MolNFT v1 · #25795 · protein

Gramicidin D from bacillus brevis (ethanol solvate)

1W5U: “Gramicidin D from bacillus brevis (ethanol solvate)”. X-ray diffraction, 3 ligands (ETA, RB, CL). MolNFT v1 #25795 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1W5U
Type: protein
Length: 60 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Gramicidin D
Ligands: ETA, RB, CL

Structure

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

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

Ligands and binding sites

ETA · Ethanolamine · ligand · 4 copies · chains A, B, C, D
RB · Rubidium ion · metal · 14 copies · chains A, B, C, D
CL · Chloride ion · ion · 6 copies · chains A, B, D, C
EOH · Ethanol · additive · chains C

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

Interfaces

6 interfaces between chains.

C–D · 1198 Å² buried · 32 hydrogen bonds · protein-protein
A–B · 1197 Å² buried · 32 hydrogen bonds · protein-protein
B–D · 190 Å² buried · 0 hydrogen bonds · protein-protein
A–C · 170 Å² buried · 0 hydrogen bonds · protein-protein
A–D · 136 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

1W5U · Gramicidin D from bacillus brevis (ethanol solvate) · 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 1W5U · PDBe 1W5U

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