Research workbench
Crystal structure of human dead-box RNA helicase DDX21 at post- hydrolysis state
Analyse Crystal structure of human dead-box RNA helicase DDX21 at post- hydrolysis state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6L5O
- Type
- protein
- Length
- 372 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleolar RNA helicase 2
- EC
- 3.6.4.13
- UniProt
- Q9NR30
- Ligands
- ADP, MG
- Pockets
- 2 · best druggability 0.36
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nucleolar RNA helicase 2 (EC 3.6.4.13) | protein | 372 | 44% helix, 18% strand | Q9NR30 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- MG · Magnesium ion · metal · chains A
- GOL · Glycerol · additive · 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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 83 | 0.36 | 0.76 | 20 | ADP, MG |
| 2 | 62 | 0.32 | 0.75 | 12 | empty |
Compared structures
- 6L5O · Crystal structure of human DEAD-box RNA helicase DDX21 at post-hydrolysis state · the same entry in another collection · chain A against A, TM-score 1.00
- Q9NR30 · AlphaFold monomer V2.0 prediction for nucleolar RNA helicase 2 (Q9NR30) · a predicted model of the same protein · chain A against A, TM-score 0.64
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 Q9NR30
- Elsewhere: RCSB PDB 6L5O · PDBe 6L5O · UniProt Q9NR30
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