Research workbench
Crystal structure of the bdellovibrio bacteriovorus nucleoside diphosphate sugar hydrolase in complex with ADP-ribose
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
- 5C7T
- Type
- protein
- Length
- 361 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
- APR, SO4
- Pockets
- 2 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nudf protein (EC 3.6.1.13) | protein | 182 | 24% helix, 43% strand | Q6MIH8 |
| B | Nudf protein (EC 3.6.1.13) | protein | 179 | 20% helix, 44% strand | Q6MIH8 |
Ligands and binding sites
- APR · Adenosine-5-diphosphoribose · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
- GOL · Glycerol · additive · 7 copies · chains A, B
- PG0 · 2-(2-methoxyethoxy)ethanol · additive · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A, B
- PGE · Triethylene glycol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 487 | 0.76 | 0.84 | 50 | APR, SO4 |
| 2 | 430 | 0.75 | 0.84 | 42 | SO4, APR |
Interfaces
1 interface between chains.
- A–B · 3214 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 5C7T · Crystal Structure of the Bdellovibrio bacteriovorus Nucleoside Diphosphate Sugar… · 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 5C7T · PDBe 5C7T · UniProt Q6MIH8
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