Schema for wgEncodeGencodePdbV50

Database: hg38 Primary Table: wgEncodeGencodePdbV50 Row Count: 394,395 Data last updated: 2026-04-24
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`	ENST00000619609.1	`varchar(255)`	values	GENCODE transcript identifier
`pdbId`	4DAT	`varchar(255)`	values	Protein Data Bank (PDB) identifier

Connected Tables and Joining Fields


	hg38.wgEncodeGencodeAttrsV50.transcriptId (via wgEncodeGencodePdbV50.transcriptId)

Sample Rows

transcriptId	pdbId
ENST00000619609.1	4DAT
ENST00000619609.1	4DAU
ENST00000619609.1	8QL0
ENST00000619609.1	9FMN
ENST00000256592.3	7T9I
ENST00000256592.3	7UTZ
ENST00000256592.3	7XW5
ENST00000367685.5	6LI0
ENST00000367685.5	6LI1
ENST00000367685.5	6LI2

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