Research workbench
X-ray crystal structure of viperin-like enzyme from trichoderma virens
Analyse X-ray crystal structure of viperin-like enzyme from trichoderma virens in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7N7I
- Type
- protein
- Length
- 837 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Viperin-like enzyme
- UniProt
- G9MQB8
- Ligands
- SAM, SF4, UTP
- Pockets
- 10 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Viperin-like enzyme | protein | 279 | 34% helix, 16% strand | G9MQB8 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 3 copies · chains A, B, C
- SF4 · Iron/sulfur cluster · ligand · 3 copies · chains A, B, C
- UTP · Uridine 5'-triphosphate · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 460 | 0.86 | 0.93 | 51 | SAM, SF4, UTP |
| 2 | 476 | 0.86 | 0.93 | 55 | SAM, SF4, UTP |
| 3 | 488 | 0.85 | 0.92 | 53 | SAM, SF4, UTP |
| 4 | 548 | 0.69 | 0.78 | 87 | empty |
| 5 | 69 | 0.64 | 0.92 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–C · 559 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 360 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 201 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7N7I · X-ray crystal structure of Viperin-like enzyme from Trichoderma virens · the same entry in another collection · chain A against A, 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 G9MQB8
- Elsewhere: RCSB PDB 7N7I · PDBe 7N7I · UniProt G9MQB8
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