Research workbench
Crystal structure of methyltransferase tled complexed with sah and teleocidin A1
Analyse Crystal structure of methyltransferase tled complexed with sah and teleocidin A1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5GM2
- Type
- protein
- Length
- 4,931 residues
- Chains
- 18
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- O-methylransferase
- UniProt
- A0A077K7L1
- Ligands
- SAH, TEX
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 10 distinct chains · 49% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, H | O-methylransferase | protein | 281 | 51% helix, 17% strand | A0A077K7L1 |
| B | O-methylransferase | protein | 282 | 51% helix, 19% strand | A0A077K7L1 |
| C, E, F, O, P | O-methylransferase | protein | 279 | 50% helix, 20% strand | A0A077K7L1 |
| G, I, Q | O-methylransferase | protein | 266 | 49% helix, 21% strand | A0A077K7L1 |
| J | O-methylransferase | protein | 272 | 50% helix, 19% strand | A0A077K7L1 |
| K | O-methylransferase | protein | 267 | 46% helix, 16% strand | A0A077K7L1 |
| L | O-methylransferase | protein | 263 | 49% helix, 21% strand | A0A077K7L1 |
| M | O-methylransferase | protein | 264 | 49% helix, 21% strand | A0A077K7L1 |
| N | O-methylransferase | protein | 274 | 49% helix, 18% strand | A0A077K7L1 |
| R | O-methylransferase | protein | 273 | 51% helix, 11% strand | A0A077K7L1 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 18 copies · chains A, B, C, D, E, F, G, H, I, K, J, L, M, N, O, P, Q, R
- TEX · (2S,5S)-9-[(3R)-3,7-dimethylocta-1,6-dien-3-yl]-5-(hydroxymethyl)-1-methyl-2-(propan-2-yl)-1,2,4,5,6,8-hexahydro-3H-[1,4]diazonino[7,6,5-cd]indol-3-one · ligand · 18 copies · chains A, B, C, D, E, F, G, H, I, K, J, L, M, N, O, P, Q, R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 412 | 0.88 | 0.96 | 61 | SAH, TEX |
| 2 | 420 | 0.88 | 0.95 | 63 | SAH, TEX |
| 3 | 436 | 0.88 | 0.95 | 60 | SAH, TEX |
| 4 | 410 | 0.87 | 0.95 | 58 | SAH, TEX |
| 5 | 424 | 0.87 | 0.95 | 62 | SAH, TEX |
Interfaces
49 interfaces between chains.
- A–B · 4972 Ų buried · 60 hydrogen bonds · protein-protein
- C–D · 4806 Ų buried · 64 hydrogen bonds · protein-protein
- O–P · 4738 Ų buried · 58 hydrogen bonds · protein-protein
- E–F · 4701 Ų buried · 58 hydrogen bonds · protein-protein
- Q–R · 4297 Ų buried · 50 hydrogen bonds · protein-protein
Compared structures
- 5GM2 · Crystal structure of methyltransferase TleD complexed with SAH and teleocidin A1 · the same entry in another collection · chain D against D, 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 A0A077K7L1
- Elsewhere: RCSB PDB 5GM2 · PDBe 5GM2 · UniProt A0A077K7L1
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