| Item | Options/Links | Description |
|---|
| Full NAKB accession id list |
csv
json
| Complete current list of structures indexed by NAKB, with mappings to PDB and NDB ids, polymer composition, and abbreviated experimental method. NAKB's primary index is the PDB id for all PDB entries. The NDB id is only used as primary index id for NDB-only entries. NAKB atlas pages can be called up by inserting either the PDB or NDB id (case insensitive) in the URL (/atlas=id). The csv and json links can be used for programmatic access. |
| NAKB Entry Summary annotations |
csv
json
| Nucleic acid, protein, and ligand annotations curated by NAKB, updated weekly. Entry Summary annotations are created by grouping/sorting NA, Protein, Ligand entity-level annotations (see below). |
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| NAKB Entity Annotations: NA |
annotations(json)
dictionary(js)
| Nucleic Acid entity annotations curated by NAKB, updated weekly (parallel annotation/PDB entity id lists). Dictionary provides annotation definitions, hierarchy. Supports NA annotation tree view. |
|---|
| NAKB Entity Annotations: Protein |
annotations(json)
dictionary(js)
| Protein entity annotations curated by NAKB, updated weekly (parallel annotation/PDB entity id lists). Dictionary provides annotation definitions, hierarchy. Supports Protein annotation tree view. |
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| NAKB Entity Annotations: Ligands |
annotations(json)
dictionary(js)
| Ligand entity annotations curated by NAKB, updated weekly (parallel annotation/PDB entity id lists). Dictionary provides annotation definitions, hierarchy. Supports Ligand annotation tree view. |
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| NDB/NAKB-only structures |
Assemblies
mmCIF
PDB format
Structure Factors
| Historically important high resolution DNA and RNA crystal structures that were originally deposited in the Cambridge Structural Database, mainly consisting of dinucleotides. |
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| Ideal DNA models |
NAKB intro
| DNA duplexes in A-form, B-form, and Z-form, generated using ideal fiber parameters. Download links are provided for model coordinates (PDB format). Source: Web-x3DNA fiber building tool. |
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NAKB logo |
png(med)
png(large)
svg |
Comprised of a generic nucleic acid strand making use of NDB colors (green: guanine, red: adenine, yellow: cytosine, blue: thymine, cyan: uracil) connected to a database symbol. Created by Maria Voigt (RCSB PDB). |
| Structure files by id set |
RCSB PDB Download Service |
Structure files for multiple PDB ids can be downloaded in bulk via the provided RCSB PDB link. To obtain a list of ids from NAKB search, first navigate to the tabular report page, then click on the ↓Ids button to download the id list. |
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