Research workbench
The crystal structure of NSUN6 from pyrococcus horikoshii with SAM
Analyse The crystal structure of NSUN6 from pyrococcus horikoshii with SAM in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZVG
- Type
- protein
- Length
- 768 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 389AA long hypothetical nucleolar protein
- UniProt
- O57712
- Ligands
- SAM
- Pockets
- 7 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | 389AA long hypothetical nucleolar protein | protein | 384 | 33% helix, 26% strand | O57712 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 2 copies · chains B, 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 709 | 0.68 | 0.76 | 74 | SAM |
| 2 | 608 | 0.65 | 0.75 | 64 | SAM |
| 3 | 250 | 0.49 | 0.74 | 31 | empty |
| 4 | 91 | 0.46 | 0.81 | 19 | empty |
| 5 | 180 | 0.43 | 0.73 | 24 | empty |
Interfaces
1 interface between chains.
- B–A · 260 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5ZVG · The crystal structure of NSun6 from Pyrococcus horikoshii with SAM · the same entry in another collection · chain A against A, TM-score 1.00
- O57712 · AlphaFold monomer V2.0 prediction for tRNA (CYTOSINE(72)-C(5))-methyltransferase (O57712) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 O57712
- Elsewhere: RCSB PDB 5ZVG · PDBe 5ZVG · UniProt O57712
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