# 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_spkb09502 # _entry.id spkb09502 # 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 H9 N O4" 147.129 GLU y "GLUTAMIC ACID" C(CC(=O)O)[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" "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" "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 GLU 2 1 n PRO 3 1 n GLY 4 1 n LEU 5 1 n TRP 6 1 n LEU 7 1 n LEU 8 1 n PHE 9 1 n GLY 10 1 n LEU 11 1 n THR 12 1 n VAL 13 1 n THR 14 1 n SER 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 @ 2025-07-07 16:31:14)" _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 89.20 _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 76.93 1 1 A GLU 2 2 78.01 1 2 A PRO 3 2 89.96 1 3 A GLY 4 2 92.17 1 4 A LEU 5 2 89.68 1 5 A TRP 6 2 91.37 1 6 A LEU 7 2 92.57 1 7 A LEU 8 2 91.79 1 8 A PHE 9 2 89.98 1 9 A GLY 10 2 94.10 1 10 A LEU 11 2 92.63 1 11 A THR 12 2 92.92 1 12 A VAL 13 2 93.80 1 13 A THR 14 2 90.96 1 14 A SER 15 2 90.76 1 15 A ALA 16 2 83.16 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 GLU . 2 A 2 A 3 1 n PRO . 3 A 3 A 4 1 n GLY . 4 A 4 A 5 1 n LEU . 5 A 5 A 6 1 n TRP . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n PHE . 9 A 9 A 10 1 n GLY . 10 A 10 A 11 1 n LEU . 11 A 11 A 12 1 n THR . 12 A 12 A 13 1 n VAL . 13 A 13 A 14 1 n THR . 14 A 14 A 15 1 n SER . 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 ? -11.567 0.064 4.872 1.00 82.84 1 A 1 ATOM 2 C CA . MET A 1 1 ? -11.523 1.074 5.934 1.00 84.33 1 A 1 ATOM 3 C C . MET A 1 1 ? -10.422 2.094 5.669 1.00 85.85 1 A 1 ATOM 4 O O . MET A 1 1 ? -10.581 3.276 5.960 1.00 81.91 1 A 1 ATOM 5 C CB . MET A 1 1 ? -11.286 0.401 7.284 1.00 78.66 1 A 1 ATOM 6 C CG . MET A 1 1 ? -12.406 -0.565 7.636 1.00 73.40 1 A 1 ATOM 7 S SD . MET A 1 1 ? -12.728 -0.592 9.389 1.00 68.10 1 A 1 ATOM 8 C CE . MET A 1 1 ? -14.184 -1.612 9.410 1.00 60.34 1 A 1 ATOM 9 N N . GLU A 1 2 ? -9.304 1.650 5.124 1.00 82.64 2 A 1 ATOM 10 C CA . GLU A 1 2 ? -8.195 2.560 4.818 1.00 86.81 2 A 1 ATOM 11 C C . GLU A 1 2 ? -7.806 2.465 3.342 1.00 89.43 2 A 1 ATOM 12 O O . GLU A 1 2 ? -6.750 1.927 3.004 1.00 87.72 2 A 1 ATOM 13 C CB . GLU A 1 2 ? -6.998 2.211 5.691 1.00 80.97 2 A 1 ATOM 14 C CG . GLU A 1 2 ? -7.326 2.304 7.165 1.00 73.41 2 A 1 ATOM 15 C CD . GLU A 1 2 ? -6.065 2.513 7.977 