# 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_spkb33439 # _entry.id spkb33439 # 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" "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 TRP 2 1 n LEU 3 1 n LEU 4 1 n ALA 5 1 n ILE 6 1 n SER 7 1 n LEU 8 1 n VAL 9 1 n GLY 10 1 n LEU 11 1 n LEU 12 1 n VAL 13 1 n VAL 14 1 n VAL 15 1 n VAL 16 1 n CYS 17 # _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 @ 2025-07-11 14:44:16)" _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 96.31 _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 91.59 1 1 A TRP 2 2 93.72 1 2 A LEU 3 2 96.86 1 3 A LEU 4 2 96.76 1 4 A ALA 5 2 98.47 1 5 A ILE 6 2 97.51 1 6 A SER 7 2 97.42 1 7 A LEU 8 2 96.78 1 8 A VAL 9 2 97.82 1 9 A GLY 10 2 98.47 1 10 A LEU 11 2 96.89 1 11 A LEU 12 2 96.66 1 12 A VAL 13 2 98.03 1 13 A VAL 14 2 98.34 1 14 A VAL 15 2 98.03 1 15 A VAL 16 2 96.89 1 16 A CYS 17 2 91.44 1 17 # _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 TRP . 2 A 2 A 3 1 n LEU . 3 A 3 A 4 1 n LEU . 4 A 4 A 5 1 n ALA . 5 A 5 A 6 1 n ILE . 6 A 6 A 7 1 n SER . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n VAL . 9 A 9 A 10 1 n GLY . 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 VAL . 14 A 14 A 15 1 n VAL . 15 A 15 A 16 1 n VAL . 16 A 16 A 17 1 n CYS . 17 A 17 # _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 ? -10.287 -0.682 10.547 1.00 96.32 1 A 1 ATOM 2 C CA . MET A 1 1 ? -9.554 -0.256 9.353 1.00 96.26 1 A 1 ATOM 3 C C . MET A 1 1 ? -8.068 -0.609 9.460 1.00 96.71 1 A 1 ATOM 4 O O . MET A 1 1 ? -7.238 0.254 9.731 1.00 95.66 1 A 1 ATOM 5 C CB . MET A 1 1 ? -9.699 1.248 9.166 1.00 93.64 1 A 1 ATOM 6 C CG . MET A 1 1 ? -9.371 2.043 10.412 1.00 89.97 1 A 1 ATOM 7 S SD . MET A 1 1 ? -9.602 3.816 10.172 1.00 87.13 1 A 1 ATOM 8 C CE . MET A 1 1 ? -11.378 3.897 10.115 1.00 77.06 1 A 1 ATOM 9 N N . TRP A 1 2 ? -7.745 -1.878 9.267 1.00 96.70 2 A 1 ATOM 10 C CA . TRP A 1 2 ? -6.368 -2.354 9.376 1.00 96.96 2 A 1 ATOM 11 C C . TRP A 1 2 ? -5.862 -2.843 8.024 1.00 97.60 2 A 1 ATOM 12 O O . TRP A 1 2 ? -4.789 -2.453 7.577 1.00 96.95 2 A 1 ATOM 13 C CB . TRP A 1 2 ? -6.291 -3.490 10.403 1.00 96.41 2 A 1 ATOM 14 C CG . TRP A 1 2 ? -7.419 -3.462 11.383 1.00 94.43 2 A 1 ATOM 15 C CD1 . TRP A 1 2 ? -7.434 -2.800 12.566 1.00 93.08 2 A 1 ATOM 16 C CD2 . TRP A 1 2 ? -8.694 -4.110 11.270 1.00 94.18 2 A 1 ATOM 17 N NE1 . TRP A 1 2 ? -8.636 -3.003 