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Crystal structure of the hexameric anti-microbial peptide channel dermcidin

Analyse Crystal structure of the hexameric anti-microbial peptide channel dermcidin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2YMK
Type: protein
Length: 140 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dcd-1
EC: 3.4.-.-
UniProt: P81605
Ligands: ZN

Structure

x-ray diffraction · 2 distinct chains · 90% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Dcd-1 (EC 3.4.-.-)	protein	46	89% helix, 0% strand	P81605
B, C	Dcd-1 (EC 3.4.-.-)	protein	47	91% helix, 0% strand	P81605

Ligands and binding sites

ZN · Zinc ion · metal · 6 copies · chains A, B, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Interfaces

3 interfaces between chains.

A–B · 45 Å² buried · 0 hydrogen bonds · protein-protein
A–C · 31 Å² buried · 0 hydrogen bonds · protein-protein
B–C · 23 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

2YMK · Crystal structure of the hexameric anti-microbial peptide channel dermcidin · the same entry in another collection · chain A against A, TM-score 1.00
P81605 · AlphaFold monomer V2.0 prediction for dermcidin (P81605) · a predicted model of the same protein · chain A against A, TM-score 0.77

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P81605
Elsewhere: RCSB PDB 2YMK · PDBe 2YMK · UniProt P81605

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