MolNFT v1 · #128101 · protein

Crystal structure of PB6, major tail tube protein of bacteriophage T5

5NGJ: “Crystal structure of PB6, major tail tube protein of bacteriophage T5”. X-ray diffraction, 1 ligand (CL), 13 pockets (best druggability 0.59). MolNFT v1 #128101 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5NGJ
Type: protein
Length: 872 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tail tube protein
UniProt: Q6QGE2
Ligands: CL
Pockets: 13 · best druggability 0.59

Structure

x-ray diffraction · 2 distinct chains · 11% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tail tube protein	protein	440	11% helix, 44% strand	Q6QGE2
B	Tail tube protein	protein	432	12% helix, 40% strand	Q6QGE2

Ligands and binding sites

CL · Chloride ion · ion · 5 copies · chains A

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

Pockets

13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	231	0.59	0.80	27	empty
2	226	0.58	0.79	28	empty
3	343	0.54	0.74	43	empty
4	115	0.46	0.79	20	empty
5	124	0.45	0.78	22	empty

Interfaces

1 interface between chains.

A–B · 852 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

5NGJ · Crystal structure of pb6, major tail tube protein of bacteriophage T5 · 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 Q6QGE2
Elsewhere: RCSB PDB 5NGJ · PDBe 5NGJ · UniProt Q6QGE2

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