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Crystal structures of thioredoxin with mesna at 2.8A resolution

Analyse Crystal structures of thioredoxin with mesna at 2.8A resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4POL
Type: protein
Length: 424 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thioredoxin
UniProt: P10599
Ligands: COM
Pockets: 4 · best druggability 0.69

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Thioredoxin	protein	106	39% helix, 30% strand	P10599

Ligands and binding sites

COM · 1-thioethanesulfonic acid · ligand · 4 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	726	0.69	0.76	77	empty
2	111	0.41	0.76	23	empty
3	90	0.39	0.77	19	empty
4	91	0.33	0.74	17	empty

Interfaces

5 interfaces between chains.

C–D · 880 Å² buried · 15 hydrogen bonds · protein-protein
A–C · 436 Å² buried · 5 hydrogen bonds · protein-protein
B–D · 427 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 218 Å² buried · 3 hydrogen bonds · protein-protein
A–D · 216 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 4 covalent (disulfide, covalent ligand).

Compared structures

4POL · Crystal structures of thioredoxin with mesna at 2.8A resolution · the same entry in another collection · chain A against A, TM-score 1.00
P10599 · AlphaFold monomer V2.0 prediction for thioredoxin (P10599) · a predicted model of the same protein · chain A against A, TM-score 0.96

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 P10599
Elsewhere: RCSB PDB 4POL · PDBe 4POL · UniProt P10599

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