# 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_spkb17957 # _entry.id spkb17957 # 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" "C3 H7 N O2 S" 121.158 CYS y CYSTEINE C([C@@H](C(=O)O)N)S ? "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" "C6 H15 N2 O2" 147.195 LYS y LYSINE C(CC[NH3+])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 LYS 2 1 n TRP 3 1 n LEU 4 1 n LEU 5 1 n LEU 6 1 n LEU 7 1 n GLY 8 1 n LEU 9 1 n VAL 10 1 n ALA 11 1 n LEU 12 1 n SER 13 1 n GLU 14 1 n CYS 15 # _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 @ 2025-07-10 20:06:07)" _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 93.97 _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 91.28 1 1 A LYS 2 2 90.88 1 2 A TRP 3 2 93.30 1 3 A LEU 4 2 96.31 1 4 A LEU 5 2 95.46 1 5 A LEU 6 2 95.70 1 6 A LEU 7 2 96.39 1 7 A GLY 8 2 98.12 1 8 A LEU 9 2 95.95 1 9 A VAL 10 2 97.59 1 10 A ALA 11 2 98.08 1 11 A LEU 12 2 95.64 1 12 A SER 13 2 95.68 1 13 A GLU 14 2 86.42 1 14 A CYS 15 2 88.39 1 15 # _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 LYS . 2 A 2 A 3 1 n TRP . 3 A 3 A 4 1 n LEU . 4 A 4 A 5 1 n LEU . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n GLY . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n VAL . 10 A 10 A 11 1 n ALA . 11 A 11 A 12 1 n LEU . 12 A 12 A 13 1 n SER . 13 A 13 A 14 1 n GLU . 14 A 14 A 15 1 n CYS . 15 A 15 # _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 ? -5.473 11.505 5.488 1.00 96.30 1 A 1 ATOM 2 C CA . MET A 1 1 ? -4.618 10.427 6.021 1.00 96.32 1 A 1 ATOM 3 C C . MET A 1 1 ? -3.889 9.710 4.886 1.00 96.65 1 A 1 ATOM 4 O O . MET A 1 1 ? -4.433 9.549 3.797 1.00 95.23 1 A 1 ATOM 5 C CB . MET A 1 1 ? -5.464 9.419 6.793 1.00 94.02 1 A 1 ATOM 6 C CG . MET A 1 1 ? -6.204 10.056 7.971 1.00 89.48 1 A 1 ATOM 7 S SD . MET A 1 1 ? -5.083 10.677 9.220 1.00 86.61 1 A 1 ATOM 8 C CE . MET A 1 1 ? -6.244 11.388 10.365 1.00 75.63 1 A 1 ATOM 9 N N . LYS A 1 2 ? -2.654 9.273 5.142 1.00 96.96 2 A 1 ATOM 10 C CA . LYS A 1 2 ? -1.848 8.571 4.148 1.00 97.07 2 A 1 ATOM 11 C C . LYS A 1 2 ? -1.482 7.158 4.601 1.00 97.34 2 A 1 ATOM 12 O O . LYS A 1 2 ? -0.602 6.528 4.022 1.00 96.91 2 A 1 ATOM 13 C CB . LYS A 1 2 ? -0.581 9.367 3.853 1.00 96.27 2 A 1 ATOM 14 C CG . LYS A 1 2 ? -0.842 10.613 3.024 1.00 91.04 2 A 1 ATOM 15 C CD . LYS A 1 2 ? 