# 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_spkb10955 # _entry.id spkb10955 # 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" "C4 H8 N2 O3" 132.118 ASN y ASPARAGINE C([C@@H](C(=O)O)N)C(=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" "C9 H11 N O3" 181.189 TYR y TYROSINE c1cc(ccc1C[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 LEU 2 1 n ASN 3 1 n VAL 4 1 n PHE 5 1 n PHE 6 1 n LEU 7 1 n THR 8 1 n SER 9 1 n LEU 10 1 n PHE 11 1 n TYR 12 1 n ALA 13 1 n ALA 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 @ 2025-07-09 19:04:41)" _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 88.04 _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 78.58 1 1 A LEU 2 2 82.79 1 2 A ASN 3 2 85.67 1 3 A VAL 4 2 91.84 1 4 A PHE 5 2 88.53 1 5 A PHE 6 2 89.31 1 6 A LEU 7 2 90.99 1 7 A THR 8 2 90.88 1 8 A SER 9 2 91.08 1 9 A LEU 10 2 91.28 1 10 A PHE 11 2 87.92 1 11 A TYR 12 2 87.57 1 12 A ALA 13 2 94.14 1 13 A ALA 14 2 92.68 1 14 A SER 15 2 86.96 1 15 A ALA 16 2 81.78 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 LEU . 2 A 2 A 3 1 n ASN . 3 A 3 A 4 1 n VAL . 4 A 4 A 5 1 n PHE . 5 A 5 A 6 1 n PHE . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n THR . 8 A 8 A 9 1 n SER . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n PHE . 11 A 11 A 12 1 n TYR . 12 A 12 A 13 1 n ALA . 13 A 13 A 14 1 n ALA . 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 ? -4.980 4.855 9.393 1.00 81.73 1 A 1 ATOM 2 C CA . MET A 1 1 ? -3.812 4.363 10.165 1.00 85.40 1 A 1 ATOM 3 C C . MET A 1 1 ? -2.579 4.246 9.266 1.00 86.19 1 A 1 ATOM 4 O O . MET A 1 1 ? -2.679 4.370 8.048 1.00 84.07 1 A 1 ATOM 5 C CB . MET A 1 1 ? -4.160 3.012 10.767 1.00 78.92 1 A 1 ATOM 6 C CG . MET A 1 1 ? -4.615 3.144 12.224 1.00 74.79 1 A 1 ATOM 7 S SD . MET A 1 1 ? -5.846 4.406 12.461 1.00 72.17 1 A 1 ATOM 8 C CE . MET A 1 1 ? -6.194 4.152 14.204 1.00 65.36 1 A 1 ATOM 9 N N . LEU A 1 2 ? -1.438 4.001 9.871 1.00 83.74 2 A 1 ATOM 10 C CA . LEU A 1 2 ? -0.181 3.899 9.128 1.00 86.63 2 A 1 ATOM 11 C C . LEU A 1 2 ? -0.050 2.545 8.434 1.00 88.92 2 A 1 ATOM 12 O O . LEU A 1 2 ? 0.295 2.473 7.253 1.00 86.66 2 A 1 ATOM 13 C CB . LEU A 1 2 ? 1.004 4.115 10.075 1.00 84.14 2 A 1 ATOM 14 C CG . LEU A 1 2 ? 2.116 4.951 9.456 1.00 80.75 2 A 1 ATOM 15 C CD1 . LEU A 1 2 ? 2.227 6.297 10.166 1.00 77.09 2 A 1 ATOM 16 C CD2 . LEU A 1 2 ? 