About the contents of the PDBj data site

This page lists the files within the PDBj data archive. Information regarding data retrieval is written on the PDBj download page.

Files within the data site

efsite/data-web/${entryId}.mpbf.gz
pdb_versioned	Shared between all wwPDB members
data
entries
${id23}/pdb0000${pdbid}/
pdb_0000${pdbid}_xyz-ext-atom_v${version}.xml.gz
pdb_0000${pdbid}_xyz-no-atom_v${version}.xml.gz
pdb_0000${pdbid}_xyz_v${version}.cif.gz
pdb_0000${pdbid}_xyz_v${version}.xml.gz
removed
${id23}/pdb0000${pdbid}/
pdb_0000${pdbid}_xyz-ext-atom_v${version}.xml.gz
pdb_0000${pdbid}_xyz-no-atom_v${version}.xml.gz
pdb_0000${pdbid}_xyz_v${version}.cif.gz
pdb_0000${pdbid}_xyz_v${version}.xml.gz
views
all
coordinates
mmcif
${id23}/pdb0000${pdbid}/
pdb_0000${pdbid}_xyz_v${version}.cif.gz
pdbml
${id23}/pdb0000${pdbid}/
pdb_0000${pdbid}_xyz_v${version}.xml.gz
latest
coordinates
mmcif
${id23}/pdb0000${pdbid}/
pdb_0000${pdbid}_xyz.cif.gz
pdbml
${id23}/pdb0000${pdbid}/
pdb_0000${pdbid}_xyz.xml.gz
pdbjplus	Data generated by PDBj for wwPDB data
data
cc	chem_comp data (Chemie)
mdl
${comp_id}.mdl.gz
mmcif
${comp_id}.cif.gz
mmjson
${comp_id}.json.gz
mmjson-plus
${comp_id}-plus.json.gz
rdf
${comp_id}.rdf.gz
svg
${comp_id}.svg.gz
xml
${comp_id}.xml.gz
ccmodel
mmcif
${model_id}.cif.gz
mmjson
${model_id}.json.gz
pdb	PDB data
mmjson
${pdbid}.json.gz
mmjson-chain
${pdbid}_${asym_id}-chain.json.gz
mmjson-noatom
${pdbid}-noatom.json.gz
mmjson-plus
${pdbid}-plus.json.gz
rdf
${pdbid}.rdf.gz
prd	BIRD data
mmcif
${prd_id}.cif.gz
mmcif-cc
${prd_id}-cc.cif.gz
mmjson
${prd_id}.json.gz
svg
${prd_id}.svg.gz
sifts	SIFTS data
rdf
pdb_chain_cath_uniprot.ttl.gz
pdb_chain_enzyme.ttl.gz
pdb_chain_go.ttl.gz
pdb_chain_interpro.ttl.gz
pdb_chain_pfam.ttl.gz
pdb_chain_scop_uniprot.ttl.gz
pdb_chain_taxonomy.ttl.gz
pdb_chain_uniprot.ttl.gz
pdb_chain_uniprot_short.ttl.gz
pdb_pubmed.ttl.gz
uniprot_pdb.ttl.gz
dictionaries	Various dictionaries in various formats
edmap2	EDMap map data
ccp4
${pdbid}_validation_${type}_map_coef.ccp4
mtz
${pdbid}_validation_${type}_map_coef.mtz
edmap.list
mine2
dump	PostgreSQL RDB dump files
rdb_docs	RDB documentation files in json format
schema	RDB schema definitions in YAML format (used by mine2updater)
statistics	RDB statistics; lists per column the number of non-null elements
promode/data_web/${entryId}/	The web-data for the secondary database Promode Elastic
pub	Shared between all wwPDB members
emdb
doc
obsoleted/${emdb_id}/header	Obsolete entries header files
${emdb_id}-v19.xml
${emdb_id}-v30.xml
${emdb_id}.xml
status
archive	Weekly update history
latest	Latest update history
structures/${emdb_id}/	Current entries data files
header