13.202 1.00 90.33 2 A 1 ATOM 18 C CE2 . TRP A 1 2 ? -9.436 -3.805 12.426 1.00 92.27 2 A 1 ATOM 19 C CE3 . TRP A 1 2 ? -9.284 -4.920 10.292 1.00 91.42 2 A 1 ATOM 20 C CZ2 . TRP A 1 2 ? -10.731 -4.289 12.628 1.00 92.92 2 A 1 ATOM 21 C CZ3 . TRP A 1 2 ? -10.562 -5.395 10.491 1.00 89.40 2 A 1 ATOM 22 C CH2 . TRP A 1 2 ? -11.285 -5.085 11.646 1.00 89.47 2 A 1 ATOM 23 N N . LEU A 1 3 ? -6.647 -3.684 7.371 1.00 97.93 3 A 1 ATOM 24 C CA . LEU A 1 3 ? -6.287 -4.226 6.066 1.00 98.11 3 A 1 ATOM 25 C C . LEU A 1 3 ? -6.119 -3.104 5.050 1.00 98.31 3 A 1 ATOM 26 O O . LEU A 1 3 ? -5.248 -3.159 4.181 1.00 98.00 3 A 1 ATOM 27 C CB . LEU A 1 3 ? -7.374 -5.197 5.592 1.00 97.99 3 A 1 ATOM 28 C CG . LEU A 1 3 ? -7.680 -6.321 6.577 1.00 96.51 3 A 1 ATOM 29 C CD1 . LEU A 1 3 ? -8.827 -7.175 6.059 1.00 94.52 3 A 1 ATOM 30 C CD2 . LEU A 1 3 ? -6.445 -7.176 6.812 1.00 93.49 3 A 1 ATOM 31 N N . LEU A 1 4 ? -6.957 -2.080 5.174 1.00 98.41 4 A 1 ATOM 32 C CA . LEU A 1 4 ? -6.911 -0.933 4.275 1.00 98.32 4 A 1 ATOM 33 C C . LEU A 1 4 ? -5.584 -0.201 4.422 1.00 98.41 4 A 1 ATOM 34 O O . LEU A 1 4 ? -4.971 0.207 3.436 1.00 98.17 4 A 1 ATOM 35 C CB . LEU A 1 4 ? -8.065 0.022 4.590 1.00 98.12 4 A 1 ATOM 36 C CG . LEU A 1 4 ? -9.419 -0.667 4.761 1.00 96.04 4 A 1 ATOM 37 C CD1 . LEU A 1 4 ? -10.502 0.362 5.035 1.00 93.59 4 A 1 ATOM 38 C CD2 . LEU A 1 4 ? -9.757 -1.490 3.525 1.00 93.00 4 A 1 ATOM 39 N N . ALA A 1 5 ? -5.139 -0.032 5.671 1.00 98.57 5 A 1 ATOM 40 C CA . ALA A 1 5 ? -3.883 0.646 5.965 1.00 98.55 5 A 1 ATOM 41 C C . ALA A 1 5 ? -2.704 -0.125 5.380 1.00 98.61 5 A 1 ATOM 42 O O . ALA A 1 5 ? -1.785 0.461 4.810 1.00 98.38 5 A 1 ATOM 43 C CB . ALA A 1 5 ? -3.710 0.801 7.471 1.00 98.24 5 A 1 ATOM 44 N N . ILE A 1 6 ? -2.737 -1.444 5.526 1.00 98.66 6 A 1 ATOM 45 C CA . ILE A 1 6 ? -1.678 -2.307 5.014 1.00 98.60 6 A 1 ATOM 46 C C . ILE A 1 6 ? -1.563 -2.175 3.500 1.00 98.58 6 A 1 ATOM 47 O O . ILE A 1 6 ? -0.462 -2.108 2.947 1.00 98.44 6 A 1 ATOM 48 C CB . ILE A 1 6 ? -1.946 -3.775 5.385 1.00 98.47 6 A 1 ATOM 49 C CG1 . ILE A 1 6 ? -1.945 -3.950 6.902 1.00 97.12 6 A 1 ATOM 50 C CG2 . ILE A 1 6 ? -0.885 -4.673 4.758 1.00 96.52 6 A 1 ATOM 51 C CD1 . ILE A 1 6 ? -2.397 -5.330 7.341 1.00 93.70 6 A 1 ATOM 52 N N . SER A 1 7 ? -2.708 -2.136 2.838 1.00 98.58 7 A 1 ATOM 53 C CA . SER A 1 7 ? -2.740 -2.011 1.385 1.00 98.50 7 A 1 ATOM 54 C C . SER A 1 7 ? -2.129 -0.689 0.939 