Research workbench

Crystal structure of unliganded griffithsin

Analyse Crystal structure of unliganded griffithsin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2GTY
Type: protein
Length: 242 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Griffithsin
UniProt: P84801
Ligands: ACE, SO4
Pockets: 2 · best druggability 0.47

Structure

x-ray diffraction · 1 distinct chain · 0% helix, 64% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Griffithsin	protein	121	0% helix, 64% strand	P84801

Ligands and binding sites

ACE · Acetyl group · ligand · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 8 copies · chains A, B
EDO · 1,2-ethanediol · additive · 6 copies · chains A, B

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	131	0.47	0.78	27	EDO
2	132	0.47	0.78	29	SO4

Interfaces

1 interface between chains.

A–B · 2213 Å² buried · 59 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

2GTY · Crystal structure of unliganded griffithsin · 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
Every structure of UniProt P84801
Elsewhere: RCSB PDB 2GTY · PDBe 2GTY · UniProt P84801

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.