MolNFT v1 · #174847 · protein

Peroxiredoxin from aeropyrum pernix K1 (apprx) C50S/F80C/C207S/C213S mutant modified with 2-(BROMOACETYL)NAPHTHALENE(NAPH@APPRX*)

7C8A: “Peroxiredoxin from aeropyrum pernix K1 (apprx) C50S/F80C/C207S/C213S mutant modified with…”. X-ray diffraction, 1 ligand (FL3), 20 pockets (best druggability 0.61). MolNFT v1 #174847 on GenesisL1: 3D structure, binding sites and…

PDB: 7C8A
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
Ligands: FL3
Pockets: 20 · best druggability 0.61

Structure

x-ray diffraction · 1 distinct chain · 34% 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	34% helix, 24% strand	Q9Y9L0

Ligands and binding sites

FL3 · 1-naphthalen-2-ylethanone · ligand · 10 copies · chains A, F, B, C, D, J, E, H, G, I
CIT · Citric acid · additive · 10 copies · chains A, B, C, D, E, F, G, H, I, 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, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	369	0.61	0.77	44	CIT, FL3
2	394	0.61	0.77	42	CIT, FL3
3	387	0.61	0.77	44	CIT, FL3
4	373	0.61	0.77	43	FL3, CIT
5	348	0.61	0.78	41	CIT, FL3

Interfaces

20 interfaces between chains.

I–J · 3589 Å² buried · 59 hydrogen bonds · protein-protein
G–H · 3587 Å² buried · 64 hydrogen bonds · protein-protein
E–F · 3580 Å² buried · 55 hydrogen bonds · protein-protein
C–D · 3535 Å² buried · 60 hydrogen bonds · protein-protein
A–B · 3534 Å² buried · 56 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 covalent (covalent ligand).

Compared structures

7C8A · Peroxiredoxin from Aeropyrum pernix K1 (ApPrx) C50S/F80C/C207S/C213S mutant modified with… · the same entry in another collection · 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 7C8A · PDBe 7C8A · UniProt Q9Y9L0

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