MolNFT v2 · #140172 · protein

Peroxiredoxin from Aeropyrum pernix (6m mutant)

5XBS: “Peroxiredoxin from Aeropyrum pernix (6m mutant)”. X-ray diffraction at 2.51, 13 pockets (best druggability 0.77). MolNFT v2 #140172 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5XBS
Type: protein
Length: 963 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.51
Source: Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)
Molecule: Peroxiredoxin
EC: 1.11.1.15
UniProt: Q9Y9L0
Pockets: 13 · best druggability 0.77

Structure

x-ray diffraction · resolution 2.51 · 4 distinct chains · 36% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Peroxiredoxin (EC 1.11.1.15)	protein	246	33% helix, 24% strand	Q9Y9L0
B	Peroxiredoxin (EC 1.11.1.15)	protein	240	37% helix, 24% strand	Q9Y9L0
C	Peroxiredoxin (EC 1.11.1.15)	protein	241	37% helix, 22% strand	Q9Y9L0
D	Peroxiredoxin (EC 1.11.1.15)	protein	236	35% helix, 23% strand	Q9Y9L0

Pockets

13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	675	0.77	0.82	60	empty
2	110	0.56	0.84	27	empty
3	90	0.52	0.84	27	empty
4	60	0.48	0.85	17	empty
5	119	0.47	0.79	17	empty

Interfaces

3 interfaces between chains.

A–B · 3392 Å² buried · 51 hydrogen bonds · protein-protein
C–D · 3254 Å² buried · 42 hydrogen bonds · protein-protein
B–D · 754 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

5XBS · Peroxiredoxin from aeropyrum pernix (6M mutant) · the same entry in another collection · chain D against D, TM-score 1.00
Q9Y9L0 · AlphaFold monomer V2.0 prediction for peroxiredoxin (Q9Y9L0) · 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 Q9Y9L0
Elsewhere: RCSB PDB 5XBS · PDBe 5XBS · UniProt Q9Y9L0

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