MolNFT v1 · #125812 · protein

Single particle reconstruction of slow bee paralysis virus virion at pH 5.5

5LK7 · VP1: “Single particle reconstruction of slow bee paralysis virus virion at pH 5.5”. Electron microscopy, 9 pockets (best druggability 0.48). MolNFT v1 #125812 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5LK7
Type: protein
Length: 739 residues
Chains: 3
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: VP1; VP2; VP3
UniProt: A7LM73
Pockets: 9 · best druggability 0.48

Structure

electron microscopy · 3 distinct chains · 8% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	VP1	protein	233	9% helix, 32% strand	A7LM73
B	VP2	protein	252	8% helix, 38% strand	A7LM73
C	VP3	protein	254	7% helix, 33% strand	A7LM73

Pockets

9 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	127	0.48	0.79	32	empty
2	156	0.46	0.76	22	empty
3	85	0.46	0.81	25	empty
4	71	0.43	0.81	14	empty
5	134	0.43	0.76	28	empty

Interfaces

3 interfaces between chains.

A–C · 4204 Å² buried · 60 hydrogen bonds · protein-protein
B–C · 1411 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 1171 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

5LK7 · Single particle reconstruction of slow bee paralysis virus virion at pH 5.5 · 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 5LK7 · PDBe 5LK7 · UniProt A7LM73

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