MolNFT v1 · #38491 · protein
Human methyltransferase 10 domain containing protein
2H00: “Human methyltransferase 10 domain containing protein”. X-ray diffraction, 2 ligands (SAH, CL), 8 pockets (best druggability 0.80). MolNFT v1 #38491 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2H00
- Type
- protein
- Length
- 638 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methyltransferase 10 domain containing protein
- Ligands
- SAH, CL
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methyltransferase 10 domain containing protein | protein | 225 | 40% helix, 20% strand | — |
| B | Methyltransferase 10 domain containing protein | protein | 210 | 40% helix, 23% strand | — |
| C | Methyltransferase 10 domain containing protein | protein | 203 | 42% helix, 24% strand | — |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 3 copies · chains A, B, C
- CL · Chloride ion · ion · 2 copies · chains B, C
- DTU · (2R,3S)-1,4-dimercaptobutane-2,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1148 | 0.80 | 0.81 | 93 | CL |
| 2 | 180 | 0.73 | 0.90 | 35 | SAH |
| 3 | 223 | 0.70 | 0.87 | 39 | SAH |
| 4 | 52 | 0.67 | 0.96 | 18 | empty |
| 5 | 299 | 0.64 | 0.80 | 40 | SAH |
Interfaces
3 interfaces between chains.
- B–C · 1098 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 881 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 97 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2H00 · Human methyltransferase 10 domain containing protein · the same entry in another collection · chain A against A, 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
- Elsewhere: RCSB PDB 2H00 · PDBe 2H00
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