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Crystal structure of nucleoside 2-deoxyribosyltransferase

Analyse Crystal structure of nucleoside 2-deoxyribosyltransferase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1F8X
Type: protein
Length: 312 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.5
Source: Lactobacillus leichmannii
Molecule: Nucleoside 2-deoxyribosyltransferase
EC: 2.4.2.6
UniProt: Q9R5V5
Pockets: 3 · best druggability 0.75

Structure

x-ray diffraction · resolution 2.5 · 1 distinct chain · 44% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Nucleoside 2-deoxyribosyltransferase (EC 2.4.2.6)	protein	156	44% helix, 16% strand	Q9R5V5

Pockets

3 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	108	0.75	0.95	30	empty
2	69	0.73	0.98	23	empty
3	67	0.29	0.73	20	empty

Interfaces

1 interface between chains.

A–B · 1621 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

1F8X · Crystal structure of nucleoside 2-deoxyribosyltransferase · the same entry in another collection · chain A against A, TM-score 1.00
Q9R5V5 · AlphaFold monomer V2.0 prediction for nucleoside deoxyribosyltransferase (Q9R5V5) · 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 Q9R5V5
Elsewhere: RCSB PDB 1F8X · PDBe 1F8X · UniProt Q9R5V5

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