MolNFT v1 · #54163 · protein + RNA
Structure of MTR4, a dexh helicase involved in nuclear RNA processing and surveillance
2XGJ · ATP-dependent RNA helicase DOB1: “Structure of MTR4, a dexh helicase involved in nuclear RNA processing and surveillance”. X-ray diffraction, 1 ligand (ADP), 14 pockets (best druggability 0.84). MolNFT v1 #54163 on GenesisL1: 3D…
- PDB
- 2XGJ
- Type
- protein + RNA
- Length
- 1,751 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent RNA helicase DOB1; RNA (5'-(*AP*AP*AP*AP*A)-3')
- EC
- 3.6.4.13, 3.6.1.-
- UniProt
- P47047
- Ligands
- ADP
- Pockets
- 14 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent RNA helicase DOB1 (EC 3.6.4.13, 3.6.1.-) | protein | 964 | 45% helix, 17% strand | P47047 |
| B | ATP-dependent RNA helicase DOB1 (EC 3.6.4.13, 3.6.1.-) | protein | 777 | 53% helix, 11% strand | P47047 |
| C, D | RNA (5'-(*AP*AP*AP*AP*A)-3') | rna | 5 | — | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 510 | 0.84 | 0.90 | 67 | empty |
| 2 | 784 | 0.83 | 0.86 | 90 | empty |
| 3 | 716 | 0.80 | 0.84 | 66 | empty |
| 4 | 579 | 0.76 | 0.83 | 70 | ADP |
| 5 | 569 | 0.74 | 0.82 | 51 | empty |
Interfaces
3 interfaces between chains.
- A–C · 716 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–B · 663 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 659 Ų buried · 19 hydrogen bonds · protein-nucleic
Compared structures
- 2XGJ · Structure of Mtr4, a DExH helicase involved in nuclear RNA processing and surveillance · the same entry in another collection · chain B against B, TM-score 1.00
- P47047 · AlphaFold monomer V2.0 prediction for ATP-dependent RNA helicase DOB1 (P47047) · a predicted model of the same protein · chain B against A, TM-score 0.93
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 P47047
- Elsewhere: RCSB PDB 2XGJ · PDBe 2XGJ · UniProt P47047
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.