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Crystal structure of LPG0406 in reduced form from legionella pneumophila

Analyse Crystal structure of LPG0406 in reduced form from legionella pneumophila in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5DIP
Type: protein
Length: 224 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Alkyl hydroperoxide reductase ahpd
EC: 1.11.1.15
UniProt: A0A0C9P2U2
Ligands: NA
Pockets: 2 · best druggability 0.44

Structure

x-ray diffraction · 1 distinct chain · 81% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Alkyl hydroperoxide reductase ahpd (EC 1.11.1.15)	protein	112	81% helix, 0% strand	A0A0C9P2U2

Ligands and binding sites

NA · Sodium ion · metal · 3 copies · chains A, B
GOL · Glycerol · additive · chains B

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	194	0.44	0.73	21	NA
2	131	0.36	0.72	20	NA

Interfaces

1 interface between chains.

A–B · 1383 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

5DIP · Crystal structure of lpg0406 in reduced form from Legionella pneumophila · 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 A0A0C9P2U2
Elsewhere: RCSB PDB 5DIP · PDBe 5DIP · UniProt A0A0C9P2U2

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