Research workbench
Crystal structure of the bdellovibrio bacteriovorus nucleoside diphosphate sugar hydrolase
Analyse Crystal structure of the bdellovibrio bacteriovorus nucleoside diphosphate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5C7Q
- Type
- protein
- Length
- 362 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nudf protein
- EC
- 3.6.1.13
- UniProt
- Q6MIH8
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nudf protein (EC 3.6.1.13) | protein | 182 | 21% helix, 43% strand | Q6MIH8 |
| B | Nudf protein (EC 3.6.1.13) | protein | 180 | 20% helix, 44% strand | Q6MIH8 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
- GOL · Glycerol · additive · 9 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
- PG0 · 2-(2-methoxyethoxy)ethanol · additive · 2 copies · chains A, B
- PGE · Triethylene glycol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 432 | 0.76 | 0.85 | 45 | SO4, GOL |
| 2 | 476 | 0.74 | 0.83 | 49 | SO4, GOL |
| 3 | 52 | 0.40 | 0.81 | 13 | PGE |
Interfaces
1 interface between chains.
- A–B · 3191 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 5C7Q · Crystal Structure of the Bdellovibrio bacteriovorus Nucleoside Diphosphate Sugar Hydrolase · 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 Q6MIH8
- Elsewhere: RCSB PDB 5C7Q · PDBe 5C7Q · UniProt Q6MIH8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.