MolNFT v1 · #84327 · protein
Structure of the C. elegans SMG5-SMG7 complex
3ZHE · Nonsense-mediated mRNA decay protein: “Structure of the C. elegans SMG5-SMG7 complex”. X-ray diffraction, 18 pockets (best druggability 0.66). MolNFT v1 #84327 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3ZHE
- Type
- protein
- Length
- 1,564 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nonsense-mediated mRNA decay protein; Protein smg-7
- UniProt
- G5ECF1, G5EF47
- Pockets
- 18 · best druggability 0.66
Structure
x-ray diffraction · 4 distinct chains · 67% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nonsense-mediated mRNA decay protein | protein | 399 | 66% helix, 3% strand | G5ECF1 |
| B | Protein smg-7 | protein | 390 | 67% helix, 1% strand | G5EF47 |
| C | Nonsense-mediated mRNA decay protein | protein | 388 | 68% helix, 2% strand | G5ECF1 |
| D | Protein smg-7 | protein | 387 | 67% helix, 1% strand | G5EF47 |
Pockets
18 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 459 | 0.66 | 0.78 | 64 | empty |
| 2 | 270 | 0.60 | 0.79 | 40 | empty |
| 3 | 304 | 0.56 | 0.76 | 32 | empty |
| 4 | 59 | 0.52 | 0.87 | 15 | empty |
| 5 | 237 | 0.52 | 0.75 | 25 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1306 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 1216 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 682 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 126 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3ZHE · Structure of the C. elegans SMG5-SMG7 complex · the same entry in another collection · chain B against B, TM-score 1.00
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 G5ECF1
- Every structure of UniProt G5EF47
- Elsewhere: RCSB PDB 3ZHE · PDBe 3ZHE · UniProt G5ECF1 · UniProt G5EF47
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