Schema for wgEncodeGencodePdbV48

Database: hg38 Primary Table: wgEncodeGencodePdbV48 Row Count: 348,897 Data last updated: 2025-05-31
Format description: GENCODE transcript to Protein Data Bank (PDB) protein structure mapping
On download server: MariaDB table dump directory

field	example	SQL type	info	description
`transcriptId`	ENST00000378391.6	`varchar(255)`	values	GENCODE transcript identifier
`pdbId`	2N1I	`varchar(255)`	values	Protein Data Bank (PDB) identifier

Connected Tables and Joining Fields


	hg38.wgEncodeGencodeAttrsV48.transcriptId (via wgEncodeGencodePdbV48.transcriptId)

Sample Rows

transcriptId	pdbId
ENST00000378391.6	2N1I
ENST00000378391.6	6BW4
ENST00000270722.10	2N1I
ENST00000270722.10	6BW4
ENST00000356607.9	2W84
ENST00000356607.9	2W85
ENST00000356607.9	4BXU
ENST00000328089.11	2JK9
ENST00000328089.11	3F2O
ENST00000357898.3	2JK9

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.