${emdb_id}-v19.xml
${emdb_id}-v30.xml
${emdb_id}.xml
images/${emdb_id}.png
map/${emdb_id}.map.gz
${emdb_id}-v19.xml
validation_reports/${emdb_id}/
${emdb_id}_full_validation.pdf.gz
${emdb_id}_validation.pdf.gz
${emdb_id}_validation.xml.gz
pdb
compatible/pdb_bundle/${id23}/${pdbid}/${pdbid}-pdb-bundle.tar.gz
data
biounit
PDB
all/${pdbid}.pdb${buid}.gz
divided/${id23}/${pdbid}/${pdbid}.pdb${buid}.gz
coordinates
all/${pdbid}.pdb${buid}.gz
divided/${id23}/${pdbid}/${pdbid}.pdb${buid}.gz
mmCIF
all/${pdbid}-assembly${buid}.gz
divided/${id23}/${pdbid}/${pdbid}-assembly${buid}.gz
bird
family
prd
component-models/complete/
monomers/${comp_id}
status	List of weekly modified entries
structures
all
XML/${pdbid}.xml.gz
XML-extatom/${pdbid}-extatom.xml.gz
XML-noatom/${pdbid}-noatom.xml.gz
mmCIF/${pdbid}.cif.gz
nmr_chemical_shifts/${pdbid}_cs.str.gz
nmr_data
${pdbid}_nmr-data.nef.gz
${pdbid}_nmr-data.str.gz
nmr_restraints/${pdbid}.mr.gz
nmr_restraints_v2/${pdbid}_mr.str.gz
pdb/pdb${pdbid}.ent.gz	PDB flatfile format
structure_factors/r${pdbid}.ent.gz	mmCIF format
divided
XML/${id23}/${pdbid}.xml.gz
XML-extatom/${id23}/${pdbid}-extatom.xml.gz
XML-noatom/${id23}/${pdbid}-noatom.xml.gz
mmCIF/${id23}/${pdbid}.cif.gz
nmr_chemical_shifts/${id23}/${pdbid}_cs.str.gz
nmr_data
${id23}/${pdbid}_nmr-data.nef.gz
${id23}/${pdbid}_nmr-data.str.gz
nmr_restraints/${id23}/${pdbid}.mr.gz
nmr_restraints_v2/${id23}/${pdbid}_mr.str.gz
pdb/${id23}/pdb${pdbid}.ent.gz	PDB flatfile format
structure_factors/${id23}/r${pdbid}.ent.gz	mmCIF format
models
current/pdb/${id23}/pdb${pdbid}.ent.gz
index
obsolete/pdb/${id23}/pdb${pdbid}.ent.gz
obsolete
XML/${id23}/${pdbid}.xml.gz
mmCIF/${id23}/${pdbid}.cif.gz
nmr_chemical_shifts/${id23}/${pdbid}_cs.str.gz
nmr_data
${id23}/${pdbid}_nmr-data.nef.gz
${id23}/${pdbid}_nmr-data.str.gz
nmr_restraints/${id23}/${pdbid}.mr.gz
nmr_restraints_v2/${id23}/${pdbid}_mr.str.gz
pdb/${id23}/pdb${pdbid}.ent.gz	PDB flatfile format
structure_factors/${id23}/r${pdbid}.ent.gz	mmCIF format
derived_data
doc
software
validation_reports${id23}/${pdbid}
${pdbid}_full_validation.pdf.gz
${pdbid}_multipercentile_validation.png.gz
${pdbid}_multipercentile_validation.svg.gz
${pdbid}_validation.pdf.gz
${pdbid}_validation.xml.gz
${pdbid}_validation_2fo-fc_map_coef.cif.gz
${pdbid}_validation_fo-fc_map_coef.cif.gz

Explanation of the variables used in the above table:

${pdbid}	PDBID of the entry
${comp_id}	comp_id (cc) of the entry
${model_id}	Model ID (ccmodel) of the entry
${prd_id}	PRD ID of the entry
${emdb_id}	EMDB ID of the entry
${id23}	2nd and 3rd character of the PDBID
${buid}	BU assembly ID
${entryId}	Entry ID of the entry (efsite, promode)
${version}	Version of the file