1.00 70.89 2 A 1 ATOM 16 O OE1 . GLU A 1 2 ? -5.519 3.619 7.928 1.00 63.82 2 A 1 ATOM 17 O OE2 . GLU A 1 2 ? -5.626 1.560 8.634 1.00 66.39 2 A 1 ATOM 18 N N . PRO A 1 3 ? -8.642 2.991 2.450 1.00 90.50 3 A 1 ATOM 19 C CA . PRO A 1 3 ? -8.355 2.942 1.007 1.00 92.47 3 A 1 ATOM 20 C C . PRO A 1 3 ? -7.094 3.715 0.641 1.00 94.10 3 A 1 ATOM 21 O O . PRO A 1 3 ? -6.330 3.295 -0.231 1.00 90.34 3 A 1 ATOM 22 C CB . PRO A 1 3 ? -9.603 3.578 0.375 1.00 88.60 3 A 1 ATOM 23 C CG . PRO A 1 3 ? -10.206 4.411 1.460 1.00 85.32 3 A 1 ATOM 24 C CD . PRO A 1 3 ? -9.883 3.709 2.756 1.00 88.41 3 A 1 ATOM 25 N N . GLY A 1 4 ? -6.878 4.845 1.296 1.00 90.79 4 A 1 ATOM 26 C CA . GLY A 1 4 ? -5.682 5.648 1.029 1.00 92.22 4 A 1 ATOM 27 C C . GLY A 1 4 ? -4.414 4.886 1.365 1.00 93.56 4 A 1 ATOM 28 O O . GLY A 1 4 ? -3.437 4.917 0.618 1.00 92.10 4 A 1 ATOM 29 N N . LEU A 1 5 ? -4.426 4.197 2.484 1.00 91.96 5 A 1 ATOM 30 C CA . LEU A 1 5 ? -3.272 3.404 2.920 1.00 93.32 5 A 1 ATOM 31 C C . LEU A 1 5 ? -3.024 2.260 1.940 1.00 94.64 5 A 1 ATOM 32 O O . LEU A 1 5 ? -1.890 1.916 1.631 1.00 93.72 5 A 1 ATOM 33 C CB . LEU A 1 5 ? -3.535 2.849 4.328 1.00 91.93 5 A 1 ATOM 34 C CG . LEU A 1 5 ? -2.350 3.036 5.276 1.00 86.03 5 A 1 ATOM 35 C CD1 . LEU A 1 5 ? -1.098 2.371 4.716 1.00 83.41 5 A 1 ATOM 36 C CD2 . LEU A 1 5 ? -2.104 4.520 5.506 1.00 82.42 5 A 1 ATOM 37 N N . TRP A 1 6 ? -4.113 1.673 1.442 1.00 93.27 6 A 1 ATOM 38 C CA . TRP A 1 6 ? -4.013 0.568 0.489 1.00 94.20 6 A 1 ATOM 39 C C . TRP A 1 6 ? -3.283 1.021 -0.771 1.00 94.85 6 A 1 ATOM 40 O O . TRP A 1 6 ? -2.411 0.328 -1.287 1.00 94.08 6 A 1 ATOM 41 C CB . TRP A 1 6 ? -5.420 0.080 0.142 1.00 93.56 6 A 1 ATOM 42 C CG . TRP A 1 6 ? -5.487 -1.409 0.127 1.00 92.78 6 A 1 ATOM 43 C CD1 . TRP A 1 6 ? -5.932 -2.206 1.134 1.00 90.02 6 A 1 ATOM 44 C CD2 . TRP A 1 6 ? -5.084 -2.285 -0.939 1.00 91.52 6 A 1 ATOM 45 N NE1 . TRP A 1 6 ? -5.831 -3.525 0.753 1.00 89.21 6 A 1 ATOM 46 C CE2 . TRP A 1 6 ? -5.314 -3.611 -0.509 1.00 90.68 6 A 1 ATOM 47 C CE3 . TRP A 1 6 ? -4.552 -2.077 -2.219 1.00 89.79 6 A 1 ATOM 48 C CZ2 . TRP A 1 6 ? -5.025 -4.710 -1.324 1.00 89.77 6 A 1 ATOM 49 C CZ3 . TRP A 1 6 ? -4.265 -3.175 -3.029 1.00 87.81 6 A 1 ATOM 50 C CH2 . TRP A 1 6 ? -4.499 -4.473 -2.580 1.00 87.61 6 A 1 ATOM 51 N N . LEU A 1 7 ? -3.622 2.193 -1.249 1.00 94.76 7 A 1 ATOM 