MolNFT v1 · #114243 · protein

Crystal structures of human peroxiredoxin 6 in sulfinic acid state

5B6N · Peroxiredoxin-6: “Crystal structures of human peroxiredoxin 6 in sulfinic acid state”. X-ray diffraction, 17 pockets (best druggability 0.73). MolNFT v1 #114243 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5B6N
Type: protein
Length: 1,316 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peroxiredoxin-6
EC: 1.11.1.15
UniProt: P30041
Pockets: 17 · best druggability 0.73

Structure

x-ray diffraction · 4 distinct chains · 24% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, E	Peroxiredoxin-6 (EC 1.11.1.15)	protein	221	26% helix, 26% strand	P30041
C	Peroxiredoxin-6 (EC 1.11.1.15)	protein	217	24% helix, 26% strand	P30041
D	Peroxiredoxin-6 (EC 1.11.1.15)	protein	213	22% helix, 19% strand	P30041
F	Peroxiredoxin-6 (EC 1.11.1.15)	protein	223	25% helix, 22% strand	P30041

Pockets

17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	334	0.73	0.85	59	empty
2	92	0.72	0.95	20	empty
3	438	0.65	0.78	48	empty
4	292	0.60	0.78	40	empty
5	275	0.58	0.78	47	empty

Interfaces

5 interfaces between chains.

A–B · 2519 Å² buried · 36 hydrogen bonds · protein-protein
E–F · 2419 Å² buried · 36 hydrogen bonds · protein-protein
C–D · 2339 Å² buried · 27 hydrogen bonds · protein-protein
B–C · 415 Å² buried · 2 hydrogen bonds · protein-protein
C–E · 23 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 modified (oxidation).

Compared structures

5B6N · Crystal structures of human peroxiredoxin 6 in sulfinic acid state · the same entry in another collection · chain B against B, TM-score 1.00
P30041 · AlphaFold monomer V2.0 prediction for peroxiredoxin-6 (P30041) · a predicted model of the same protein · chain A 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 P30041
Elsewhere: RCSB PDB 5B6N · PDBe 5B6N · UniProt P30041

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