Research workbench

The capsid of myoviridae phage XM1

Analyse The capsid of myoviridae phage XM1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7KMX
Type: protein
Length: 3,178 residues
Chains: 14
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Minor capsid protein; Major capsid protein
Pockets: 20 · best druggability 0.70

Structure

electron microscopy · 2 distinct chains · 17% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
a, b, c, d, e, f, g	Minor capsid protein	protein	160	0% helix, 42% strand	—
A, B, C, D, E, F, G	Major capsid protein	protein	294	26% helix, 32% strand	—

Pockets

20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	419	0.70	0.81	41	empty
2	734	0.70	0.77	74	empty
3	599	0.69	0.78	72	empty
4	582	0.67	0.77	53	empty
5	315	0.66	0.81	41	empty

Interfaces

29 interfaces between chains.

A–B · 2464 Å² buried · 35 hydrogen bonds · protein-protein
E–F · 2439 Å² buried · 31 hydrogen bonds · protein-protein
D–E · 2429 Å² buried · 27 hydrogen bonds · protein-protein
C–D · 2422 Å² buried · 38 hydrogen bonds · protein-protein
A–F · 2410 Å² buried · 41 hydrogen bonds · protein-protein

Compared structures

7KMX · The capsid of Myoviridae Phage XM1 · 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 7KMX · PDBe 7KMX

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