MolNFT v1 · #18083 · protein

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

1PDL · Tail-associated lysozyme: “Fitting of GP5 in the cryoem reconstruction of the bacteriophage T4 baseplate”. Electron microscopy, 8 pockets (best druggability 0.52). MolNFT v1 #18083 on GenesisL1: 3D structure, binding sites and…

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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