Research workbench
Cocrystal structure of nudix domain of shewanella oneidensis nrtr complexed with ADP ribose
Analyse Cocrystal structure of nudix domain of shewanella oneidensis nrtr complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GZ8
- Type
- protein
- Length
- 618 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MUTT/NUDIX family protein
- UniProt
- Q8EFJ3
- Ligands
- APR
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | MUTT/NUDIX family protein | protein | 154 | 26% helix, 35% strand | Q8EFJ3 |
| C | MUTT/NUDIX family protein | protein | 156 | 25% helix, 34% strand | Q8EFJ3 |
Ligands and binding sites
- APR · Adenosine-5-diphosphoribose · ligand · 4 copies · chains A, B, C, D
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 | 519 | 0.73 | 0.81 | 70 | APR |
| 2 | 498 | 0.73 | 0.82 | 71 | APR |
| 3 | 800 | 0.71 | 0.77 | 62 | empty |
| 4 | 94 | 0.33 | 0.73 | 15 | empty |
| 5 | 89 | 0.32 | 0.72 | 16 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1590 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1567 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 653 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 636 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 97 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3GZ8 · Cocrystal structure of NUDIX domain of Shewanella oneidensis NrtR complexed with ADP… · 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 Q8EFJ3
- Elsewhere: RCSB PDB 3GZ8 · PDBe 3GZ8 · UniProt Q8EFJ3
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