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Structure of linear gramicidin D obtained using type I crystals grown in a monovaccenin lipid cubic phase

Analyse Structure of linear gramicidin D obtained using type I crystals grown in a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3ZQ8
Type: protein
Length: 60 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Val-gramicidin a
Ligands: ETA, MVC

Structure

x-ray diffraction · 1 distinct chain · 0% helix, 87% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Val-gramicidin a	protein	15	0% helix, 87% strand	—

Ligands and binding sites

ETA · Ethanolamine · ligand · 4 copies · chains A, B, C, D
MVC · Monovaccenin · ligand · 3 copies · chains C, D

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

Interfaces

6 interfaces between chains.

A–B · 1137 Å² buried · 34 hydrogen bonds · protein-protein
C–D · 1107 Å² buried · 34 hydrogen bonds · protein-protein
A–C · 283 Å² buried · 1 hydrogen bond · protein-protein
B–C · 269 Å² buried · 0 hydrogen bonds · protein-protein
A–D · 222 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 24 d-amino, 4 covalent, 4 modified (D-amino acid, covalent ligand, nonstandard).

Compared structures

3ZQ8 · STRUCTURE OF LINEAR GRAMICIDIN D OBTAINED USING TYPE I CRYSTALS GROWN IN A monovaccenin… · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 3ZQ8 · PDBe 3ZQ8

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