0.461 11.288 2.654 1.00 87.73 2 A 1 ATOM 16 C CE . LYS A 1 2 ? 0.228 12.450 1.715 1.00 81.03 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? 1.509 13.116 1.352 1.00 73.60 2 A 1 ATOM 18 N N . TRP A 1 3 ? -2.175 6.675 5.621 1.00 96.70 3 A 1 ATOM 19 C CA . TRP A 1 3 ? -1.911 5.339 6.145 1.00 97.32 3 A 1 ATOM 20 C C . TRP A 1 3 ? -2.301 4.264 5.133 1.00 97.86 3 A 1 ATOM 21 O O . TRP A 1 3 ? -1.753 3.164 5.139 1.00 97.25 3 A 1 ATOM 22 C CB . TRP A 1 3 ? -2.674 5.137 7.452 1.00 96.86 3 A 1 ATOM 23 C CG . TRP A 1 3 ? -4.139 5.400 7.329 1.00 94.74 3 A 1 ATOM 24 C CD1 . TRP A 1 3 ? -4.744 6.608 7.297 1.00 91.46 3 A 1 ATOM 25 C CD2 . TRP A 1 3 ? -5.186 4.419 7.218 1.00 93.89 3 A 1 ATOM 26 N NE1 . TRP A 1 3 ? -6.104 6.449 7.166 1.00 90.17 3 A 1 ATOM 27 C CE2 . TRP A 1 3 ? -6.399 5.113 7.116 1.00 93.18 3 A 1 ATOM 28 C CE3 . TRP A 1 3 ? -5.198 3.025 7.202 1.00 91.02 3 A 1 ATOM 29 C CZ2 . TRP A 1 3 ? -7.621 4.443 6.997 1.00 90.57 3 A 1 ATOM 30 C CZ3 . TRP A 1 3 ? -6.414 2.360 7.085 1.00 87.76 3 A 1 ATOM 31 C CH2 . TRP A 1 3 ? -7.609 3.071 6.974 1.00 87.46 3 A 1 ATOM 32 N N . LEU A 1 4 ? -3.228 4.589 4.249 1.00 98.14 4 A 1 ATOM 33 C CA . LEU A 1 4 ? -3.669 3.658 3.215 1.00 98.26 4 A 1 ATOM 34 C C . LEU A 1 4 ? -2.550 3.377 2.222 1.00 98.42 4 A 1 ATOM 35 O O . LEU A 1 4 ? -2.472 2.290 1.650 1.00 98.28 4 A 1 ATOM 36 C CB . LEU A 1 4 ? -4.885 4.229 2.487 1.00 98.16 4 A 1 ATOM 37 C CG . LEU A 1 4 ? -6.148 4.308 3.338 1.00 95.56 4 A 1 ATOM 38 C CD1 . LEU A 1 4 ? -7.246 5.041 2.586 1.00 91.82 4 A 1 ATOM 39 C CD2 . LEU A 1 4 ? -6.620 2.914 3.722 1.00 91.80 4 A 1 ATOM 40 N N . LEU A 1 5 ? -1.678 4.350 2.019 1.00 98.02 5 A 1 ATOM 41 C CA . LEU A 1 5 ? -0.553 4.192 1.103 1.00 98.04 5 A 1 ATOM 42 C C . LEU A 1 5 ? 0.407 3.125 1.610 1.00 98.19 5 A 1 ATOM 43 O O . LEU A 1 5 ? 0.940 2.332 0.831 1.00 98.15 5 A 1 ATOM 44 C CB . LEU A 1 5 ? 0.181 5.521 0.943 1.00 97.96 5 A 1 ATOM 45 C CG . LEU A 1 5 ? -0.657 6.613 0.284 1.00 93.08 5 A 1 ATOM 46 C CD1 . LEU A 1 5 ? 0.115 7.923 0.266 1.00 89.62 5 A 1 ATOM 47 C CD2 . LEU A 1 5 ? -1.039 6.212 -1.134 1.00 90.59 5 A 1 ATOM 48 N N . LEU A 1 6 ? 0.611 3.104 2.916 1.00 98.16 6 A 1 ATOM 49 C CA . LEU A 1 6 ? 