52 C CA . LEU A 1 7 ? -2.969 2.743 -2.443 1.00 95.03 7 A 1 ATOM 53 C C . LEU A 1 7 ? -1.480 2.971 -2.184 1.00 95.87 7 A 1 ATOM 54 O O . LEU A 1 7 ? -0.638 2.646 -3.020 1.00 95.15 7 A 1 ATOM 55 C CB . LEU A 1 7 ? -3.646 4.062 -2.816 1.00 94.43 7 A 1 ATOM 56 C CG . LEU A 1 7 ? -4.969 3.849 -3.556 1.00 90.77 7 A 1 ATOM 57 C CD1 . LEU A 1 7 ? -5.800 5.126 -3.527 1.00 87.59 7 A 1 ATOM 58 C CD2 . LEU A 1 7 ? -4.696 3.451 -5.006 1.00 86.97 7 A 1 ATOM 59 N N . LEU A 1 8 ? -1.169 3.523 -1.037 1.00 93.81 8 A 1 ATOM 60 C CA . LEU A 1 8 ? 0.229 3.771 -0.664 1.00 94.33 8 A 1 ATOM 61 C C . LEU A 1 8 ? 1.009 2.463 -0.614 1.00 95.10 8 A 1 ATOM 62 O O . LEU A 1 8 ? 2.131 2.372 -1.113 1.00 94.59 8 A 1 ATOM 63 C CB . LEU A 1 8 ? 0.263 4.465 0.700 1.00 93.53 8 A 1 ATOM 64 C CG . LEU A 1 8 ? 0.531 5.966 0.588 1.00 89.88 8 A 1 ATOM 65 C CD1 . LEU A 1 8 ? 0.156 6.666 1.890 1.00 87.06 8 A 1 ATOM 66 C CD2 . LEU A 1 8 ? 2.004 6.207 0.276 1.00 86.05 8 A 1 ATOM 67 N N . PHE A 1 9 ? 0.407 1.462 -0.023 1.00 92.85 9 A 1 ATOM 68 C CA . PHE A 1 9 ? 1.045 0.152 0.085 1.00 93.19 9 A 1 ATOM 69 C C . PHE A 1 9 ? 1.315 -0.423 -1.300 1.00 94.44 9 A 1 ATOM 70 O O . PHE A 1 9 ? 2.389 -0.968 -1.558 1.00 93.65 9 A 1 ATOM 71 C CB . PHE A 1 9 ? 0.130 -0.781 0.875 1.00 92.53 9 A 1 ATOM 72 C CG . PHE A 1 9 ? 0.833 -2.050 1.268 1.00 90.18 9 A 1 ATOM 73 C CD1 . PHE A 1 9 ? 1.828 -2.031 2.231 1.00 87.38 9 A 1 ATOM 74 C CD2 . PHE A 1 9 ? 0.495 -3.253 0.662 1.00 87.25 9 A 1 ATOM 75 C CE1 . PHE A 1 9 ? 2.486 -3.196 2.591 1.00 86.73 9 A 1 ATOM 76 C CE2 . PHE A 1 9 ? 1.153 -4.426 1.019 1.00 85.68 9 A 1 ATOM 77 C CZ . PHE A 1 9 ? 2.148 -4.398 1.983 1.00 85.94 9 A 1 ATOM 78 N N . GLY A 1 10 ? 0.331 -0.293 -2.189 1.00 93.90 10 A 1 ATOM 79 C CA . GLY A 1 10 ? 0.494 -0.799 -3.553 1.00 93.88 10 A 1 ATOM 80 C C . GLY A 1 10 ? 1.685 -0.159 -4.244 1.00 94.87 10 A 1 ATOM 81 O O . GLY A 1 10 ? 2.470 -0.833 -4.913 1.00 93.74 10 A 1 ATOM 82 N N . LEU A 1 11 ? 1.832 1.143 -4.080 1.00 94.96 11 A 1 ATOM 83 C CA . LEU A 1 11 ? 2.955 1.868 -4.679 1.00 95.08 11 A 1 ATOM 84 C C . LEU A 1 11 ? 4.281 1.350 -4.129 1.00 95.89 11 A 1 ATOM 85 O O . LEU A 1 11 ? 5.236 1.139 -4.876 1.00 94.74 11 A 1 ATOM 86 C CB . LEU A 1 11 ? 2.817 3.362 -4.368 1.00 94.12 11 A 1 ATOM 87 C CG . LEU A 1 11 ? 3.811 4.200 -5.166 1.00 90.88 11 A 1 ATOM 88 C CD1 . LEU A 1 11 ? 