MolNFT v1 · #55125 · protein

Crystal structure of the second glutaredoxin domain of human TXNL2

2YAN · Glutaredoxin-3: “Crystal structure of the second glutaredoxin domain of human TXNL2”. X-ray diffraction, 4 ligands (GSH, FE, SO4), 2 pockets (best druggability 0.48). MolNFT v1 #55125 on GenesisL1: 3D structure, binding sites and…

PDB: 2YAN
Type: protein
Length: 210 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glutaredoxin-3
UniProt: O76003
Ligands: GSH, FE, SO4, CL
Pockets: 2 · best druggability 0.48

Structure

x-ray diffraction · 1 distinct chain · 49% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Glutaredoxin-3	protein	105	49% helix, 18% strand	O76003

Ligands and binding sites

GSH · Glutathione · ligand · 2 copies · chains A, B
FE · Fe (III) ion · metal · chains A
SO4 · Sulfate ion · ion · chains A
CL · Chloride ion · ion · chains A
EDO · 1,2-ethanediol · additive · 7 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	146	0.48	0.78	17	EDO
2	61	0.46	0.84	15	empty

Interfaces

1 interface between chains.

A–B · 671 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

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

Compared structures

2YAN · Crystal structure of the second glutaredoxin domain of human TXNL2 · the same entry in another collection · chain A against A, TM-score 1.00
O76003 · AlphaFold monomer V2.0 prediction for glutaredoxin-3 (O76003) · a predicted model of the same protein · chain A against A, TM-score 0.94

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 O76003
Elsewhere: RCSB PDB 2YAN · PDBe 2YAN · UniProt O76003

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