1.494 2.114 3.528 1.00 98.11 6 A 1 ATOM 50 C C . LEU A 1 6 ? 0.907 0.718 3.378 1.00 98.27 6 A 1 ATOM 51 O O . LEU A 1 6 ? 1.621 -0.235 3.054 1.00 98.22 6 A 1 ATOM 52 C CB . LEU A 1 6 ? 1.706 2.442 5.008 1.00 97.89 6 A 1 ATOM 53 C CG . LEU A 1 6 ? 2.461 3.745 5.252 1.00 93.22 6 A 1 ATOM 54 C CD1 . LEU A 1 6 ? 2.484 4.065 6.743 1.00 90.40 6 A 1 ATOM 55 C CD2 . LEU A 1 6 ? 3.883 3.650 4.719 1.00 91.33 6 A 1 ATOM 56 N N . LEU A 1 7 ? -0.403 0.600 3.599 1.00 98.27 7 A 1 ATOM 57 C CA . LEU A 1 7 ? -1.088 -0.680 3.464 1.00 98.18 7 A 1 ATOM 58 C C . LEU A 1 7 ? -1.050 -1.154 2.019 1.00 98.38 7 A 1 ATOM 59 O O . LEU A 1 7 ? -0.891 -2.347 1.750 1.00 98.28 7 A 1 ATOM 60 C CB . LEU A 1 7 ? -2.536 -0.546 3.938 1.00 97.89 7 A 1 ATOM 61 C CG . LEU A 1 7 ? -2.686 -0.317 5.438 1.00 94.91 7 A 1 ATOM 62 C CD1 . LEU A 1 7 ? -4.146 -0.053 5.779 1.00 92.57 7 A 1 ATOM 63 C CD2 . LEU A 1 7 ? -2.173 -1.516 6.221 1.00 92.60 7 A 1 ATOM 64 N N . GLY A 1 8 ? -1.187 -0.218 1.096 1.00 98.00 8 A 1 ATOM 65 C CA . GLY A 1 8 ? -1.135 -0.547 -0.320 1.00 98.06 8 A 1 ATOM 66 C C . GLY A 1 8 ? 0.213 -1.113 -0.712 1.00 98.31 8 A 1 ATOM 67 O O . GLY A 1 8 ? 0.299 -2.061 -1.495 1.00 98.11 8 A 1 ATOM 68 N N . LEU A 1 9 ? 1.275 -0.530 -0.167 1.00 98.18 9 A 1 ATOM 69 C CA . LEU A 1 9 ? 2.632 -0.995 -0.441 1.00 98.18 9 A 1 ATOM 70 C C . LEU A 1 9 ? 2.840 -2.404 0.095 1.00 98.34 9 A 1 ATOM 71 O O . LEU A 1 9 ? 3.426 -3.254 -0.579 1.00 98.01 9 A 1 ATOM 72 C CB . LEU A 1 9 ? 3.646 -0.043 0.195 1.00 97.89 9 A 1 ATOM 73 C CG . LEU A 1 9 ? 5.100 -0.371 -0.135 1.00 94.10 9 A 1 ATOM 74 C CD1 . LEU A 1 9 ? 5.375 -0.141 -1.612 1.00 91.24 9 A 1 ATOM 75 C CD2 . LEU A 1 9 ? 6.038 0.481 0.710 1.00 91.65 9 A 1 ATOM 76 N N . VAL A 1 10 ? 2.355 -2.653 1.307 1.00 98.42 10 A 1 ATOM 77 C CA . VAL A 1 10 ? 2.476 -3.969 1.929 1.00 98.26 10 A 1 ATOM 78 C C . VAL A 1 10 ? 1.664 -4.995 1.153 1.00 98.26 10 A 1 ATOM 79 O O . VAL A 1 10 ? 2.119 -6.120 0.925 1.00 97.90 10 A 1 ATOM 80 C CB . VAL A 1 10 ? 2.020 -3.929 3.395 1.00 97.87 10 A 1 ATOM 81 C CG1 . VAL A 1 10 ? 2.025 -5.323 4.005 1.00 95.91 10 A 1 ATOM 82 C CG2 . VAL A 1 10 ? 2.923 -3.009 4.195 1.00 96.48 10 A 1 ATOM 83 N N . ALA A 1 11 ? 0.465 -4.611 0.741 1.00 98.27 11 A 1 ATOM 84 C CA . ALA A 1 11 ? -0.409 -5.504 -0.014 1.00 98.23 11 A 1 ATOM 85 C C . ALA A 1 11 ? 