Research workbench
Crystal structure of human dead-box RNA helicase DDX21 in complex with AMP
Analyse Crystal structure of human dead-box RNA helicase DDX21 in complex with AMP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6L5M
- Type
- protein
- Length
- 1,830 residues
- Chains
- 5
- 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
- AMP
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Nucleolar RNA helicase 2 (EC 3.6.4.13) | protein | 366 | 41% helix, 17% strand | Q9NR30 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 5 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 822 | 0.71 | 0.76 | 81 | AMP |
| 2 | 321 | 0.55 | 0.75 | 39 | empty |
| 3 | 340 | 0.55 | 0.75 | 46 | empty |
| 4 | 211 | 0.50 | 0.76 | 29 | empty |
| 5 | 215 | 0.49 | 0.75 | 26 | empty |
Interfaces
6 interfaces between chains.
- B–C · 583 Ų buried · 1 hydrogen bond · protein-protein
- D–E · 541 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 516 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 467 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 185 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6L5M · Crystal structure of human DEAD-box RNA helicase DDX21 in complex with AMP · the same entry in another collection · chain E against E, TM-score 1.00
- Q9NR30 · AlphaFold monomer V2.0 prediction for nucleolar RNA helicase 2 (Q9NR30) · a predicted model of the same protein · chain E against A, TM-score 0.58
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 6L5M · PDBe 6L5M · UniProt Q9NR30
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