3.435 4.199 9.535 1.00 74.38 2 A 1 ATOM 17 N N . ASN A 1 3 ? -0.325 1.485 9.176 1.00 88.08 3 A 1 ATOM 18 C CA . ASN A 1 3 ? -0.232 0.131 8.631 1.00 90.30 3 A 1 ATOM 19 C C . ASN A 1 3 ? -1.285 -0.102 7.552 1.00 91.86 3 A 1 ATOM 20 O O . ASN A 1 3 ? -1.007 -0.673 6.503 1.00 91.46 3 A 1 ATOM 21 C CB . ASN A 1 3 ? -0.402 -0.893 9.757 1.00 86.69 3 A 1 ATOM 22 C CG . ASN A 1 3 ? 0.614 -2.008 9.660 1.00 82.00 3 A 1 ATOM 23 O OD1 . ASN A 1 3 ? 0.354 -3.051 9.079 1.00 77.99 3 A 1 ATOM 24 N ND2 . ASN A 1 3 ? 1.786 -1.800 10.238 1.00 76.97 3 A 1 ATOM 25 N N . VAL A 1 4 ? -2.476 0.352 7.817 1.00 92.95 4 A 1 ATOM 26 C CA . VAL A 1 4 ? -3.583 0.207 6.867 1.00 93.69 4 A 1 ATOM 27 C C . VAL A 1 4 ? -3.301 0.995 5.593 1.00 94.69 4 A 1 ATOM 28 O O . VAL A 1 4 ? -3.600 0.540 4.485 1.00 94.17 4 A 1 ATOM 29 C CB . VAL A 1 4 ? -4.903 0.683 7.499 1.00 92.30 4 A 1 ATOM 30 C CG1 . VAL A 1 4 ? -6.052 0.524 6.514 1.00 87.40 4 A 1 ATOM 31 C CG2 . VAL A 1 4 ? -5.198 -0.102 8.774 1.00 87.67 4 A 1 ATOM 32 N N . PHE A 1 5 ? -2.726 2.155 5.751 1.00 92.08 5 A 1 ATOM 33 C CA . PHE A 1 5 ? -2.396 3.000 4.610 1.00 92.15 5 A 1 ATOM 34 C C . PHE A 1 5 ? -1.295 2.359 3.773 1.00 93.52 5 A 1 ATOM 35 O O . PHE A 1 5 ? -1.313 2.421 2.546 1.00 93.08 5 A 1 ATOM 36 C CB . PHE A 1 5 ? -1.944 4.371 5.108 1.00 91.49 5 A 1 ATOM 37 C CG . PHE A 1 5 ? -2.623 5.492 4.369 1.00 89.18 5 A 1 ATOM 38 C CD1 . PHE A 1 5 ? -2.343 5.725 3.036 1.00 85.62 5 A 1 ATOM 39 C CD2 . PHE A 1 5 ? -3.540 6.306 5.022 1.00 85.84 5 A 1 ATOM 40 C CE1 . PHE A 1 5 ? -2.971 6.751 2.348 1.00 83.38 5 A 1 ATOM 41 C CE2 . PHE A 1 5 ? -4.166 7.340 4.340 1.00 84.18 5 A 1 ATOM 42 C CZ . PHE A 1 5 ? -3.880 7.561 3.004 1.00 83.27 5 A 1 ATOM 43 N N . PHE A 1 6 ? -0.360 1.732 4.442 1.00 91.97 6 A 1 ATOM 44 C CA . PHE A 1 6 ? 0.750 1.064 3.766 1.00 92.19 6 A 1 ATOM 45 C C . PHE A 1 6 ? 0.241 -0.120 2.952 1.00 93.52 6 A 1 ATOM 46 O O . PHE A 1 6 ? 0.701 -0.366 1.840 1.00 93.32 6 A 1 ATOM 47 C CB . PHE A 1 6 ? 1.767 0.595 4.803 1.00 91.57 6 A 1 ATOM 48 C CG . PHE A 1 6 ? 3.103 0.262 4.192 1.00 89.80 6 A 1 ATOM 49 C CD1 . PHE A 1 6 ? 3.877 1.254 3.613 1.00 86.97 6 A 1 ATOM 50 C CD2 . PHE A 1 6 ? 3.569 -1.039 4.208 1.00 87.50 6 A 1 ATOM 51 C CE1 . PHE A 1 6 ? 5.105 0.957 3.047 1.00 85.48 6 A 1 ATOM 52 C CE2 . PHE A 1 6 ? 4.802 -1.349 3.642 1.00 85.12 6 A 1 ATOM 53 C CZ . PHE A 1 6 ? 