Research workbench
Crystal structure of a dead box protein from the hyperthermophile methanococcus jannaschii
Analyse Crystal structure of a dead box protein from the hyperthermophile methanococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1HV8
- Type
- protein
- Length
- 726 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative ATP-dependent RNA helicase MJ0669
- UniProt
- Q58083
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Putative ATP-dependent RNA helicase MJ0669 | protein | 363 | 42% helix, 17% strand | Q58083 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 503 | 0.78 | 0.85 | 55 | SO4 |
| 2 | 853 | 0.74 | 0.78 | 74 | SO4 |
| 3 | 504 | 0.63 | 0.76 | 76 | empty |
| 4 | 127 | 0.42 | 0.76 | 25 | SO4 |
Interfaces
1 interface between chains.
- A–B · 740 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 1HV8 · Crystal structure of a dead box protein from the hyperthermophile methanococcus jannaschii · the same entry in another collection · chain A against A, TM-score 1.00
- Q58083 · AlphaFold monomer V2.0 prediction for probable ATP-dependent RNA helicase MJ0669 (Q58083) · a predicted model of the same protein · chain A against A, TM-score 0.71
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 Q58083
- Elsewhere: RCSB PDB 1HV8 · PDBe 1HV8 · UniProt Q58083
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