Research workbench
X-ray crystal structure of the MTR4 nvl complex
Analyse X-ray crystal structure of the MTR4 nvl complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RO1
- Type
- protein
- Length
- 937 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exosome RNA helicase MTR4; Nuclear valosin-containing protein-like
- EC
- 3.6.4.13
- UniProt
- P42285, O15381
- Ligands
- ADP, SO4, CL
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Exosome RNA helicase MTR4 (EC 3.6.4.13) | protein | 919 | 48% helix, 16% strand | P42285 |
| B | Nuclear valosin-containing protein-like | protein | 18 | 0% helix, 17% strand | O15381 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1046 | 0.77 | 0.79 | 111 | SO4 |
| 2 | 422 | 0.74 | 0.84 | 56 | ADP |
| 3 | 205 | 0.52 | 0.77 | 26 | empty |
| 4 | 157 | 0.42 | 0.74 | 23 | empty |
| 5 | 66 | 0.38 | 0.78 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 553 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6RO1 · X-ray crystal structure of the MTR4 NVL complex · the same entry in another collection · chain A against A, TM-score 1.00
- P42285 · AlphaFold monomer V2.0 prediction for exosome RNA helicase MTR4 (P42285) · a predicted model of the same protein · chain A against A, TM-score 0.77
- O15381 · AlphaFold monomer V2.0 prediction for nuclear valosin-containing protein-like (O15381) · a predicted model of the same protein · chain B against A, TM-score 0.18
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 P42285
- Every structure of UniProt O15381
- Elsewhere: RCSB PDB 6RO1 · PDBe 6RO1 · UniProt P42285 · UniProt O15381
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