MolNFT v1 · #142166 · protein
The crystal structure of NSUN6 from pyrococcus horikoshii with sah
5ZVE · 389AA long hypothetical nucleolar protein: “The crystal structure of NSUN6 from pyrococcus horikoshii with sah”. X-ray diffraction, 1 ligand (SAH), 7 pockets (best druggability 0.67). MolNFT v1 #142166 on GenesisL1: 3D structure…
- PDB
- 5ZVE
- 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
- SAH
- Pockets
- 7 · best druggability 0.67
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
- SAH · S-adenosyl-L-homocysteine · 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 | 671 | 0.67 | 0.76 | 73 | SAH |
| 2 | 632 | 0.65 | 0.75 | 61 | SAH |
| 3 | 239 | 0.48 | 0.74 | 31 | empty |
| 4 | 155 | 0.44 | 0.75 | 23 | empty |
| 5 | 76 | 0.43 | 0.80 | 18 | empty |
Interfaces
1 interface between chains.
- B–A · 275 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5ZVE · The crystal structure of NSun6 from Pyrococcus horikoshii with SAH · the same entry in another collection · chain B against B, 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 5ZVE · PDBe 5ZVE · UniProt O57712
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