5.570 -0.349 3.062 1.00 84.96 6 A 1 ATOM 54 N N . LEU A 1 7 ? -0.703 -0.835 3.522 1.00 93.00 7 A 1 ATOM 55 C CA . LEU A 1 7 ? -1.285 -1.993 2.849 1.00 93.79 7 A 1 ATOM 56 C C . LEU A 1 7 ? -2.091 -1.560 1.632 1.00 94.62 7 A 1 ATOM 57 O O . LEU A 1 7 ? -2.004 -2.169 0.567 1.00 94.88 7 A 1 ATOM 58 C CB . LEU A 1 7 ? -2.184 -2.756 3.825 1.00 93.43 7 A 1 ATOM 59 C CG . LEU A 1 7 ? -2.510 -4.176 3.377 1.00 87.12 7 A 1 ATOM 60 C CD1 . LEU A 1 7 ? -1.330 -5.102 3.638 1.00 85.62 7 A 1 ATOM 61 C CD2 . LEU A 1 7 ? -3.745 -4.681 4.097 1.00 85.47 7 A 1 ATOM 62 N N . THR A 1 8 ? -2.857 -0.523 1.797 1.00 92.42 8 A 1 ATOM 63 C CA . THR A 1 8 ? -3.687 -0.007 0.713 1.00 92.71 8 A 1 ATOM 64 C C . THR A 1 8 ? -2.823 0.576 -0.404 1.00 93.71 8 A 1 ATOM 65 O O . THR A 1 8 ? -3.153 0.458 -1.588 1.00 92.84 8 A 1 ATOM 66 C CB . THR A 1 8 ? -4.671 1.036 1.278 1.00 92.00 8 A 1 ATOM 67 O OG1 . THR A 1 8 ? -6.000 0.530 1.114 1.00 87.22 8 A 1 ATOM 68 C CG2 . THR A 1 8 ? -4.594 2.383 0.576 1.00 85.26 8 A 1 ATOM 69 N N . SER A 1 9 ? -1.733 1.184 -0.023 1.00 92.05 9 A 1 ATOM 70 C CA . SER A 1 9 ? -0.812 1.778 -0.985 1.00 92.26 9 A 1 ATOM 71 C C . SER A 1 9 ? -0.129 0.692 -1.805 1.00 92.99 9 A 1 ATOM 72 O O . SER A 1 9 ? 0.075 0.841 -3.008 1.00 91.98 9 A 1 ATOM 73 C CB . SER A 1 9 ? 0.227 2.622 -0.255 1.00 91.53 9 A 1 ATOM 74 O OG . SER A 1 9 ? 0.421 3.846 -0.926 1.00 85.65 9 A 1 ATOM 75 N N . LEU A 1 10 ? 0.207 -0.400 -1.148 1.00 93.86 10 A 1 ATOM 76 C CA . LEU A 1 10 ? 0.859 -1.523 -1.816 1.00 93.90 10 A 1 ATOM 77 C C . LEU A 1 10 ? -0.101 -2.194 -2.789 1.00 94.42 10 A 1 ATOM 78 O O . LEU A 1 10 ? 0.289 -2.610 -3.878 1.00 93.73 10 A 1 ATOM 79 C CB . LEU A 1 10 ? 1.345 -2.532 -0.775 1.00 93.29 10 A 1 ATOM 80 C CG . LEU A 1 10 ? 2.561 -3.330 -1.229 1.00 89.64 10 A 1 ATOM 81 C CD1 . LEU A 1 10 ? 3.810 -2.860 -0.499 1.00 85.69 10 A 1 ATOM 82 C CD2 . LEU A 1 10 ? 2.335 -4.814 -0.991 1.00 85.68 10 A 1 ATOM 83 N N . PHE A 1 11 ? -1.352 -2.297 -2.390 1.00 93.22 11 A 1 ATOM 84 C CA . PHE A 1 11 ? -2.380 -2.912 -3.224 1.00 92.26 11 A 1 ATOM 85 C C . PHE A 1 11 ? -2.559 -2.130 -4.520 1.00 93.20 11 A 1 ATOM 86 O O . PHE A 1 11 ? -2.732 -2.713 -5.591 1.00 92.57 11 A 1 ATOM 87 C CB . PHE A 1 11 ? -3.698 -2.959 -2.455 1.00 91.06 11 A 1 ATOM 88 C CG . PHE A 1 11 ? -4.604 -4.066 -2.930 1.00 87.66 11 A 1 ATOM 89 C CD1 . PHE A 1 11 ? -5.343 -3.924 -4.092 1.00 84.19 11 A 1 ATOM 90 C CD2 . PHE A 1 11 ? -4.705 -5.245 -2.205 1.00 84.77 11 A 1 ATOM 91 C CE1 . PHE A 1 11 ? -6.174 -4.944 -4.534 1.00 82.87 11 A 1 ATOM 92 C CE2 . PHE A 