MolNFT v1 · #128817 · protein + RNA

Structure of NRD1 RNA binding domain in complex with RNA (cguaaa)

5O1Z · Protein NRD1: “Structure of NRD1 RNA binding domain in complex with RNA (cguaaa)”. X-ray diffraction, 1 pocket (best druggability 0.34). MolNFT v1 #128817 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5O1Z
Type: protein + RNA
Length: 169 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein NRD1; RNA (5'-R(*CP*GP*UP*AP*AP*A)-3')
UniProt: P53617
Pockets: 1 · best druggability 0.34

Structure

x-ray diffraction · 2 distinct chains · 20% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein NRD1	protein	163	20% helix, 26% strand	P53617
B	RNA (5'-R(CPGPUPAPAPA)-3')	rna	6	—	—

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	54	0.34	0.78	15	empty

Interfaces

1 interface between chains.

A–B · 708 Å² buried · 9 hydrogen bonds · protein-nucleic

Compared structures

5O1Z · Structure of Nrd1 RNA binding domain in complex with RNA (CGUAAA) · 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 5O1Z · PDBe 5O1Z · UniProt P53617

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