0.233 -5.899 -1.336 1.00 98.26 11 A 1 ATOM 86 O O . ALA A 1 11 ? 0.129 -7.047 -1.771 1.00 97.75 11 A 1 ATOM 87 C CB . ALA A 1 11 ? -1.753 -4.833 -0.262 1.00 97.90 11 A 1 ATOM 88 N N . LEU A 1 12 ? 0.905 -4.946 -1.975 1.00 98.29 12 A 1 ATOM 89 C CA . LEU A 1 12 ? 1.589 -5.212 -3.234 1.00 98.11 12 A 1 ATOM 90 C C . LEU A 1 12 ? 2.762 -6.158 -3.021 1.00 98.01 12 A 1 ATOM 91 O O . LEU A 1 12 ? 3.041 -7.014 -3.864 1.00 97.22 12 A 1 ATOM 92 C CB . LEU A 1 12 ? 2.084 -3.902 -3.844 1.00 97.78 12 A 1 ATOM 93 C CG . LEU A 1 12 ? 2.686 -4.052 -5.236 1.00 95.11 12 A 1 ATOM 94 C CD1 . LEU A 1 12 ? 1.617 -4.463 -6.236 1.00 90.45 12 A 1 ATOM 95 C CD2 . LEU A 1 12 ? 3.335 -2.746 -5.669 1.00 90.17 12 A 1 ATOM 96 N N . SER A 1 13 ? 3.451 -6.000 -1.908 1.00 97.88 13 A 1 ATOM 97 C CA . SER A 1 13 ? 4.590 -6.849 -1.568 1.00 97.70 13 A 1 ATOM 98 C C . SER A 1 13 ? 4.146 -8.281 -1.304 1.00 97.67 13 A 1 ATOM 99 O O . SER A 1 13 ? 4.815 -9.235 -1.706 1.00 96.45 13 A 1 ATOM 100 C CB . SER A 1 13 ? 5.311 -6.301 -0.340 1.00 96.73 13 A 1 ATOM 101 O OG . SER A 1 13 ? 6.462 -7.071 -0.060 1.00 87.67 13 A 1 ATOM 102 N N . GLU A 1 14 ? 3.008 -8.434 -0.623 1.00 95.32 14 A 1 ATOM 103 C CA . GLU A 1 14 ? 2.469 -9.759 -0.311 1.00 93.94 14 A 1 ATOM 104 C C . GLU A 1 14 ? 1.830 -10.392 -1.534 1.00 92.73 14 A 1 ATOM 105 O O . GLU A 1 14 ? 2.030 -11.581 -1.802 1.00 87.72 14 A 1 ATOM 106 C CB . GLU A 1 14 ? 1.441 -9.654 0.818 1.00 92.10 14 A 1 ATOM 107 C CG . GLU A 1 14 ? 2.088 -9.282 2.144 1.00 84.84 14 A 1 ATOM 108 C CD . GLU A 1 14 ? 1.064 -9.185 3.254 1.00 80.87 14 A 1 ATOM 109 O OE1 . GLU A 1 14 ? -0.114 -8.927 2.954 1.00 74.48 14 A 1 ATOM 110 O OE2 . GLU A 1 14 ? 1.437 -9.366 4.428 1.00 75.79 14 A 1 ATOM 111 N N . CYS A 1 15 ? 1.050 -9.588 -2.266 1.00 94.42 15 A 1 ATOM 112 C CA . CYS A 1 15 ? 0.368 -10.032 -3.483 1.00 93.47 15 A 1 ATOM 113 C C . CYS A 1 15 ? -0.588 -11.194 -3.195 1.00 92.57 15 A 1 ATOM 114 O O . CYS A 1 15 ? -1.711 -11.178 -3.717 1.00 88.61 15 A 1 ATOM 115 C CB . CYS A 1 15 ? 1.385 -10.443 -4.559 1.00 89.80 15 A 1 ATOM 116 S SG . CYS A 1 15 ? 0.635 -10.686 -6.168 1.00 82.18 15 A 1 ATOM 117 O OXT . CYS A 1 15 ? -0.209 -12.087 -2.433 1.00 77.70 15 A 1 #