MolNFT v1 · #103707 · protein

Crystal structures of thioredoxin with mesna at 1.85A resolution

4POM: “Crystal structures of thioredoxin with mesna at 1.85A resolution”. X-ray diffraction, 1 ligand (COM), 4 pockets (best druggability 0.68). MolNFT v1 #103707 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4POM
Type: protein
Length: 428 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 0.68

Structure

x-ray diffraction · 1 distinct chain · 40% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Thioredoxin	protein	107	40% helix, 28% strand	P10599

Ligands and binding sites

COM · 1-thioethanesulfonic acid · ligand · 2 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	670	0.68	0.77	65	empty
2	109	0.43	0.77	21	empty
3	70	0.37	0.77	15	empty
4	52	0.29	0.76	16	empty

Interfaces

5 interfaces between chains.

C–D · 819 Å² buried · 13 hydrogen bonds · protein-protein
A–C · 429 Å² buried · 5 hydrogen bonds · protein-protein
B–D · 428 Å² buried · 5 hydrogen bonds · protein-protein
A–D · 240 Å² buried · 4 hydrogen bonds · protein-protein
B–C · 232 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 2 covalent (disulfide, covalent ligand).

Compared structures

4POM · Crystal structures of thioredoxin with mesna at 1.85A 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 0.97

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 4POM · PDBe 4POM · UniProt P10599

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