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Human peroxiredoxin-1 C83S mutant

Analyse Human peroxiredoxin-1 C83S mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4XCS
Type: protein
Length: 1,066 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peroxiredoxin-1
EC: 1.11.1.15
UniProt: Q06830
Ligands: CPS
Pockets: 9 · best druggability 0.84

Structure

x-ray diffraction · 3 distinct chains · 29% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, F	Peroxiredoxin-1 (EC 1.11.1.15)	protein	179	30% helix, 23% strand	Q06830
B, D	Peroxiredoxin-1 (EC 1.11.1.15)	protein	176	29% helix, 27% strand	Q06830
E	Peroxiredoxin-1 (EC 1.11.1.15)	protein	177	28% helix, 25% strand	Q06830

Ligands and binding sites

CPS · 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate · ligand · 3 copies · chains A, B, C, D, E, F
GOL · Glycerol · additive · 3 copies · chains A, C, F

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

Pockets

9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1051	0.84	0.85	114	GOL
2	324	0.73	0.85	37	GOL
3	338	0.72	0.85	36	GOL
4	634	0.67	0.76	79	empty
5	64	0.61	0.91	19	empty

Interfaces

9 interfaces between chains.

C–D · 1575 Å² buried · 24 hydrogen bonds · protein-protein
E–F · 1567 Å² buried · 25 hydrogen bonds · protein-protein
A–B · 1552 Å² buried · 25 hydrogen bonds · protein-protein
C–E · 637 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 381 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

4XCS · Human peroxiredoxin-1 C83S mutant · the same entry in another collection · chain F against F, TM-score 1.00
Q06830 · AlphaFold monomer V2.0 prediction for peroxiredoxin-1 (Q06830) · a predicted model of the same protein · chain E against A, TM-score 0.95

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 Q06830
Elsewhere: RCSB PDB 4XCS · PDBe 4XCS · UniProt Q06830

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