MolNFT v1 · #78518 · protein

Crystal structure of saccharomyces cerevisiae TSA1C47S mutant protein

3SBC · Peroxiredoxin TSA1: “Crystal structure of saccharomyces cerevisiae TSA1C47S mutant protein”. X-ray diffraction, 1 ligand (DTV), 20 pockets (best druggability 0.59). MolNFT v1 #78518 on GenesisL1: 3D structure, binding sites and…

PDB: 3SBC
Type: protein
Length: 1,951 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peroxiredoxin TSA1
EC: 1.11.1.15
UniProt: P34760
Ligands: DTV
Pockets: 20 · best druggability 0.59

Structure

x-ray diffraction · 4 distinct chains · 32% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E, G, H, I, J	Peroxiredoxin TSA1 (EC 1.11.1.15)	protein	195	33% helix, 25% strand	P34760
B	Peroxiredoxin TSA1 (EC 1.11.1.15)	protein	197	32% helix, 26% strand	P34760
C	Peroxiredoxin TSA1 (EC 1.11.1.15)	protein	196	33% helix, 24% strand	P34760
D, F	Peroxiredoxin TSA1 (EC 1.11.1.15)	protein	194	32% helix, 23% strand	P34760

Ligands and binding sites

DTV · (2S,3S)-1,4-dimercaptobutane-2,3-diol · ligand · chains B, C, D
DTU · (2R,3S)-1,4-dimercaptobutane-2,3-diol · additive · 5 copies · chains A, B, C, D, E, F, G, H, I, J

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

Pockets

20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	135	0.59	0.84	32	empty
2	159	0.59	0.82	32	empty
3	151	0.58	0.83	18	empty
4	134	0.58	0.83	26	empty
5	122	0.58	0.84	20	empty

Interfaces

20 interfaces between chains.

A–B · 2209 Å² buried · 40 hydrogen bonds · protein-protein
E–F · 2151 Å² buried · 38 hydrogen bonds · protein-protein
C–D · 2143 Å² buried · 33 hydrogen bonds · protein-protein
G–H · 2124 Å² buried · 40 hydrogen bonds · protein-protein
I–J · 2086 Å² buried · 34 hydrogen bonds · protein-protein

Compared structures

3SBC · Crystal structure of Saccharomyces cerevisiae TSA1C47S mutant protein · the same entry in another collection · chain J against J, TM-score 1.00
P34760 · AlphaFold monomer V2.0 prediction for peroxiredoxin TSA1 (P34760) · a predicted model of the same protein · chain D against A, TM-score 0.99

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 P34760
Elsewhere: RCSB PDB 3SBC · PDBe 3SBC · UniProt P34760

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