MolNFT v1 · #154946 · protein

Peroxiredoxin from aeropyrum pernix K1 (apprx) 0CYS F46A mutant

6KRM: “Peroxiredoxin from aeropyrum pernix K1 (apprx) 0CYS F46A mutant”. X-ray diffraction, 20 pockets (best druggability 0.66). MolNFT v1 #154946 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6KRM
Type: protein
Length: 2,440 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peroxiredoxin
EC: 1.11.1.15
UniProt: Q9Y9L0
Pockets: 20 · best druggability 0.66

Structure

x-ray diffraction · 1 distinct chain · 35% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I, J	Peroxiredoxin (EC 1.11.1.15)	protein	244	35% helix, 24% strand	Q9Y9L0

Ligands and binding sites

CIT · Citric acid · additive · 10 copies · chains A, B, I, D, C, E, F, H, G, 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	234	0.66	0.83	25	empty
2	181	0.65	0.85	25	empty
3	171	0.60	0.83	28	empty
4	141	0.58	0.84	24	empty
5	315	0.57	0.76	39	CIT

Interfaces

20 interfaces between chains.

A–B · 3672 Å² buried · 58 hydrogen bonds · protein-protein
G–H · 3619 Å² buried · 53 hydrogen bonds · protein-protein
E–F · 3615 Å² buried · 54 hydrogen bonds · protein-protein
C–D · 3605 Å² buried · 55 hydrogen bonds · protein-protein
I–J · 3564 Å² buried · 55 hydrogen bonds · protein-protein

Compared structures

6KRM · Peroxiredoxin from Aeropyrum pernix K1 (ApPrx) 0Cys F46A mutant · the same entry in another collection · chain J against J, TM-score 1.00
Q9Y9L0 · AlphaFold monomer V2.0 prediction for peroxiredoxin (Q9Y9L0) · a predicted model of the same protein · chain A against A, TM-score 1.00

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 6KRM · PDBe 6KRM · UniProt Q9Y9L0

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