# 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_abundant-rose
#
_entry.id abundant-rose
#
loop_
_atom_type.symbol
C 
N 
O 
P 
#
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
"C10 H14 N5 O7 P" 347.221 A y "ADENOSINE-5'-MONOPHOSPHATE"                     c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N ? "RNA LINKING" 
"C13 H18 N5 O7 P" 387.285 P n "2'-DEOXY-N1,N2-PROPANO GUANOSINE MONOPHOSPHATE" c1nc2c(n1[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O)N=C4NCCCN4C2=O     ? "DNA LINKING" 
"C10 H15 N2 O8 P" 322.208 T y "THYMIDINE-5'-MONOPHOSPHATE"                     CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O           ? "DNA 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             branched
#
_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 (3.0.1 @ 2025-04-17 11:50:50)"
_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 80.25
_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 A . 2 78.76 1 1 
A T . 2 83.81 1 2 
A P . 2 78.71 1 3 
#
_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_branch_scheme.asym_id
_pdbx_branch_scheme.auth_asym_id
_pdbx_branch_scheme.auth_seq_num
_pdbx_branch_scheme.entity_id
_pdbx_branch_scheme.hetero
_pdbx_branch_scheme.mon_id
_pdbx_branch_scheme.num
_pdbx_branch_scheme.pdb_asym_id
_pdbx_branch_scheme.pdb_ins_code
_pdbx_branch_scheme.pdb_seq_num
A A 1 1 n A 1 A . 1 
A A 2 1 n T 2 A . 2 
A A 3 1 n P 3 A . 3 
#
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 ?                                                                              
#
_software.classification other
_software.date           ?
_software.description    "Structure prediction"
_software.name           AlphaFold
_software.pdbx_ordinal   1
_software.type           package
_software.version        "AlphaFold-beta-20231127 (25b635fa27adb4b12654a9dc6367a96b1463ec03aa886066ffc6cf0691bbe007)"
#
_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
HETATM 1  O OP3   . A A 1 . ? 3.483  -6.011 -4.815 1.00 52.46 1 A 1 
HETATM 2  P P     . A A 1 . ? 3.472  -5.284 -3.488 1.00 71.01 1 A 1 
HETATM 3  O OP1   . A A 1 . ? 3.401  -6.196 -2.333 1.00 60.93 1 A 1 
HETATM 4  O OP2   . A A 1 . ? 4.581  -4.310 -3.480 1.00 60.56 1 A 1 
HETATM 5  O "O5'" . A A 1 . ? 2.101  -4.414 -3.447 1.00 76.74 1 A 1 
HETATM 6  C "C5'" . A A 1 . ? 1.701  -3.716 -4.613 1.00 83.91 1 A 1 
HETATM 7  C "C4'" . A A 1 . ? 0.292  -3.186 -4.460 1.00 85.22 1 A 1 
HETATM 8  O "O4'" . A A 1 . ? -0.585 -4.199 -3.963 1.00 86.58 1 A 1 
HETATM 9  C "C3'" . A A 1 . ? 0.176  -2.020 -3.460 1.00 84.36 1 A 1 
HETATM 10 O "O3'" . A A 1 . ? 0.466  -0.783 -4.089 1.00 82.54 1 A 1 
HETATM 11 C "C2'" . A A 1 . ? -1.289 -2.118 -3.012 1.00 80.51 1 A 1 
HETATM 12 O "O2'" . A A 1 . ? -2.112 -1.539 -4.028 1.00 76.96 1 A 1 
HETATM 13 C "C1'" . A A 1 . ? -1.516 -3.626 -3.052 1.00 85.52 1 A 1 
HETATM 14 N N9    . A A 1 . ? -1.331 -4.243 -1.717 1.00 87.94 1 A 1 
HETATM 15 C C8    . A A 1 . ? -0.339 -5.050 -1.311 1.00 86.14 1 A 1 
HETATM 16 N N7    . A A 1 . ? -0.487 -5.416 -0.064 1.00 83.62 1 A 1 
HETATM 17 C C5    . A A 1 . ? -1.617 -4.849 0.364  1.00 84.60 1 A 1 
HETATM 18 C C6    . A A 1 . ? -2.339 -4.827 1.573  1.00 81.29 1 A 1 
HETATM 19 N N6    . A A 1 . ? -1.930 -5.494 2.638  1.00 76.63 1 A 1 
HETATM 20 N N1    . A A 1 . ? -3.453 -4.105 1.630  1.00 80.64 1 A 1 
HETATM 21 C C2    . A A 1 . ? -3.904 -3.419 0.587  1.00 77.48 1 A 1 
