Research workbench

Fitting of GP5 in the cryoem reconstruction of the bacteriophage T4 baseplate

Analyse Fitting of GP5 in the cryoem reconstruction of the bacteriophage T4 baseplate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1PDL
Type: protein
Length: 1,662 residues
Chains: 3
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tail-associated lysozyme
EC: 3.2.1.17
UniProt: P16009
Pockets: 8 · best druggability 0.52

Structure

electron microscopy · 1 distinct chain · 0% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Tail-associated lysozyme (EC 3.2.1.17)	protein	554	0% helix, 0% strand	P16009

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	224	0.52	0.74	49	empty
2	177	0.46	0.73	40	empty
3	129	0.41	0.73	33	empty
4	92	0.35	0.72	27	empty
5	79	0.33	0.73	30	empty

Interfaces

3 interfaces between chains.

A–B · 2941 Å² buried · 0 hydrogen bonds · protein-protein
B–C · 2939 Å² buried · 0 hydrogen bonds · protein-protein
A–C · 2935 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

1PDL · Fitting of gp5 in the cryoEM reconstruction of the bacteriophage T4 baseplate · 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 P16009
Elsewhere: RCSB PDB 1PDL · PDBe 1PDL · UniProt P16009

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