MolNFT v1 · #66563 · protein + RNA
Crystal structure of small RNA methyltransferase HEN1
3HTX: “Crystal structure of small RNA methyltransferase HEN1”. X-ray diffraction, 2 ligands (SAH, MG), 20 pockets (best druggability 0.83). MolNFT v1 #66563 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3HTX
- Type
- protein + RNA
- Length
- 1,662 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HEN1; 5'-R(*GP*AP*UP*UP*UP*CP*UP*CP*UP*CP*UP*GP*CP*AP*AP*GP*CP*GP *AP*AP*AP*G)-3'…
- UniProt
- Q945R3
- Ligands
- SAH, MG
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HEN1 | protein | 779 | 33% helix, 23% strand | Q945R3 |
| B, E | 5'-R(*GP*AP*UP*UP*UP*CP*UP*CP*UP*CP*UP*GP*CP*AP*AP*GP*CP*GP *AP*AP*AP*G)-3' | rna | 22 | — | — |
| C, F | 5'-R(P*UP*UP*CP*GP*CP*UP*UP*GP*CP*AP*GP*AP*GP*AP*GP*AP*AP*A P*UP*CP*AP*C)-3' | rna | 22 | — | — |
| D | HEN1 | protein | 795 | 32% helix, 23% strand | Q945R3 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 2 copies · chains A, B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 921 | 0.83 | 0.85 | 86 | empty |
| 2 | 1133 | 0.81 | 0.82 | 94 | empty |
| 3 | 674 | 0.68 | 0.77 | 48 | empty |
| 4 | 223 | 0.68 | 0.85 | 30 | SAH |
| 5 | 665 | 0.67 | 0.77 | 53 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1533 Ų buried · 27 hydrogen bonds · protein-nucleic
- D–E · 1432 Ų buried · 28 hydrogen bonds · protein-nucleic
- A–C · 1296 Ų buried · 28 hydrogen bonds · protein-nucleic
- D–F · 1258 Ų buried · 18 hydrogen bonds · protein-nucleic
- E–F · 969 Ų buried · 80 hydrogen bonds · nucleic-nucleic
Compared structures
- 3HTX · Crystal structure of small RNA methyltransferase HEN1 · the same entry in another collection · chain F against F, 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 Q945R3
- Elsewhere: RCSB PDB 3HTX · PDBe 3HTX · UniProt Q945R3
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