Research workbench
M. jannaschii NEP1 complexed with sinefungin
Analyse M. jannaschii NEP1 complexed with sinefungin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BBH
- Type
- protein
- Length
- 408 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribosome biogenesis protein NEP1-like
- UniProt
- Q57977
- Ligands
- SFG
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ribosome biogenesis protein NEP1-like | protein | 204 | 34% helix, 24% strand | Q57977 |
Ligands and binding sites
- SFG · Sinefungin · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 384 | 0.72 | 0.83 | 57 | SFG |
| 2 | 285 | 0.65 | 0.81 | 37 | SFG |
| 3 | 86 | 0.60 | 0.88 | 17 | GOL |
| 4 | 124 | 0.44 | 0.76 | 20 | empty |
| 5 | 67 | 0.36 | 0.78 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1344 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
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 Q57977
- Elsewhere: RCSB PDB 3BBH · PDBe 3BBH · UniProt Q57977
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