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Crystal structure of nudix hydrolase from nitrosomonas europaea
Analyse Crystal structure of nudix hydrolase from nitrosomonas europaea in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CNG
- Type
- protein
- Length
- 708 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nudix hydrolase
- UniProt
- Q82VD6
- Ligands
- ZN, NA, CL
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Nudix hydrolase | protein | 177 | 20% helix, 38% strand | Q82VD6 |
| B | Nudix hydrolase | protein | 176 | 18% helix, 39% strand | Q82VD6 |
| C | Nudix hydrolase | protein | 178 | 20% helix, 39% strand | Q82VD6 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 7 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1145 | 0.77 | 0.79 | 107 | EDO, NA, GOL |
| 2 | 214 | 0.51 | 0.76 | 38 | EDO, GOL |
| 3 | 275 | 0.50 | 0.74 | 31 | empty |
| 4 | 209 | 0.49 | 0.75 | 38 | NA, CL, GOL |
| 5 | 179 | 0.48 | 0.76 | 24 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1575 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1556 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 414 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 407 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 252 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 3CNG · Crystal structure of NUDIX hydrolase from Nitrosomonas europaea · 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 Q82VD6
- Elsewhere: RCSB PDB 3CNG · PDBe 3CNG · UniProt Q82VD6
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