ECODEvolutionary Classification of Protein Domains

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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.

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e5dc2B2 - ECOD Domain | ECOD

ECOD/Domains/e5dc2B2

e5dc2B2

UID: 001888609

PDB

Range: B:251-408
PDB: 5DC2 chain B(all domains)
UniProt: O53223 (all domains)
Gene: ldtB

Molecule: L,D-transpeptidase 2

3D Structure

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Related Domains

Browse other domains in YkuD →

Classification

AArchitecturebeta complex topology(a.5)

XX-groupL,D-transpeptidase catalytic domain-like(4091)

HH-groupL,D-transpeptidase catalytic domain-like(4091.1)

TT-groupL,D-transpeptidase catalytic domain-like(4091.1.1)

FFamilyYkuD(4091.1.1.1)

Ligands

in contact, ≤ 4 Å

(4S)-4-methyl-2,5,7-trioxoheptanoic acid58U

+ 5 additives (Triethylene glycol, Sulfate ion, 1,2-ETHANEDIOL, …)

Triethylene glycolPGE
DrugBank DB02327
Sulfate ionSO4

Pfam Families

L,D-transpeptidase catalytic domain

ClanCL0508YkuD

External Links

ECOD PDB View: 5DC2 RCSB PDB: 5DC2 PDBe: 5DC2 UniProt: O53223

Downloads

Download Domain PDB Download Domain FASTA Full PDB Structure

DrugBank DB14546

1,2-ETHANEDIOLEDO

GlycerolGOL

DI(HYDROXYETHYL)ETHERPEG

Shown in the structure viewer. Drug annotations from DrugDomain.