Research workbench
Crystal structure of E. COLI dead-box protein srmb bound to regulator of ribonuclease activity a (rraa)
Analyse Crystal structure of E. COLI dead-box protein srmb bound to regulator of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YJT
- Type
- protein
- Length
- 644 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Regulator of ribonuclease activity a; ATP-dependent RNA helicase srmb
- EC
- 3.6.4.13
- UniProt
- D8AM26, P21507
- Pockets
- 6 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Regulator of ribonuclease activity a | protein | 158 | 20% helix, 37% strand | D8AM26 |
| D | ATP-dependent RNA helicase srmb (EC 3.6.4.13) | protein | 170 | 37% helix, 18% strand | P21507 |
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 123 | 0.62 | 0.87 | 21 | empty |
| 2 | 108 | 0.43 | 0.78 | 16 | empty |
| 3 | 78 | 0.40 | 0.79 | 19 | empty |
| 4 | 75 | 0.38 | 0.78 | 22 | empty |
| 5 | 58 | 0.36 | 0.79 | 20 | empty |
Interfaces
4 interfaces between chains.
- A–D · 791 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 499 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 498 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 492 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 2YJT · Crystal structure of E. coli DEAD-box protein SrmB bound to regulator of ribonuclease… · the same entry in another collection · chain A against A, TM-score 1.00
- P21507 · AlphaFold monomer V2.0 prediction for ATP-dependent RNA helicase srmb (P21507) · a predicted model of the same protein · chain D against A, TM-score 0.97
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 D8AM26
- Every structure of UniProt P21507
- Elsewhere: RCSB PDB 2YJT · PDBe 2YJT · UniProt D8AM26 · UniProt P21507
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.