATOM 56 C CG1 . VAL A 1 7 ? 1.983 -1.748 5.123 1.00 96.47 7 A 1 ATOM 57 C CG2 . VAL A 1 7 ? 0.660 -0.116 6.457 1.00 96.37 7 A 1 ATOM 58 N N . LEU A 1 8 ? -0.998 -1.915 2.703 1.00 97.93 8 A 1 ATOM 59 C CA . LEU A 1 8 ? -1.223 -2.866 1.609 1.00 97.77 8 A 1 ATOM 60 C C . LEU A 1 8 ? -1.282 -2.129 0.276 1.00 97.94 8 A 1 ATOM 61 O O . LEU A 1 8 ? -0.810 -2.629 -0.740 1.00 97.68 8 A 1 ATOM 62 C CB . LEU A 1 8 ? -2.534 -3.611 1.866 1.00 97.51 8 A 1 ATOM 63 C CG . LEU A 1 8 ? -2.356 -4.771 2.850 1.00 94.91 8 A 1 ATOM 64 C CD1 . LEU A 1 8 ? -3.689 -5.138 3.477 1.00 92.63 8 A 1 ATOM 65 C CD2 . LEU A 1 8 ? -1.781 -5.982 2.114 1.00 92.69 8 A 1 ATOM 66 N N . GLY A 1 9 ? -1.863 -0.960 0.296 1.00 97.89 9 A 1 ATOM 67 C CA . GLY A 1 9 ? -1.955 -0.157 -0.921 1.00 97.83 9 A 1 ATOM 68 C C . GLY A 1 9 ? -0.583 0.217 -1.443 1.00 98.11 9 A 1 ATOM 69 O O . GLY A 1 9 ? -0.300 0.103 -2.635 1.00 97.88 9 A 1 ATOM 70 N N . ILE A 1 10 ? 0.255 0.661 -0.543 1.00 97.55 10 A 1 ATOM 71 C CA . ILE A 1 10 ? 1.614 1.039 -0.920 1.00 97.53 10 A 1 ATOM 72 C C . ILE A 1 10 ? 2.410 -0.194 -1.337 1.00 97.96 10 A 1 ATOM 73 O O . ILE A 1 10 ? 3.190 -0.154 -2.287 1.00 97.65 10 A 1 ATOM 74 C CB . ILE A 1 10 ? 2.293 1.759 0.255 1.00 97.23 10 A 1 ATOM 75 C CG1 . ILE A 1 10 ? 1.704 3.173 0.383 1.00 96.03 10 A 1 ATOM 76 C CG2 . ILE A 1 10 ? 3.803 1.842 0.035 1.00 96.04 10 A 1 ATOM 77 C CD1 . ILE A 1 10 ? 2.096 3.843 1.669 1.00 92.42 10 A 1 ATOM 78 N N . LEU A 1 11 ? 2.200 -1.269 -0.615 1.00 98.08 11 A 1 ATOM 79 C CA . LEU A 1 11 ? 2.895 -2.519 -0.935 1.00 98.05 11 A 1 ATOM 80 C C . LEU A 1 11 ? 2.516 -2.981 -2.339 1.00 98.39 11 A 1 ATOM 81 O O . LEU A 1 11 ? 3.352 -3.491 -3.081 1.00 98.27 11 A 1 ATOM 82 C CB . LEU A 1 11 ? 2.512 -3.586 0.090 1.00 97.92 11 A 1 ATOM 83 C CG . LEU A 1 11 ? 3.727 -4.146 0.827 1.00 95.30 11 A 1 ATOM 84 C CD1 . LEU A 1 11 ? 4.051 -3.281 2.043 1.00 93.67 11 A 1 ATOM 85 C CD2 . LEU A 1 11 ? 3.466 -5.579 1.256 1.00 94.19 11 A 1 ATOM 86 N N . LEU A 1 12 ? 1.265 -2.792 -2.690 1.00 98.17 12 A 1 ATOM 87 C CA . LEU A 1 12 ? 0.786 -3.189 -4.016 1.00 98.15 12 A 1 ATOM 88 C C . LEU A 1 12 ? 1.461 -2.352 -5.094 1.00 98.46 12 A 1 ATOM 89 O O . LEU A 1 12 ? 