MolNFT v1 · #128816 · protein + RNA
Structure of NRD1 RNA binding domain in complex with RNA (guaa)
5O1Y · Protein NRD1: “Structure of NRD1 RNA binding domain in complex with RNA (guaa)”. X-ray diffraction, 1 pocket (best druggability 0.38). MolNFT v1 #128816 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5O1Y
- Type
- protein + RNA
- Length
- 167 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein NRD1; RNA (5'-R(*GP*UP*AP*A)-3')
- UniProt
- P53617
- Pockets
- 1 · best druggability 0.38
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(*GP*UP*AP*A)-3') | rna | 4 | — | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 72 | 0.38 | 0.78 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 581 Ų buried · 9 hydrogen bonds · protein-nucleic
Compared structures
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 5O1Y · PDBe 5O1Y · UniProt P53617
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