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Crystal structure of the carboxy-terminal region of the bacteriophage T4 proximal long tail fibre protein GP34, residues 795 to 1289, at 1.9 ångström.

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PDB: 5NXF
Type: protein
Length: 1,483 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Long-tail fiber proximal subunit
UniProt: P18771
Ligands: URE, NA, PO4
Pockets: 8 · best druggability 0.83

Structure

x-ray diffraction · 2 distinct chains · 9% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Long-tail fiber proximal subunit	protein	495	9% helix, 43% strand	P18771
B, C	Long-tail fiber proximal subunit	protein	494	9% helix, 43% strand	P18771

Ligands and binding sites

URE · Urea · ligand · chains C
NA · Sodium ion · metal · chains A, C
PO4 · Phosphate ion · ion · 3 copies · chains A, B, C
GOL · Glycerol · additive · 17 copies · chains A, C, B
ACT · Acetate ion · additive · 2 copies · chains A, B, C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	169	0.83	0.98	33	empty
2	175	0.49	0.77	32	empty
3	154	0.44	0.76	30	GOL
4	101	0.44	0.79	25	empty
5	107	0.40	0.76	27	GOL

Interfaces

3 interfaces between chains.

A–C · 11344 Å² buried · 218 hydrogen bonds · protein-protein
B–C · 11302 Å² buried · 231 hydrogen bonds · protein-protein
A–B · 11294 Å² buried · 223 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 15 modified (engineered).

Compared structures

5NXF · Crystal structure of the carboxy-terminal region of the bacteriophage T4 proximal long… · the same entry in another collection · chain B against B, 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 P18771
Elsewhere: RCSB PDB 5NXF · PDBe 5NXF · UniProt P18771

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