# ECOD develop291: coordinates and ligand contacts of every domain

Per-domain coordinate files for all domains of ECOD develop291, the last
PDB-only ECOD release (2024-04-12, PDB entries up to 2023-10-20). The release
itself only distributed coordinates for representative subsets. This record
holds the full set the legacy website (`prodata.swmed.edu/ecod/`) served.

The classification, release files and database are in the companion record
(see Related works). Please cite:

> Schaeffer RD, Liao Y, Cheng H, Grishin NV (2017). ECOD: new developments in the
> evolutionary classification of domains. *Nucleic Acids Res* 45:D296–D302.
> https://doi.org/10.1093/nar/gkw1137

## Files

| File | Contents | Files inside |
|---|---|---|
| `ecod.develop291.pdbnum.pdb.tar.zst` | Domain coordinates, **author (PDB) residue numbering**; matches `pdb_range` in `ecod.develop291.domains.txt`. PDB header records of the source entry are kept. This is the format of the release's own `.pdb.tar.gz` files. | 1,070,536 |
| `ecod.develop291.seqres.pdb.tar.zst` | The same coordinates, **residues numbered by SEQRES position**; matches `seqid_range`. | 1,080,346 |
| `ecod.develop291.ligand_contact.txt.tar.zst` | Ligands within 4 Å of the domain, one file per domain (with a comment line if there are none). | 1,082,375 |
| `ecod.develop291.missing_files.tsv` | Domains that lack one or more of these files: `uid`, `domain_id`, `manual_rep`, `missing` (comma-separated). | 13,650 rows |
| `MANIFEST.tsv` | Size and MD5 of every file. | |

Paths inside the archives are `./<uid[2:7]>/<uid>/<uid>.<type>`, where `uid` is
the 9-digit zero-padded ECOD uid, e.g. `./00002/000000267/000000267.pdbnum.pdb`.
Unpack with `tar --zstd -xf FILE` (or `zstd -dc FILE | tar -x`). To extract one
domain, use `tar --zstd -xf FILE ./00002/000000267/000000267.pdbnum.pdb`.

## Coverage

There are 1,083,021 domains in the release. The website never had every file:

| File | Present | Missing |
|---|---|---|
| `.pdbnum.pdb` | 1,070,536 | 12,485 (all automatic, non-representative domains) |
| `.seqres.pdb` | 1,080,346 | 2,675 |
| `.ligand_contact.txt` | 1,082,375 | 646 |

2,147 domains have neither coordinate file. The pipeline's own domain tree has
none of the missing `.pdbnum.pdb` files. It has 171 of the missing `.seqres.pdb`,
but those were regenerated in July 2024, after the release, and are not included.

Files left over in the website tree for domains that are not in develop291 are
not included.

## License and attribution

CC BY 4.0. Coordinates are derived from PDB entries (wwPDB, CC0).

Contact: Grishin lab, UT Southwestern Medical Center (http://prodata.swmed.edu/ecod/).