MolNFT v1 · #28608 · protein

Variable small protein 1 of borrelia turicatae (vspa or VSP1)

1YJG · Surface protein vspa: “Variable small protein 1 of borrelia turicatae (vspa or VSP1)”. X-ray diffraction, 2 pockets (best druggability 0.70). MolNFT v1 #28608 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1YJG
Type: protein
Length: 626 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Surface protein vspa
UniProt: O34000
Pockets: 2 · best druggability 0.70

Structure

x-ray diffraction · 2 distinct chains · 71% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, E	Surface protein vspa	protein	157	71% helix, 5% strand	O34000
D	Surface protein vspa	protein	155	71% helix, 5% strand	O34000

Pockets

2 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	695	0.70	0.78	76	empty
2	155	0.62	0.84	27	empty

Interfaces

5 interfaces between chains.

A–B · 1959 Å² buried · 17 hydrogen bonds · protein-protein
D–E · 1939 Å² buried · 17 hydrogen bonds · protein-protein
B–D · 309 Å² buried · 1 hydrogen bond · protein-protein
B–E · 70 Å² buried · 1 hydrogen bond · protein-protein
A–D · 66 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

1YJG · Variable Small Protein 1 of Borrelia turicatae (VspA or Vsp1) · 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 O34000
Elsewhere: RCSB PDB 1YJG · PDBe 1YJG · UniProt O34000

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