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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e6iyvA1 - ECOD Domain | ECOD

ECOD/Domains/e6iyvA1

e6iyvA1

UID: 002453160

PDB

Range: A:234-407
PDB: 6IYV chain A(all domains)
UniProt: I6Y9J2 (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

(2S,3R,4S)-4-({(3S,5S)-5-[(3-carboxyphenyl)carbamoyl]pyrrolidin-3-yl}sulfanyl)-2-[(1S,2R)-1-formyl-2-hydroxypropyl]-3-methyl-3,4-dihydro-2H-pyrrole-5-carboxylic acid2RG

+ 3 additives (Glycerin, Tromethamine, DI(HYDROXYETHYL)ETHER)

GlycerinGOL
DrugBank DB09462

Pfam Families

L,D-transpeptidase catalytic domain

ClanCL0508YkuD

External Links

ECOD PDB View: 6IYV RCSB PDB: 6IYV PDBe: 6IYV UniProt: I6Y9J2

Downloads

Download Domain PDB Download Domain FASTA Full PDB Structure

TromethamineTRS

DrugBank DB03754

DI(HYDROXYETHYL)ETHERPEG

Shown in the structure viewer. Drug annotations from DrugDomain.