Research workbench
Human methyltransferase-like protein 21D
Analyse Human methyltransferase-like protein 21D in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LG1
- Type
- protein
- Length
- 647 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein-lysine methyltransferase METTL21D
- EC
- 2.1.1.-
- UniProt
- Q9H867
- Ligands
- SAM, UNX
- Pockets
- 6 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein-lysine methyltransferase METTL21D (EC 2.1.1.-) | protein | 217 | 32% helix, 25% strand | Q9H867 |
| B | Protein-lysine methyltransferase METTL21D (EC 2.1.1.-) | protein | 213 | 33% helix, 25% strand | Q9H867 |
| C | Protein-lysine methyltransferase METTL21D (EC 2.1.1.-) | protein | 217 | 33% helix, 25% strand | Q9H867 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 3 copies · chains A, B, C
- UNX · Unknown atom or ion · ion · 23 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 512 | 0.60 | 0.74 | 60 | UNX |
| 2 | 233 | 0.59 | 0.80 | 36 | SAM |
| 3 | 162 | 0.56 | 0.81 | 28 | SAM, UNX |
| 4 | 151 | 0.55 | 0.81 | 31 | SAM, UNX |
| 5 | 258 | 0.51 | 0.75 | 26 | empty |
Interfaces
2 interfaces between chains.
- B–C · 831 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 337 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
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 Q9H867
- Elsewhere: RCSB PDB 4LG1 · PDBe 4LG1 · UniProt Q9H867
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