MolNFT v1 · #147576 · protein
Nuct from helicobacter pylori
6EHI · Nuclease nuct: “Nuct from helicobacter pylori”. X-ray diffraction, 1 ligand (CL), 17 pockets (best druggability 0.82). MolNFT v1 #147576 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6EHI
- Type
- protein
- Length
- 1,908 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nuclease nuct
- UniProt
- A0A1V3AA65
- Ligands
- CL
- Pockets
- 17 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, F, I, J, K, L | Nuclease nuct | protein | 159 | 34% helix, 31% strand | A0A1V3AA65 |
| B, G | Nuclease nuct | protein | 158 | 35% helix, 31% strand | A0A1V3AA65 |
| D, H | Nuclease nuct | protein | 160 | 34% helix, 31% strand | A0A1V3AA65 |
Ligands and binding sites
- CL · Chloride ion · ion · 6 copies · chains A, B, C, D, E, G, F, H, I, J, K, L
- ACT · Acetate ion · additive · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- GOL · Glycerol · additive · 12 copies · chains A, B, C, D, E, G, F, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 790 | 0.82 | 0.85 | 92 | empty |
| 2 | 1142 | 0.76 | 0.78 | 97 | empty |
| 3 | 227 | 0.67 | 0.85 | 32 | empty |
| 4 | 757 | 0.66 | 0.74 | 57 | empty |
| 5 | 483 | 0.66 | 0.78 | 51 | empty |
Interfaces
25 interfaces between chains.
- K–L · 2072 Ų buried · 31 hydrogen bonds · protein-protein
- F–H · 2070 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 2042 Ų buried · 30 hydrogen bonds · protein-protein
- E–G · 1989 Ų buried · 32 hydrogen bonds · protein-protein
- I–J · 1984 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide (disulfide).
Compared structures
- 6EHI · NucT from Helicobacter pylori · 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 A0A1V3AA65
- Elsewhere: RCSB PDB 6EHI · PDBe 6EHI · UniProt A0A1V3AA65
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