MolNFT v1 · #119660 · protein

Crystallographic structure of mutant D60S of thioredoxin from litopenaeus vannamei

5G30: “Crystallographic structure of mutant D60S of thioredoxin from litopenaeus vannamei”. X-ray diffraction, 1 pocket (best druggability 0.78). MolNFT v1 #119660 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5G30
Type: protein
Length: 420 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thioredoxin
EC: 1.8.1.9
UniProt: B1PWB9
Pockets: 1 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Thioredoxin (EC 1.8.1.9)	protein	105	41% helix, 27% strand	B1PWB9

Ligands and binding sites

ACT · Acetate ion · additive · 3 copies · chains C, A, D
PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains C, D

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	1017	0.78	0.80	95	PEG

Interfaces

5 interfaces between chains.

B–C · 627 Å² buried · 9 hydrogen bonds · protein-protein
A–D · 617 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 286 Å² buried · 7 hydrogen bonds · protein-protein
C–D · 261 Å² buried · 3 hydrogen bonds · protein-protein
B–D · 44 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

5G30 · Crystallographic structure of mutant D60S of thioredoxin from Litopenaeus vannamei · 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 B1PWB9
Elsewhere: RCSB PDB 5G30 · PDBe 5G30 · UniProt B1PWB9

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