MolNFT v1 · #117540 · protein

VB6-bound protein

5EB3 · Yfir: “VB6-bound protein”. X-ray diffraction, 2 ligands (UEG, SO4), 6 pockets (best druggability 0.44). MolNFT v1 #117540 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5EB3
Type: protein
Length: 301 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Yfir
UniProt: Q9I4L4
Ligands: UEG, SO4
Pockets: 6 · best druggability 0.44

Structure

x-ray diffraction · 2 distinct chains · 33% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Yfir	protein	153	34% helix, 24% strand	Q9I4L4
B	Yfir	protein	148	32% helix, 25% strand	Q9I4L4

Ligands and binding sites

UEG · 4,5-bis(hydroxymethyl)-2-methyl-pyridin-3-ol · ligand · chains A
SO4 · Sulfate ion · ion · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

6 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	59	0.44	0.83	14	empty
2	105	0.44	0.78	18	empty
3	75	0.41	0.79	16	empty
4	102	0.39	0.76	22	empty
5	115	0.39	0.75	20	empty

Interfaces

1 interface between chains.

A–B · 760 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

5EB3 · VB6-bound protein · 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 Q9I4L4
Elsewhere: RCSB PDB 5EB3 · PDBe 5EB3 · UniProt Q9I4L4

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