MolNFT v1 · #65515 · protein
Cocrystal structure of nudix domain of shewanella oneidensis nrtr complexed with ADP ribose
3GZ8 · MUTT/NUDIX family protein: “Cocrystal structure of nudix domain of shewanella oneidensis nrtr complexed with ADP ribose”. X-ray diffraction, 1 ligand (APR), 5 pockets (best druggability 0.73). MolNFT v1 #65515 on GenesisL1: 3D…
- 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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