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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e4benD4 - ECOD Domain | ECOD

ECOD/Domains/e4benD4

e4benD4

UID: 000972573

PDB

Range: D:67-163,D:239-284
PDB: 4BEN chain D(all domains)
UniProt: P39045 (all domains)
Gene: dac

Molecule: D-ALANYL-D-ALANINE CARBOXYPEPTIDASE

3D Structure

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Related Domains

Browse other domains in Peptidase_S13 →

Classification

AArchitecturea/b three-layered sandwiches(a.17)

XX-groupDTD-like(2494)

HH-groupInserted a+b domain in Dac-like proteins(2494.2)

TT-groupInserted a+b domain in Dac-like proteins(2494.2.1)

FFamilyPeptidase_S13(2494.2.1.1)

Ligands

in contact, ≤ 4 Å

Magnesium ionMG
metal
(5R)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-3-[(2-{[(E)-iminomethyl]amino}ethyl)sulfanyl]-4,5-dihydro-1H-pyrrole-2-carboxylic acidIM2
within 5 Å only

+ 2 additives (Glycerin, Sulfate ion)

GlycerinGOL

Pfam Families

PF02113Peptidase_S13

D-Ala-D-Ala carboxypeptidase 3 (S13) family

ClanCL0013Beta-lactamase

External Links

ECOD PDB View: 4BEN RCSB PDB: 4BEN PDBe: 4BEN UniProt: P39045

Downloads

Download Domain PDB Download Domain FASTA Full PDB Structure

DrugBank DB09462

Sulfate ionSO4

DrugBank DB14546

Shown in the structure viewer. Drug annotations from DrugDomain.