1.00 98.56 7 A 1 ATOM 55 O O . SER A 1 7 ? -1.352 -0.638 -0.013 1.00 98.16 7 A 1 ATOM 56 C CB . SER A 1 7 ? -4.178 -2.106 0.884 1.00 98.20 7 A 1 ATOM 57 O OG . SER A 1 7 ? -4.732 -3.369 1.196 1.00 92.50 7 A 1 ATOM 58 N N . LEU A 1 8 ? -2.482 0.381 1.648 1.00 98.50 8 A 1 ATOM 59 C CA . LEU A 1 8 ? -1.972 1.709 1.329 1.00 98.48 8 A 1 ATOM 60 C C . LEU A 1 8 ? -0.462 1.765 1.499 1.00 98.56 8 A 1 ATOM 61 O O . LEU A 1 8 ? 0.246 2.337 0.670 1.00 98.41 8 A 1 ATOM 62 C CB . LEU A 1 8 ? -2.632 2.748 2.235 1.00 98.35 8 A 1 ATOM 63 C CG . LEU A 1 8 ? -4.131 2.920 1.991 1.00 95.22 8 A 1 ATOM 64 C CD1 . LEU A 1 8 ? -4.736 3.846 3.030 1.00 92.87 8 A 1 ATOM 65 C CD2 . LEU A 1 8 ? -4.380 3.455 0.590 1.00 93.83 8 A 1 ATOM 66 N N . VAL A 1 9 ? 0.031 1.170 2.587 1.00 98.45 9 A 1 ATOM 67 C CA . VAL A 1 9 ? 1.463 1.138 2.866 1.00 98.40 9 A 1 ATOM 68 C C . VAL A 1 9 ? 2.197 0.384 1.766 1.00 98.48 9 A 1 ATOM 69 O O . VAL A 1 9 ? 3.253 0.814 1.295 1.00 98.22 9 A 1 ATOM 70 C CB . VAL A 1 9 ? 1.745 0.476 4.222 1.00 98.05 9 A 1 ATOM 71 C CG1 . VAL A 1 9 ? 3.243 0.319 4.436 1.00 96.56 9 A 1 ATOM 72 C CG2 . VAL A 1 9 ? 1.133 1.294 5.340 1.00 96.56 9 A 1 ATOM 73 N N . GLY A 1 10 ? 1.626 -0.747 1.369 1.00 98.46 10 A 1 ATOM 74 C CA . GLY A 1 10 ? 2.229 -1.547 0.309 1.00 98.45 10 A 1 ATOM 75 C C . GLY A 1 10 ? 2.306 -0.782 -0.994 1.00 98.60 10 A 1 ATOM 76 O O . GLY A 1 10 ? 3.298 -0.864 -1.721 1.00 98.36 10 A 1 ATOM 77 N N . LEU A 1 11 ? 1.256 -0.028 -1.285 1.00 98.49 11 A 1 ATOM 78 C CA . LEU A 1 11 ? 1.193 0.779 -2.499 1.00 98.45 11 A 1 ATOM 79 C C . LEU A 1 11 ? 2.318 1.804 -2.500 1.00 98.60 11 A 1 ATOM 80 O O . LEU A 1 11 ? 2.982 2.028 -3.514 1.00 98.26 11 A 1 ATOM 81 C CB . LEU A 1 11 ? -0.163 1.493 -2.583 1.00 98.24 11 A 1 ATOM 82 C CG . LEU A 1 11 ? -0.655 1.796 -4.002 1.00 95.61 11 A 1 ATOM 83 C CD1 . LEU A 1 11 ? 0.333 2.678 -4.747 1.00 93.63 11 A 1 ATOM 84 C CD2 . LEU A 1 11 ? -0.886 0.492 -4.753 1.00 93.87 11 A 1 ATOM 85 N N . LEU A 1 12 ? 2.520 2.432 -1.340 1.00 98.38 12 A 1 ATOM 86 C CA . LEU A 1 12 ? 3.569 3.438 -1.192 1.00 98.40 12 A 1 ATOM 87 C C . LEU A 1 12 ? 4.937 2.831 -1.471 1.00 98.58 12 A 1 ATOM 88 O O . LEU A 1 12 ? 5.775 3.438 -2.143 1.00 98.38 12 A 1 ATOM 89 C CB . LEU A 1 12 ? 3.548 4.008 0.228 1.00 98.24 12 A 1 ATOM 90 C CG . LEU A 1 12 ? 4.587 5.096 0.480 1.00 95.40 12 A 1 ATOM 91 C CD1 . LEU A 1 12 ? 4.261 6.337 -0.337 1.00 92.43 12 A 1 ATOM 92 C CD2 . LEU A 1 12 ? 