MolNFT v1 · #158078 · protein
Crystal structure of ravd (residues 1-200) from legionella pneumophila (strain corby) complexed with met-1 linked di-ubiquitin
6NJD: “Crystal structure of ravd (residues 1-200) from legionella pneumophila (strain corby) complexed with met-1…”. X-ray diffraction, 1 ligand (MG), 8 pockets (best druggability 0.76). MolNFT v1 #158078 on GenesisL1: 3D structure…
- PDB
- 6NJD
- Type
- protein
- Length
- 668 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Di-ubiquitin; Ravd
- UniProt
- F5H747
- Ligands
- MG
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 28% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Di-ubiquitin | protein | 153 | 24% helix, 36% strand | F5H747 |
| B | Ravd | protein | 191 | 31% helix, 27% strand | — |
| C | Di-ubiquitin | protein | 141 | 23% helix, 29% strand | F5H747 |
| D | Ravd | protein | 183 | 33% helix, 25% strand | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 229 | 0.76 | 0.90 | 32 | empty |
| 2 | 704 | 0.75 | 0.80 | 96 | empty |
| 3 | 225 | 0.74 | 0.89 | 40 | empty |
| 4 | 57 | 0.68 | 0.96 | 21 | empty |
| 5 | 231 | 0.62 | 0.81 | 34 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1637 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1552 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 327 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 283 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 160 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 6NJD · Crystal structure of RavD (residues 1-200) from Legionella pneumophila (strain Corby)… · 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 F5H747
- Elsewhere: RCSB PDB 6NJD · PDBe 6NJD · UniProt F5H747
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.