1 11 ? -5.537 -6.270 -2.644 1.00 82.94 11 A 1 ATOM 93 C CZ . PHE A 1 11 ? -6.271 -6.117 -3.810 1.00 82.37 11 A 1 ATOM 94 N N . TYR A 1 12 ? -2.519 -0.832 -4.412 1.00 92.72 12 A 1 ATOM 95 C CA . TYR A 1 12 ? -2.679 0.026 -5.580 1.00 92.41 12 A 1 ATOM 96 C C . TYR A 1 12 ? -1.467 -0.081 -6.500 1.00 93.24 12 A 1 ATOM 97 O O . TYR A 1 12 ? -1.601 -0.061 -7.724 1.00 92.67 12 A 1 ATOM 98 C CB . TYR A 1 12 ? -2.873 1.477 -5.135 1.00 91.10 12 A 1 ATOM 99 C CG . TYR A 1 12 ? -4.079 2.117 -5.794 1.00 87.18 12 A 1 ATOM 100 C CD1 . TYR A 1 12 ? -4.044 2.499 -7.129 1.00 84.99 12 A 1 ATOM 101 C CD2 . TYR A 1 12 ? -5.249 2.330 -5.068 1.00 85.12 12 A 1 ATOM 102 C CE1 . TYR A 1 12 ? -5.152 3.079 -7.732 1.00 83.54 12 A 1 ATOM 103 C CE2 . TYR A 1 12 ? -6.362 2.912 -5.667 1.00 83.91 12 A 1 ATOM 104 C CZ . TYR A 1 12 ? -6.305 3.284 -6.998 1.00 83.12 12 A 1 ATOM 105 O OH . TYR A 1 12 ? -7.400 3.862 -7.595 1.00 80.85 12 A 1 ATOM 106 N N . ALA A 1 13 ? -0.294 -0.195 -5.898 1.00 94.50 13 A 1 ATOM 107 C CA . ALA A 1 13 ? 0.946 -0.315 -6.666 1.00 94.60 13 A 1 ATOM 108 C C . ALA A 1 13 ? 1.021 -1.666 -7.366 1.00 95.16 13 A 1 ATOM 109 O O . ALA A 1 13 ? 1.457 -1.758 -8.512 1.00 93.44 13 A 1 ATOM 110 C CB . ALA A 1 13 ? 2.145 -0.131 -5.745 1.00 93.00 13 A 1 ATOM 111 N N . ALA A 1 14 ? 0.597 -2.706 -6.669 1.00 94.05 14 A 1 ATOM 112 C CA . ALA A 1 14 ? 0.621 -4.058 -7.224 1.00 93.19 14 A 1 ATOM 113 C C . ALA A 1 14 ? -0.398 -4.208 -8.347 1.00 93.68 14 A 1 ATOM 114 O O . ALA A 1 14 ? -0.227 -5.024 -9.248 1.00 91.60 14 A 1 ATOM 115 C CB . ALA A 1 14 ? 0.345 -5.074 -6.119 1.00 90.90 14 A 1 ATOM 116 N N . SER A 1 15 ? -1.458 -3.430 -8.284 1.00 91.83 15 A 1 ATOM 117 C CA . SER A 1 15 ? -2.504 -3.466 -9.299 1.00 90.05 15 A 1 ATOM 118 C C . SER A 1 15 ? -1.993 -2.938 -10.634 1.00 88.60 15 A 1 ATOM 119 O O . SER A 1 15 ? -2.506 -3.298 -11.695 1.00 85.30 15 A 1 ATOM 120 C CB . SER A 1 15 ? -3.705 -2.647 -8.842 1.00 86.76 15 A 1 ATOM 121 O OG . SER A 1 15 ? -4.896 -3.218 -9.318 1.00 79.21 15 A 1 ATOM 122 N N . ALA A 1 16 ? -0.996 -2.100 -10.566 1.00 88.97 16 A 1 ATOM 123 C CA . ALA A 1 16 ? -0.423 -1.499 -11.770 1.00 85.84 16 A 1 ATOM 124 C C . ALA A 1 16 ? 0.754 -2.331 -12.279 1.00 83.49 16 A 1 ATOM 125 O O . ALA A 1 16 ? 0.590 -3.086 -13.242 1.00 78.67 16 A 1 ATOM 126 C CB . ALA A 1 16 ? 0.014 -0.067 -11.478 1.00 79.55 16 A 1 ATOM 127 O OXT . ALA A 1 16 ? 1.831 -2.231 -11.711 1.00 74.13 16 A 1 #