3.127 4.787 -6.400 1.00 88.19 11 A 1 ATOM 89 C CD2 . LEU A 1 11 ? 4.370 5.323 -4.303 1.00 87.18 11 A 1 ATOM 90 N N . THR A 1 12 ? 4.330 1.149 -2.831 1.00 95.01 12 A 1 ATOM 91 C CA . THR A 1 12 ? 5.549 0.649 -2.185 1.00 95.16 12 A 1 ATOM 92 C C . THR A 1 12 ? 5.934 -0.716 -2.740 1.00 95.52 12 A 1 ATOM 93 O O . THR A 1 12 ? 7.108 -0.974 -3.010 1.00 94.22 12 A 1 ATOM 94 C CB . THR A 1 12 ? 5.318 0.555 -0.678 1.00 93.42 12 A 1 ATOM 95 O OG1 . THR A 1 12 ? 5.187 1.872 -0.159 1.00 88.76 12 A 1 ATOM 96 C CG2 . THR A 1 12 ? 6.496 -0.114 0.006 1.00 88.37 12 A 1 ATOM 97 N N . VAL A 1 13 ? 4.953 -1.575 -2.927 1.00 95.69 13 A 1 ATOM 98 C CA . VAL A 1 13 ? 5.207 -2.916 -3.458 1.00 95.75 13 A 1 ATOM 99 C C . VAL A 1 13 ? 5.814 -2.821 -4.853 1.00 95.83 13 A 1 ATOM 100 O O . VAL A 1 13 ? 6.758 -3.542 -5.184 1.00 94.40 13 A 1 ATOM 101 C CB . VAL A 1 13 ? 3.902 -3.720 -3.500 1.00 94.41 13 A 1 ATOM 102 C CG1 . VAL A 1 13 ? 4.127 -5.048 -4.201 1.00 89.92 13 A 1 ATOM 103 C CG2 . VAL A 1 13 ? 3.397 -3.962 -2.087 1.00 90.60 13 A 1 ATOM 104 N N . THR A 1 14 ? 5.276 -1.938 -5.673 1.00 94.42 14 A 1 ATOM 105 C CA . THR A 1 14 ? 5.786 -1.757 -7.038 1.00 93.85 14 A 1 ATOM 106 C C . THR A 1 14 ? 7.246 -1.310 -7.015 1.00 93.83 14 A 1 ATOM 107 O O . THR A 1 14 ? 8.056 -1.764 -7.824 1.00 91.89 14 A 1 ATOM 108 C CB . THR A 1 14 ? 4.938 -0.710 -7.766 1.00 91.23 14 A 1 ATOM 109 O OG1 . THR A 1 14 ? 3.620 -1.221 -7.926 1.00 86.02 14 A 1 ATOM 110 C CG2 . THR A 1 14 ? 5.505 -0.418 -9.146 1.00 85.49 14 A 1 ATOM 111 N N . SER A 1 15 ? 7.583 -0.421 -6.101 1.00 94.14 15 A 1 ATOM 112 C CA . SER A 1 15 ? 8.959 0.068 -5.968 1.00 93.68 15 A 1 ATOM 113 C C . SER A 1 15 ? 9.903 -1.050 -5.543 1.00 93.70 15 A 1 ATOM 114 O O . SER A 1 15 ? 11.058 -1.090 -5.961 1.00 90.16 15 A 1 ATOM 115 C CB . SER A 1 15 ? 9.008 1.193 -4.940 1.00 90.79 15 A 1 ATOM 116 O OG . SER A 1 15 ? 8.432 2.364 -5.476 1.00 82.07 15 A 1 ATOM 117 N N . ALA A 1 16 ? 9.403 -1.946 -4.711 1.00 90.92 16 A 1 ATOM 118 C CA . ALA A 1 16 ? 10.215 -3.057 -4.221 1.00 88.51 16 A 1 ATOM 119 C C . ALA A 1 16 ? 10.389 -4.136 -5.292 1.00 85.17 16 A 1 ATOM 120 O O . ALA A 1 16 ? 9.833 -4.017 -6.392 1.00 79.88 16 A 1 ATOM 121 C CB . ALA A 1 16 ? 9.566 -3.635 -2.964 1.00 81.37 16 A 1 ATOM 122 O OXT . ALA A 1 16 ? 11.088 -5.121 -5.044 1.00 73.10 16 A 1 #