Research workbench
Crystal structure of tea N9-methyltransferase CkTcS in complex with SAH and 1,3,7-trimethyluric acid
Analyse Crystal structure of tea N9-methyltransferase CkTcS in complex with SAH and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LYH
- Type
- protein
- Length
- 2,834 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.15
- Source
- Camellia sinensis var. assamica
- Molecule
- N-methyltransferase CkTcS
- Ligands
- SAH, EXU
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · resolution 3.15 · 7 distinct chains · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | N-methyltransferase CkTcS | protein | 350 | 42% helix, 19% strand | — |
| A | N-methyltransferase CkTcS | protein | 358 | 41% helix, 18% strand | — |
| C | N-methyltransferase CkTcS | protein | 347 | 43% helix, 18% strand | — |
| D, E | N-methyltransferase CkTcS | protein | 358 | 43% helix, 19% strand | — |
| F | N-methyltransferase CkTcS | protein | 351 | 40% helix, 19% strand | — |
| G | N-methyltransferase CkTcS | protein | 357 | 43% helix, 18% strand | — |
| H | N-methyltransferase CkTcS | protein | 355 | 42% helix, 18% strand | — |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 8 copies · chains B, A, C, D, E, F, G, H
- EXU · 1,3,7-trimethyl-9H-purine-2,6,8-trione · ligand · 8 copies · chains B, A, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 414 | 0.84 | 0.92 | 54 | SAH, EXU |
| 2 | 368 | 0.83 | 0.92 | 64 | SAH, EXU |
| 3 | 1192 | 0.83 | 0.84 | 156 | SAH, EXU |
| 4 | 363 | 0.82 | 0.91 | 58 | SAH, EXU |
| 5 | 279 | 0.82 | 0.93 | 61 | SAH, EXU |
Interfaces
8 interfaces between chains.
- A–D · 1074 Ų buried · 15 hydrogen bonds · protein-protein
- A–E · 652 Ų buried · 3 hydrogen bonds · protein-protein
- D–G · 636 Ų buried · 1 hydrogen bond · protein-protein
- B–H · 363 Ų buried · 1 hydrogen bond · protein-protein
- C–F · 287 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6LYH · Crystal structure of tea N9-methyltransferase cktcs in complex with sah and… · 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 6LYH · PDBe 6LYH
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