MolNFT v1 · #114242 · protein

Crystal structure of human peroxiredoxin 6 in reduced state

5B6M · Peroxiredoxin-6: “Crystal structure of human peroxiredoxin 6 in reduced state”. X-ray diffraction, 20 pockets (best druggability 0.76). MolNFT v1 #114242 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5B6M
Type: protein
Length: 1,311 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: 20 · best druggability 0.76

Structure

x-ray diffraction · 4 distinct chains · 27% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, E	Peroxiredoxin-6 (EC 1.11.1.15)	protein	221	29% helix, 27% strand	P30041
C	Peroxiredoxin-6 (EC 1.11.1.15)	protein	214	28% helix, 26% strand	P30041
D	Peroxiredoxin-6 (EC 1.11.1.15)	protein	211	23% helix, 20% strand	P30041
F	Peroxiredoxin-6 (EC 1.11.1.15)	protein	223	29% helix, 25% strand	P30041

Pockets

20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	106	0.76	0.96	24	empty
2	90	0.72	0.95	24	empty
3	137	0.70	0.90	28	empty
4	250	0.67	0.83	30	empty
5	432	0.64	0.77	40	empty

Interfaces

5 interfaces between chains.

A–B · 2448 Å² buried · 34 hydrogen bonds · protein-protein
E–F · 2443 Å² buried · 37 hydrogen bonds · protein-protein
C–D · 2232 Å² buried · 31 hydrogen bonds · protein-protein
B–C · 394 Å² buried · 6 hydrogen bonds · protein-protein
C–E · 26 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5B6M · Crystal structure of human peroxiredoxin 6 in reduced state · the same entry in another collection · chain F against F, TM-score 1.00
P30041 · AlphaFold monomer V2.0 prediction for peroxiredoxin-6 (P30041) · a predicted model of the same protein · chain F 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 5B6M · PDBe 5B6M · UniProt P30041

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