Research workbench
Structure of the putative methyltransferase LPG2936 from legionella pneumophila in complex with the bound cofactor SAM
Analyse Structure of the putative methyltransferase LPG2936 from legionella pneumophila… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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