MolNFT v1 · #49933 · protein

Crystal structure of a ribokinase-like superfamily protein (EF1790) from enterococcus faecalis V583 at 1.95 a resolution

2R3E · Yjef-related protein: “Crystal structure of a ribokinase-like superfamily protein (EF1790) from enterococcus faecalis V583 at 1.95 a…”. X-ray diffraction, 2 pockets (best druggability 0.51). MolNFT v1 #49933 on GenesisL1: 3D…

PDB: 2R3E
Type: protein
Length: 276 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Yjef-related protein
UniProt: Q833Y3
Pockets: 2 · best druggability 0.51

Structure

x-ray diffraction · 1 distinct chain · 51% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Yjef-related protein	protein	276	51% helix, 15% strand	Q833Y3

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 2 copies · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	215	0.51	0.76	35	empty
2	51	0.26	0.74	14	empty

Modifications

Observed in the structure: 7 modified (engineered).

Compared structures

2R3E · CRYSTAL STRUCTURE OF a ribokinase-like superfamily protein (EF1790) FROM ENTEROCOCCUS… · the same entry in another collection · chain A against A, TM-score 1.00
Q833Y3 · AlphaFold monomer V2.0 prediction for ADP-dependent (S)-NAD(P)H-hydrate dehydratase… · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q833Y3
Elsewhere: RCSB PDB 2R3E · PDBe 2R3E · UniProt Q833Y3

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