MolNFT v1 · #125813 · protein

Single particle reconstruction of slow bee paralysis virus empty particle

5LK8 · VP1: “Single particle reconstruction of slow bee paralysis virus empty particle”. Electron microscopy, 10 pockets (best druggability 0.52). MolNFT v1 #125813 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5LK8
Type: protein
Length: 693 residues
Chains: 3
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: VP1; VP2; VP3
UniProt: A7LM73
Pockets: 10 · best druggability 0.52

Structure

electron microscopy · 3 distinct chains · 10% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	VP1	protein	223	10% helix, 30% strand	A7LM73
B	VP2	protein	215	12% helix, 32% strand	A7LM73
C	VP3	protein	255	8% helix, 27% strand	A7LM73

Pockets

10 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	95	0.52	0.83	18	empty
2	214	0.52	0.77	32	empty
3	118	0.45	0.77	19	empty
4	58	0.43	0.83	14	empty
5	71	0.39	0.79	22	empty

Interfaces

3 interfaces between chains.

A–C · 3670 Å² buried · 51 hydrogen bonds · protein-protein
B–C · 1221 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 886 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

5LK8 · single particle reconstruction of slow bee paralysis virus empty 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
Every structure of UniProt A7LM73
Elsewhere: RCSB PDB 5LK8 · PDBe 5LK8 · UniProt A7LM73

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