Research workbench
Crystal structure of the regulatory domain of human LGP2
Analyse Crystal structure of the regulatory domain of human LGP2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2W4R
- Type
- protein
- Length
- 501 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable ATP-dependent RNA helicase DHX58
- EC
- 3.6.1.-
- UniProt
- Q96C10
- Ligands
- HG, SO4
- Pockets
- 5 · best druggability 0.66
Structure
x-ray diffraction · 4 distinct chains · 21% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable ATP-dependent RNA helicase DHX58 (EC 3.6.1.-) | protein | 127 | 17% helix, 41% strand | Q96C10 |
| B | Probable ATP-dependent RNA helicase DHX58 (EC 3.6.1.-) | protein | 125 | 24% helix, 42% strand | Q96C10 |
| C | Probable ATP-dependent RNA helicase DHX58 (EC 3.6.1.-) | protein | 124 | 20% helix, 40% strand | Q96C10 |
| D | Probable ATP-dependent RNA helicase DHX58 (EC 3.6.1.-) | protein | 125 | 22% helix, 39% strand | Q96C10 |
Ligands and binding sites
- HG · Mercury (II) ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 574 | 0.66 | 0.76 | 55 | empty |
| 2 | 83 | 0.42 | 0.79 | 16 | empty |
| 3 | 73 | 0.34 | 0.76 | 16 | empty |
| 4 | 55 | 0.30 | 0.76 | 15 | empty |
| 5 | 55 | 0.26 | 0.73 | 14 | empty |
Interfaces
5 interfaces between chains.
- A–B · 456 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 316 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 232 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 140 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 10 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2W4R · Crystal structure of the regulatory domain of human LGP2 · the same entry in another collection · chain D against D, TM-score 1.00
- Q96C10 · AlphaFold monomer V2.0 prediction for probable ATP-dependent RNA helicase DHX58 (Q96C10) · a predicted model of the same protein · chain C against A, TM-score 0.94
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 Q96C10
- Elsewhere: RCSB PDB 2W4R · PDBe 2W4R · UniProt Q96C10
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