4.639 5.443 1.960 1.00 93.51 12 A 1 ATOM 93 N N . VAL A 1 13 ? 5.166 1.626 -0.941 1.00 98.50 13 A 1 ATOM 94 C CA . VAL A 1 13 ? 6.437 0.931 -1.129 1.00 98.53 13 A 1 ATOM 95 C C . VAL A 1 13 ? 6.681 0.648 -2.604 1.00 98.63 13 A 1 ATOM 96 O O . VAL A 1 13 ? 7.800 0.799 -3.101 1.00 98.38 13 A 1 ATOM 97 C CB . VAL A 1 13 ? 6.458 -0.389 -0.346 1.00 98.24 13 A 1 ATOM 98 C CG1 . VAL A 1 13 ? 7.743 -1.158 -0.625 1.00 97.03 13 A 1 ATOM 99 C CG2 . VAL A 1 13 ? 6.319 -0.118 1.140 1.00 96.92 13 A 1 ATOM 100 N N . VAL A 1 14 ? 5.636 0.237 -3.303 1.00 98.74 14 A 1 ATOM 101 C CA . VAL A 1 14 ? 5.736 -0.064 -4.729 1.00 98.75 14 A 1 ATOM 102 C C . VAL A 1 14 ? 6.140 1.174 -5.514 1.00 98.80 14 A 1 ATOM 103 O O . VAL A 1 14 ? 6.950 1.101 -6.442 1.00 98.61 14 A 1 ATOM 104 C CB . VAL A 1 14 ? 4.401 -0.596 -5.276 1.00 98.57 14 A 1 ATOM 105 C CG1 . VAL A 1 14 ? 4.481 -0.793 -6.786 1.00 97.42 14 A 1 ATOM 106 C CG2 . VAL A 1 14 ? 4.040 -1.902 -4.591 1.00 97.51 14 A 1 ATOM 107 N N . VAL A 1 15 ? 5.559 2.315 -5.149 1.00 98.67 15 A 1 ATOM 108 C CA . VAL A 1 15 ? 5.856 3.575 -5.825 1.00 98.65 15 A 1 ATOM 109 C C . VAL A 1 15 ? 7.306 3.983 -5.601 1.00 98.68 15 A 1 ATOM 110 O O . VAL A 1 15 ? 7.983 4.455 -6.520 1.00 98.34 15 A 1 ATOM 111 C CB . VAL A 1 15 ? 4.934 4.698 -5.331 1.00 98.41 15 A 1 ATOM 112 C CG1 . VAL A 1 15 ? 5.307 6.022 -5.986 1.00 96.67 15 A 1 ATOM 113 C CG2 . VAL A 1 15 ? 3.487 4.352 -5.630 1.00 96.79 15 A 1 ATOM 114 N N . VAL A 1 16 ? 7.776 3.835 -4.360 1.00 98.24 16 A 1 ATOM 115 C CA . VAL A 1 16 ? 9.146 4.191 -4.006 1.00 98.16 16 A 1 ATOM 116 C C . VAL A 1 16 ? 10.152 3.227 -4.623 1.00 98.17 16 A 1 ATOM 117 O O . VAL A 1 16 ? 11.191 3.640 -5.155 1.00 97.36 16 A 1 ATOM 118 C CB . VAL A 1 16 ? 9.334 4.204 -2.481 1.00 97.60 16 A 1 ATOM 119 C CG1 . VAL A 1 16 ? 10.785 4.506 -2.123 1.00 94.29 16 A 1 ATOM 120 C CG2 . VAL A 1 16 ? 8.410 5.225 -1.843 1.00 94.44 16 A 1 ATOM 121 N N . CYS A 1 17 ? 9.851 1.931 -4.545 1.00 96.77 17 A 1 ATOM 122 C CA . CYS A 1 17 ? 10.737 0.892 -5.061 1.00 95.46 17 A 1 ATOM 123 C C . CYS A 1 17 ? 10.424 0.564 -6.523 1.00 94.26 17 A 1 ATOM 124 O O . CYS A 1 17 ? 9.553 1.214 -7.127 1.00 91.47 17 A 1 ATOM 125 C CB . CYS A 1 17 ? 10.618 -0.366 -4.191 1.00 92.07 17 A 1 ATOM 126 S SG . CYS A 1 17 ? 11.151 -0.127 -2.487 1.00 85.08 17 A 1 ATOM 127 O OXT . CYS A 1 17 ? 11.041 -0.373 -7.090 1.00 84.94 17 A 1 #