Research workbench
Human nuclear exosome targeting (next) complex bound to RNA (substrate 2)
Analyse Human nuclear exosome targeting (next) complex bound to RNA (substrate 2) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7S7C
- Type
- protein + RNA
- Length
- 1,666 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exosome RNA helicase MTR4; Zinc finger cchc domain-containing protein 8; RNA-binding…
- EC
- 3.6.4.13
- UniProt
- P42285, Q6NZY4, Q9Y580
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 7 distinct chains · 39% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Exosome RNA helicase MTR4 (EC 3.6.4.13) | protein | 924 | 47% helix, 15% strand | P42285 |
| B | Zinc finger cchc domain-containing protein 8 | protein | 330 | 31% helix, 5% strand | Q6NZY4 |
| C | RNA-binding protein 7 | protein | 79 | 20% helix, 28% strand | Q9Y580 |
| D | RNA (30-mer) | rna | 27 | — | — |
| L | RNA (30-mer) | rna | 10 | — | — |
| E | Exosome RNA helicase MTR4 (EC 3.6.4.13) | protein | 147 | 34% helix, 27% strand | P42285 |
| F | Zinc finger cchc domain-containing protein 8 | protein | 149 | 26% helix, 14% strand | Q6NZY4 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 404 | 0.81 | 0.90 | 47 | empty |
| 2 | 1044 | 0.79 | 0.81 | 91 | empty |
| 3 | 512 | 0.68 | 0.79 | 44 | empty |
| 4 | 138 | 0.62 | 0.86 | 26 | empty |
| 5 | 130 | 0.61 | 0.86 | 20 | empty |
Interfaces
10 interfaces between chains.
- A–B · 5531 Ų buried · 41 hydrogen bonds · protein-protein
- B–F · 3990 Ų buried · 34 hydrogen bonds · protein-protein
- E–F · 1994 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1422 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 1298 Ų buried · 27 hydrogen bonds · protein-nucleic
Compared structures
- 7S7C · Human Nuclear Exosome Targeting (NEXT) complex bound to RNA (substrate 2) · the same entry in another collection · chain F against F, TM-score 1.00
- Q9Y580 · AlphaFold monomer V2.0 prediction for RNA-binding protein 7 (Q9Y580) · a predicted model of the same protein · chain C against A, TM-score 0.95
- P42285 · AlphaFold monomer V2.0 prediction for exosome RNA helicase MTR4 (P42285) · a predicted model of the same protein · chain E against A, TM-score 0.93
- Q6NZY4 · AlphaFold monomer V2.0 prediction for zinc finger cchc domain- containing protein 8… · a predicted model of the same protein · chain F against A, TM-score 0.50
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
- Every structure of UniProt Q9Y580
- Elsewhere: RCSB PDB 7S7C · PDBe 7S7C · UniProt P42285 · UniProt Q6NZY4 · UniProt Q9Y580
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