Research workbench
Crystal structure of the E3 ubiquitin ligase ravn from legionella pneumophila
Analyse Crystal structure of the E3 ubiquitin ligase ravn 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
- 5MIY
- Type
- protein
- Length
- 372 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin ligase ravn
- EC
- 6.3.2.19
- UniProt
- A0A130MLL2
- Ligands
- NA, SO4
- Pockets
- 5 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 24% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin ligase ravn (EC 6.3.2.19) | protein | 127 | 24% helix, 26% strand | A0A130MLL2 |
| B | E3 ubiquitin ligase ravn (EC 6.3.2.19) | protein | 123 | 27% helix, 28% strand | A0A130MLL2 |
| C | E3 ubiquitin ligase ravn (EC 6.3.2.19) | protein | 122 | 20% helix, 30% strand | A0A130MLL2 |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains A, C
- SO4 · Sulfate ion · ion · 13 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 278 | 0.59 | 0.78 | 27 | EDO |
| 2 | 149 | 0.46 | 0.76 | 25 | NA |
| 3 | 58 | 0.45 | 0.84 | 18 | empty |
| 4 | 51 | 0.39 | 0.81 | 17 | empty |
| 5 | 61 | 0.38 | 0.79 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–C · 971 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 527 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 365 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5MIY · Crystal structure of the E3 ubiquitin ligase RavN from Legionella pneumophila · 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 A0A130MLL2
- Elsewhere: RCSB PDB 5MIY · PDBe 5MIY · UniProt A0A130MLL2
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