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Structure of NRD1 RNA binding domain

Analyse Structure of NRD1 RNA binding domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5O1X
Type: protein
Length: 162 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein NRD1
UniProt: P53617
Ligands: SCN
Pockets: 2 · best druggability 0.42

Structure

x-ray diffraction · 1 distinct chain · 22% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein NRD1	protein	162	22% helix, 26% strand	P53617

Ligands and binding sites

SCN · Thiocyanate ion · ion · 8 copies · chains A
EDO · 1,2-ethanediol · additive · 7 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, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	86	0.42	0.79	19	empty
2	51	0.27	0.75	16	empty

Compared structures

5O1X · Structure of Nrd1 RNA binding domain · the same entry in another collection · chain A against A, TM-score 1.00
P53617 · AlphaFold monomer V2.0 prediction for protein NRD1 (P53617) · 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 P53617
Elsewhere: RCSB PDB 5O1X · PDBe 5O1X · UniProt P53617

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