MolNFT v1 · #104854 · protein

The crystal structure of an effector protein vipe from legionella pneumophila subsp. pneumophila str. philadelphia 1

4QN8: “The crystal structure of an effector protein vipe from legionella pneumophila subsp. pneumophila str.…”. X-ray diffraction, 5 pockets (best druggability 0.67). MolNFT v1 #104854 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 4QN8
Type: protein
Length: 455 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Vipe
UniProt: Q5ZRR7
Pockets: 5 · best druggability 0.67

Structure

x-ray diffraction · 2 distinct chains · 65% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Vipe	protein	153	64% helix, 1% strand	Q5ZRR7
C	Vipe	protein	149	66% helix, 1% strand	Q5ZRR7

Ligands and binding sites

BME · Beta-mercaptoethanol · additive · 4 copies · chains A, B, C

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

Pockets

5 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	464	0.67	0.79	55	empty
2	125	0.52	0.81	26	empty
3	84	0.42	0.79	25	empty
4	88	0.40	0.78	24	empty
5	64	0.37	0.79	24	empty

Interfaces

3 interfaces between chains.

A–C · 794 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 767 Å² buried · 12 hydrogen bonds · protein-protein
B–C · 138 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 15 modified (engineered).

Compared structures

4QN8 · The crystal structure of an effector protein VipE from Legionella pneumophila subsp.… · 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 Q5ZRR7
Elsewhere: RCSB PDB 4QN8 · PDBe 4QN8 · UniProt Q5ZRR7

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