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Structure of linear gramicidin D obtained using type I crystals grown in a 7.7 monoacylglycerol lipid cubic phase.

Analyse Structure of linear gramicidin D obtained using type I crystals grown in a 7.7… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2Y5M
Type: protein
Length: 90 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Val-gramicidin a
Ligands: ETA
Pockets: 1 · best druggability 0.60

Structure

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

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

Ligands and binding sites

ETA · Ethanolamine · ligand · 6 copies · chains A, B, C, D, E, F
15P · Polyethylene glycol (N=34) · additive · 3 copies · chains A, B, C, D, E, F

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

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	345	0.60	0.76	32	15P

Interfaces

12 interfaces between chains.

A–B · 1113 Å² buried · 32 hydrogen bonds · protein-protein
E–F · 1066 Å² buried · 31 hydrogen bonds · protein-protein
C–D · 1064 Å² buried · 31 hydrogen bonds · protein-protein
A–E · 154 Å² buried · 0 hydrogen bonds · protein-protein
B–F · 109 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 36 d-amino, 6 covalent, 6 modified (D-amino acid, covalent ligand, nonstandard).

Compared structures

2Y5M · Structure of linear gramicidin D obtained using type I crystals grown in a 7.7… · 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 2Y5M · PDBe 2Y5M

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