MolNFT v1 · #65513 · protein + DNA
Crystal structure of shewanella oneidensis nrtr complexed with a 27MER DNA
3GZ6 · MUTT/NUDIX family protein: “Crystal structure of shewanella oneidensis nrtr complexed with a 27MER DNA”. X-ray diffraction, 1 ligand (NA), 7 pockets (best druggability 0.59). MolNFT v1 #65513 on GenesisL1: 3D structure, binding…
- PDB
- 3GZ6
- Type
- protein + DNA
- Length
- 492 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MUTT/NUDIX family protein; DNA (27-mer)
- UniProt
- Q8EFJ3
- Ligands
- NA
- Pockets
- 7 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | MUTT/NUDIX family protein | protein | 219 | 34% helix, 28% strand | Q8EFJ3 |
| D | DNA (27-mer) | dna | 27 | — | — |
| C | DNA (27-mer) | dna | 27 | — | — |
Ligands and binding sites
- NA · Sodium ion · metal · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 238 | 0.59 | 0.80 | 30 | empty |
| 2 | 57 | 0.58 | 0.90 | 16 | empty |
| 3 | 256 | 0.58 | 0.79 | 31 | empty |
| 4 | 421 | 0.56 | 0.74 | 41 | NA |
| 5 | 280 | 0.51 | 0.74 | 37 | empty |
Interfaces
6 interfaces between chains.
- D–C · 1175 Ų buried · 105 hydrogen bonds · nucleic-nucleic
- A–B · 1027 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 671 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–D · 669 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–C · 581 Ų buried · 11 hydrogen bonds · protein-nucleic
Compared structures
- 3GZ6 · Crystal structure of Shewanella oneidensis NrtR complexed with a 27mer DNA · 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 3GZ6 · PDBe 3GZ6 · UniProt Q8EFJ3
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