Research workbench

Caulobacter bacteriophage 5 - virus-like particle

Analyse Caulobacter bacteriophage 5 - virus-like particle in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2W4Y
Type: protein
Length: 366 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Caulobacter 5 virus-like particle
Ligands: AMP, CA
Pockets: 5 · best druggability 0.73

Structure

x-ray diffraction · 1 distinct chain · 18% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Caulobacter 5 virus-like particle	protein	122	18% helix, 49% strand	—

Ligands and binding sites

AMP · Adenosine monophosphate · ligand · 3 copies · chains A, C, B
CA · Calcium ion · metal · 4 copies · 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1065	0.73	0.76	111	AMP
2	391	0.58	0.75	46	AMP
3	63	0.31	0.75	13	empty
4	61	0.30	0.75	13	empty
5	55	0.27	0.73	12	empty

Interfaces

3 interfaces between chains.

A–C · 420 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 410 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 308 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

2W4Y · Caulobacter bacteriophage 5 - virus-like particle · 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
Elsewhere: RCSB PDB 2W4Y · PDBe 2W4Y

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.