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Crystal structure of an archaeal peroxiredoxin from the aerobic hyperthermophilic crenarchaeon aeropyrum pernix K1

Analyse Crystal structure of an archaeal peroxiredoxin from the aerobic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2CV4
Type: protein
Length: 2,408 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peroxiredoxin
UniProt: Q9Y9L0
Pockets: 20 · best druggability 0.58

Structure

x-ray diffraction · 3 distinct chains · 33% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, I	Peroxiredoxin	protein	241	32% helix, 24% strand	Q9Y9L0
D, G	Peroxiredoxin	protein	242	33% helix, 24% strand	Q9Y9L0
E, F, H, J	Peroxiredoxin	protein	240	34% helix, 25% strand	Q9Y9L0

Ligands and binding sites

IPA · Isopropyl alcohol · additive · 9 copies · chains A, B, C, D, E, F, G, H, I, J
MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, F

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

Pockets

20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	344	0.58	0.76	45	empty
2	327	0.57	0.76	45	empty
3	328	0.57	0.76	32	empty
4	303	0.56	0.76	38	empty
5	283	0.56	0.77	37	empty

Interfaces

20 interfaces between chains.

C–D · 3530 Å² buried · 54 hydrogen bonds · protein-protein
A–B · 3498 Å² buried · 54 hydrogen bonds · protein-protein
I–J · 3485 Å² buried · 54 hydrogen bonds · protein-protein
G–H · 3467 Å² buried · 55 hydrogen bonds · protein-protein
E–F · 3343 Å² buried · 52 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 50 modified, 10 disulfide (engineered, disulfide, oxidation).

Compared structures

2CV4 · Crystal Structure of an Archaeal Peroxiredoxin from the Aerobic Hyperthermophilic… · 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 D 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 2CV4 · PDBe 2CV4 · UniProt Q9Y9L0

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