MolNFT v1 · #119998 · protein
Crystal structure of methyltransferase tled complexed with sah
5GM1 · O-methylransferase: “Crystal structure of methyltransferase tled complexed with sah”. X-ray diffraction, 1 ligand (SAH), 20 pockets (best druggability 0.87). MolNFT v1 #119998 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5GM1
- Type
- protein
- Length
- 5,045 residues
- Chains
- 18
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- O-methylransferase
- UniProt
- A0A077K7L1
- Ligands
- SAH
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 5 distinct chains · 51% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, J, M, N, Q, R | O-methylransferase | protein | 281 | 51% helix, 19% strand | A0A077K7L1 |
| B, D, F, G, I, L, O, P | O-methylransferase | protein | 280 | 52% helix, 19% strand | A0A077K7L1 |
| C | O-methylransferase | protein | 280 | 50% helix, 20% strand | A0A077K7L1 |
| E, H | O-methylransferase | protein | 279 | 51% helix, 20% strand | A0A077K7L1 |
| K | O-methylransferase | protein | 281 | 49% helix, 20% strand | A0A077K7L1 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 19 copies · chains A, B, C, D, E, F, G, H, I, J, K, 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 | 414 | 0.87 | 0.95 | 60 | SAH |
| 2 | 383 | 0.87 | 0.96 | 56 | SAH |
| 3 | 386 | 0.87 | 0.95 | 59 | SAH |
| 4 | 381 | 0.87 | 0.95 | 59 | SAH |
| 5 | 419 | 0.87 | 0.95 | 60 | SAH |
Interfaces
51 interfaces between chains.
- M–N · 5097 Ų buried · 76 hydrogen bonds · protein-protein
- Q–R · 5039 Ų buried · 71 hydrogen bonds · protein-protein
- I–J · 4970 Ų buried · 68 hydrogen bonds · protein-protein
- A–B · 4958 Ų buried · 71 hydrogen bonds · protein-protein
- K–L · 4924 Ų buried · 72 hydrogen bonds · protein-protein
Compared structures
- 5GM1 · Crystal structure of methyltransferase TleD complexed with SAH · 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
- Every structure of UniProt A0A077K7L1
- Elsewhere: RCSB PDB 5GM1 · PDBe 5GM1 · UniProt A0A077K7L1
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