1.828 -2.861 -6.150 1.00 98.22 12 A 1 ATOM 90 C CB . LEU A 1 12 ? -0.729 -3.003 -4.062 1.00 97.85 12 A 1 ATOM 91 C CG . LEU A 1 12 ? -1.467 -4.311 -3.765 1.00 95.05 12 A 1 ATOM 92 C CD1 . LEU A 1 12 ? -2.799 -4.027 -3.084 1.00 94.02 12 A 1 ATOM 93 C CD2 . LEU A 1 12 ? -1.702 -5.068 -5.067 1.00 94.21 12 A 1 ATOM 94 N N . VAL A 1 13 ? 1.629 -1.083 -4.817 1.00 98.50 13 A 1 ATOM 95 C CA . VAL A 1 13 ? 2.277 -0.185 -5.776 1.00 98.53 13 A 1 ATOM 96 C C . VAL A 1 13 ? 3.745 -0.565 -5.938 1.00 98.70 13 A 1 ATOM 97 O O . VAL A 1 13 ? 4.302 -0.487 -7.036 1.00 98.47 13 A 1 ATOM 98 C CB . VAL A 1 13 ? 2.151 1.268 -5.300 1.00 98.13 13 A 1 ATOM 99 C CG1 . VAL A 1 13 ? 2.908 2.206 -6.228 1.00 96.35 13 A 1 ATOM 100 C CG2 . VAL A 1 13 ? 0.684 1.669 -5.248 1.00 96.35 13 A 1 ATOM 101 N N . LEU A 1 14 ? 4.360 -0.954 -4.846 1.00 98.62 14 A 1 ATOM 102 C CA . LEU A 1 14 ? 5.771 -1.340 -4.880 1.00 98.64 14 A 1 ATOM 103 C C . LEU A 1 14 ? 5.937 -2.731 -5.484 1.00 98.72 14 A 1 ATOM 104 O O . LEU A 1 14 ? 6.913 -2.996 -6.187 1.00 98.40 14 A 1 ATOM 105 C CB . LEU A 1 14 ? 6.323 -1.319 -3.453 1.00 98.48 14 A 1 ATOM 106 C CG . LEU A 1 14 ? 6.420 0.095 -2.875 1.00 97.35 14 A 1 ATOM 107 C CD1 . LEU A 1 14 ? 6.447 0.043 -1.354 1.00 95.48 14 A 1 ATOM 108 C CD2 . LEU A 1 14 ? 7.685 0.780 -3.387 1.00 95.33 14 A 1 ATOM 109 N N . VAL A 1 15 ? 4.998 -3.597 -5.202 1.00 98.33 15 A 1 ATOM 110 C CA . VAL A 1 15 ? 5.040 -4.971 -5.714 1.00 98.18 15 A 1 ATOM 111 C C . VAL A 1 15 ? 4.345 -5.066 -7.073 1.00 98.23 15 A 1 ATOM 112 O O . VAL A 1 15 ? 4.283 -6.133 -7.684 1.00 96.86 15 A 1 ATOM 113 C CB . VAL A 1 15 ? 4.383 -5.927 -4.698 1.00 97.18 15 A 1 ATOM 114 C CG1 . VAL A 1 15 ? 4.448 -7.376 -5.172 1.00 91.44 15 A 1 ATOM 115 C CG2 . VAL A 1 15 ? 5.087 -5.813 -3.350 1.00 92.53 15 A 1 ATOM 116 N N . GLY A 1 16 ? 3.834 -3.976 -7.540 1.00 95.95 16 A 1 ATOM 117 C CA . GLY A 1 16 ? 3.132 -3.981 -8.821 1.00 94.62 16 A 1 ATOM 118 C C . GLY A 1 16 ? 3.994 -3.471 -9.954 1.00 92.44 16 A 1 ATOM 119 O O . GLY A 1 16 ? 5.047 -2.879 -9.691 1.00 87.10 16 A 1 ATOM 120 O OXT . GLY A 1 16 ? 3.611 -3.647 -11.113 1.00 91.44 16 A 1 #