Research workbench

Crystal structure of heamophilus influenza hybrid-PRX5

Analyse Crystal structure of heamophilus influenza hybrid-PRX5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1NM3
Type: protein
Length: 476 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein HI0572
UniProt: P44758
Ligands: SO4
Pockets: 7 · best druggability 0.62

Structure

x-ray diffraction · 2 distinct chains · 30% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein HI0572	protein	237	31% helix, 28% strand	P44758
B	Protein HI0572	protein	239	29% helix, 28% strand	P44758

Ligands and binding sites

SO4 · Sulfate ion · ion · 4 copies · chains A, B

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

Pockets

7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	180	0.62	0.84	27	empty
2	87	0.52	0.83	20	empty
3	96	0.41	0.77	22	empty
4	89	0.39	0.77	17	empty
5	102	0.39	0.76	19	empty

Interfaces

1 interface between chains.

A–B · 848 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 14 modified, 2 disulfide (engineered, disulfide).

Compared structures

1NM3 · Crystal structure of Heamophilus influenza hybrid-Prx5 · the same entry in another collection · chain A against A, TM-score 1.00
P44758 · AlphaFold monomer V2.0 prediction for hybrid peroxiredoxin HYPRX5 (P44758) · a predicted model of the same protein · chain B against A, TM-score 0.93

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 P44758
Elsewhere: RCSB PDB 1NM3 · PDBe 1NM3 · UniProt P44758

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.