MolNFT v1 · #120044 · protein

Crystal structure of lapb from legionella pneumophila

5GNE · Leucine aminopeptidase: “Crystal structure of lapb from legionella pneumophila”. X-ray diffraction, 2 ligands (ZN, SO4), 9 pockets (best druggability 0.69). MolNFT v1 #120044 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 5GNE
Type: protein
Length: 732 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Leucine aminopeptidase
UniProt: Q5ZZH8
Ligands: ZN, SO4
Pockets: 9 · best druggability 0.69

Structure

x-ray diffraction · 1 distinct chain · 42% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Leucine aminopeptidase	protein	366	42% helix, 19% strand	Q5ZZH8

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains A, B
SO4 · Sulfate ion · ion · 2 copies · chains A, B

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

Pockets

9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	265	0.69	0.85	29	ZN
2	470	0.67	0.79	29	empty
3	212	0.65	0.84	28	ZN
4	260	0.56	0.78	26	empty
5	219	0.50	0.76	24	empty

Interfaces

1 interface between chains.

A–B · 810 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

5GNE · Crystal structure of LapB 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 Q5ZZH8
Elsewhere: RCSB PDB 5GNE · PDBe 5GNE · UniProt Q5ZZH8

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