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Atomic structure of bacteriophage SF6 tail needle knob

Analyse Atomic structure of bacteriophage SF6 tail needle knob in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3RWN
Type: protein
Length: 462 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Gene 9 protein
UniProt: Q716G6
Ligands: GLU, PO4
Pockets: 5 · best druggability 0.86

Structure

x-ray diffraction · 3 distinct chains · 13% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Gene 9 protein	protein	155	13% helix, 45% strand	Q716G6
B	Gene 9 protein	protein	154	13% helix, 45% strand	Q716G6
C	Gene 9 protein	protein	153	12% helix, 45% strand	Q716G6

Ligands and binding sites

GLU · Glutamic acid · ligand · 3 copies · chains A, C, B
PO4 · Phosphate ion · ion · 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, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	307	0.86	0.96	32	empty
2	620	0.81	0.86	44	empty
3	87	0.62	0.89	22	GLU
4	80	0.59	0.88	19	GLU
5	91	0.59	0.87	20	GLU

Interfaces

3 interfaces between chains.

A–B · 1219 Å² buried · 24 hydrogen bonds · protein-protein
B–C · 1190 Å² buried · 25 hydrogen bonds · protein-protein
A–C · 1189 Å² buried · 26 hydrogen bonds · protein-protein

Compared structures

3RWN · Atomic structure of bacteriophage sf6 tail needle knob · 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 Q716G6
Elsewhere: RCSB PDB 3RWN · PDBe 3RWN · UniProt Q716G6

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