HETATM 22 N N3    . A A 1 . ? -3.296 -3.386 -0.583 1.00 81.50 1 A 1 
HETATM 23 C C4    . A A 1 . ? -2.168 -4.091 -0.690 1.00 84.27 1 A 1 
HETATM 24 O OP3   . T A 1 . ? 1.546  1.262  -3.774 1.00 59.37 2 A 1 
HETATM 25 P P     . T A 1 . ? 1.092  0.378  -3.060 1.00 85.89 2 A 1 
HETATM 26 O OP1   . T A 1 . ? 2.006  -0.279 -2.121 1.00 75.49 2 A 1 
HETATM 27 O OP2   . T A 1 . ? 1.398  1.224  -3.997 1.00 72.13 2 A 1 
HETATM 28 O "O5'" . T A 1 . ? -0.213 0.864  -2.243 1.00 85.33 2 A 1 
HETATM 29 C "C5'" . T A 1 . ? -1.334 1.404  -2.917 1.00 85.70 2 A 1 
HETATM 30 C "C4'" . T A 1 . ? -2.504 1.636  -1.931 1.00 88.20 2 A 1 
HETATM 31 O "O4'" . T A 1 . ? -2.698 0.477  -1.131 1.00 88.12 2 A 1 
HETATM 32 C "C3'" . T A 1 . ? -2.285 2.811  -0.989 1.00 87.08 2 A 1 
HETATM 33 O "O3'" . T A 1 . ? -3.463 3.596  -0.917 1.00 87.13 2 A 1 
HETATM 34 C "C2'" . T A 1 . ? -2.064 2.209  0.347  1.00 86.19 2 A 1 
HETATM 35 C "C1'" . T A 1 . ? -2.742 0.879  0.263  1.00 86.25 2 A 1 
HETATM 36 N N1    . T A 1 . ? -2.080 -0.123 1.078  1.00 89.36 2 A 1 
HETATM 37 C C2    . T A 1 . ? -2.729 -0.511 2.226  1.00 87.40 2 A 1 
HETATM 38 O O2    . T A 1 . ? -3.803 -0.029 2.557  1.00 83.51 2 A 1 
HETATM 39 N N3    . T A 1 . ? -2.142 -1.452 2.974  1.00 85.28 2 A 1 
HETATM 40 C C4    . T A 1 . ? -0.938 -2.038 2.660  1.00 87.08 2 A 1 
HETATM 41 O O4    . T A 1 . ? -0.467 -2.895 3.410  1.00 81.68 2 A 1 
HETATM 42 C C5    . T A 1 . ? -0.260 -1.625 1.451  1.00 87.44 2 A 1 
HETATM 43 C C7    . T A 1 . ? 1.013  -2.189 1.044  1.00 84.18 2 A 1 
HETATM 44 C C6    . T A 1 . ? -0.864 -0.659 0.695  1.00 87.15 2 A 1 
HETATM 45 P P     . P A 1 . ? -3.282 5.323  -0.916 1.00 86.66 3 A 1 
HETATM 46 O OP1   . P A 1 . ? -1.815 5.210  -0.801 1.00 74.51 3 A 1 
HETATM 47 O OP2   . P A 1 . ? -4.153 4.949  -1.962 1.00 67.14 3 A 1 
HETATM 48 O OP3   . P A 1 . ? -3.380 6.800  -1.271 1.00 58.27 3 A 1 
HETATM 49 O "O5'" . P A 1 . ? -3.941 5.313  0.562  1.00 83.25 3 A 1 
HETATM 50 C "C5'" . P A 1 . ? -5.355 5.399  0.756  1.00 83.38 3 A 1 
HETATM 51 C "C4'" . P A 1 . ? -5.692 5.502  2.246  1.00 86.32 3 A 1 
HETATM 52 O "O4'" . P A 1 . ? -5.439 4.246  2.880  1.00 85.09 3 A 1 
HETATM 53 C "C3'" . P A 1 . ? -4.870 6.548  2.982  1.00 83.27 3 A 1 
HETATM 54 O "O3'" . P A 1 . ? -5.732 7.430  3.677  1.00 77.21 3 A 1 
HETATM 55 C "C2'" . P A 1 . ? -4.092 5.749  4.034  1.00 82.99 3 A 1 
HETATM 56 C "C1'" . P A 1 . ? -4.951 4.523  4.194  1.00 85.61 3 A 1 
HETATM 57 N N9    . P A 1 . ? -4.357 3.328  4.795  1.00 85.47 3 A 1 
HETATM 58 C C8    . P A 1 . ? -4.986 2.541  5.728  1.00 82.88 3 A 1 
HETATM 59 N N7    . P A 1 . ? -4.214 1.519  6.083  1.00 81.20 3 A 1 
HETATM 60 C C5    . P A 1 . ? -3.058 1.661  5.398  1.00 82.05 3 A 1 
HETATM 61 C C6    . P A 1 . ? -1.880 0.867  5.385  1.00 78.95 3 A 1 
HETATM 62 O O6    . P A 1 . ? -1.734 -0.150 6.052  1.00 73.50 3 A 1 
HETATM 63 N N1    . P A 1 . ? -0.877 1.329  4.522  1.00 76.52 3 A 1 
HETATM 64 C C2    . P A 1 . ? -1.031 2.465  3.753  1.00 77.09 3 A 1 
HETATM 65 N N2    . P A 1 . ? -0.080 2.888  2.931  1.00 72.58 3 A 1 
HETATM 66 N N3    . P A 1 . ? -2.135 3.201  3.789  1.00 76.97 3 A 1 
HETATM 67 C C4    . P A 1 . ? -3.133 2.803  4.588  1.00 83.82 3 A 1 
HETATM 68 C C6A   . P A 1 . ? 1.052  2.211  2.795  1.00 71.67 3 A 1 
HETATM 69 C C7A   . P A 1 . ? 1.259  1.070  3.524  1.00 72.75 3 A 1 
HETATM 70 C C8A   . P A 1 . ? 0.291  0.618  4.395  1.00 77.32 3 A 1 
#
