Research workbench
Crystal structure of HMETTL16 catalytic domain in complex with MAT2A 3'UTR hairpin 1
Analyse Crystal structure of HMETTL16 catalytic domain in complex with MAT2A 3'UTR… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DU4
- Type
- protein + RNA
- Length
- 316 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase; HP1X-RNA (29-mer)
- EC
- 2.1.1.346, 2.1.1.62
- UniProt
- Q86W50
- Pockets
- 8 · best druggability 0.44
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase (EC 2.1.1.346, 2.1.1.62) | protein | 287 | 37% helix, 18% strand | Q86W50 |
| B | HP1X-RNA (29-mer) | rna | 29 | — | — |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 143 | 0.44 | 0.76 | 27 | empty |
| 2 | 215 | 0.41 | 0.72 | 18 | TRS |
| 3 | 73 | 0.40 | 0.80 | 18 | empty |
| 4 | 94 | 0.37 | 0.75 | 16 | empty |
| 5 | 80 | 0.32 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2022 Ų buried · 54 hydrogen bonds · protein-nucleic
Compared structures
- 6DU4 · Crystal structure of hMettl16 catalytic domain in complex with MAT2A 3'UTR hairpin 1 · the same entry in another collection · chain A against A, TM-score 1.00
- Q86W50 · AlphaFold monomer V2.0 prediction for RNA N6-adenosine- methyltransferase METTL16 (Q86W50) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q86W50
- Elsewhere: RCSB PDB 6DU4 · PDBe 6DU4 · UniProt Q86W50
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.