MolNFT v1 · #129059 · protein
Structure of the putative methyltransferase LPG2936 from legionella pneumophila in complex with the bound cofactor SAM
5O96 · Ribosomal RNA small subunit methyltransferase E: “Structure of the putative methyltransferase LPG2936 from legionella pneumophila in complex with the bound…”. X-ray diffraction, 1 ligand (SAM), 20 pockets (best druggability 0.81).…
- PDB
- 5O96
- Type
- protein
- Length
- 1,937 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribosomal RNA small subunit methyltransferase E
- EC
- 2.1.1.193
- UniProt
- Q5ZRE6
- Ligands
- SAM
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E, F, G, H | Ribosomal RNA small subunit methyltransferase E (EC 2.1.1.193) | protein | 242 | 33% helix, 27% strand | Q5ZRE6 |
| D | Ribosomal RNA small subunit methyltransferase E (EC 2.1.1.193) | protein | 243 | 33% helix, 26% strand | Q5ZRE6 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 8 copies · chains A, B, 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 907 | 0.81 | 0.83 | 75 | empty |
| 2 | 1101 | 0.78 | 0.80 | 114 | SAM |
| 3 | 204 | 0.65 | 0.84 | 25 | SAM |
| 4 | 425 | 0.63 | 0.77 | 39 | SAM |
| 5 | 340 | 0.63 | 0.79 | 36 | SAM |
Interfaces
12 interfaces between chains.
- C–D · 1560 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 1520 Ų buried · 32 hydrogen bonds · protein-protein
- E–F · 1506 Ų buried · 33 hydrogen bonds · protein-protein
- G–H · 1486 Ų buried · 34 hydrogen bonds · protein-protein
- D–H · 992 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5O96 · Structure of the putative methyltransferase Lpg2936 from Legionella pneumophila in… · the same entry in another collection · chain F against F, 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 Q5ZRE6
- Elsewhere: RCSB PDB 5O96 · PDBe 5O96 · UniProt Q5ZRE6
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