Research workbench
Human MTR4 helicase in complex with ZCCHC8-ctd
Analyse Human MTR4 helicase in complex with ZCCHC8-ctd in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6C90
- Type
- protein
- Length
- 736 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exosome RNA helicase MTR4,EXOSOME RNA helicase MTR4; Zinc finger cchc domain-containing…
- EC
- 3.6.4.13
- UniProt
- P42285, Q6NZY4
- Ligands
- ADP, MG
- Pockets
- 6 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Exosome RNA helicase MTR4,EXOSOME RNA helicase MTR4 (EC 3.6.4.13) | protein | 694 | 47% helix, 14% strand | P42285 |
| B | Zinc finger cchc domain-containing protein 8 | protein | 42 | 38% helix, 2% strand | Q6NZY4 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- MLI · Malonate ion · additive · 4 copies · chains A
- TLA · L(+)-tartaric acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 906 | 0.84 | 0.86 | 120 | MLI |
| 2 | 598 | 0.72 | 0.80 | 53 | ADP |
| 3 | 184 | 0.50 | 0.77 | 25 | empty |
| 4 | 87 | 0.40 | 0.77 | 20 | empty |
| 5 | 50 | 0.38 | 0.81 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 2331 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 6C90 · Human Mtr4 helicase in complex with ZCCHC8-CTD · 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 0.98
- Q6NZY4 · AlphaFold monomer V2.0 prediction for zinc finger cchc domain- containing protein 8… · a predicted model of the same protein · chain B against A, TM-score 0.29
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 Q6NZY4
- Elsewhere: RCSB PDB 6C90 · PDBe 6C90 · UniProt P42285 · UniProt Q6NZY4
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