ECODEvolutionary Classification of Protein Domains

Home Browse Search Download Help

About ECOD

ECOD (Evolutionary Classification of Protein Domains) is a hierarchical classification of protein domains based on evolutionary relationships. It combines automated sequence and structure analysis with manual curation.

Quick Links

Browse Classification
Search
Download Data
Documentation
Privacy

Resources

Grishin Lab
UT Southwestern
RCSB PDB
AlphaFold DB
ecod.database@gmail.com

© 2014-2026 Grishin Lab / HHMI / UTSW

e3n9bB1 - ECOD Domain | ECOD

ECOD/Domains/e3n9bB1

e3n9bB1

UID: 000397372

PDB

Range: B:30-187
PDB: 3N9B chain B(all domains)
UniProt: Q9I1X7 (all domains)
Gene: ligD

Molecule: Probable ATP-dependent DNA ligase

3D Structure

Loading viewer...

Related Domains

Browse other domains in LigD_N →

Classification

AArchitecturebeta barrels(a.1)

XX-groupOncogene product-like(58)

HH-groupLigD phosphoesterase domain(58.2)

TT-groupLigD phosphoesterase domain(58.2.1)

FFamilyLigD_N(58.2.1.1)

Ligands

in contact, ≤ 4 Å

Chloride ionCL
MANGANESE (II) IONMN
metal

+ 2 additives (Sulfate ion, DI(HYDROXYETHYL)ETHER)

Sulfate ionSO4

Pfam Families

DNA Ligase D 3'-phosphoesterase domain

External Links

ECOD PDB View: 3N9B RCSB PDB: 3N9B PDBe: 3N9B UniProt: Q9I1X7

Downloads

Download Domain PDB Download Domain FASTA Full PDB Structure

DrugBank DB14546

DI(HYDROXYETHYL)ETHERPEG

within 5 Å only

Shown in the structure viewer. Drug annotations from DrugDomain.