Research workbench
VRR_NUC domain protein
Analyse VRR_NUC domain protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QBL
- Type
- protein
- Length
- 735 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vrr-nuc
- UniProt
- A5WF35
- Ligands
- MG
- Pockets
- 5 · best druggability 0.54
Structure
x-ray diffraction · 6 distinct chains · 37% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vrr-nuc | protein | 122 | 39% helix, 20% strand | A5WF35 |
| B | Vrr-nuc | protein | 121 | 37% helix, 21% strand | A5WF35 |
| D | Vrr-nuc | protein | 121 | 38% helix, 21% strand | A5WF35 |
| E | Vrr-nuc | protein | 126 | 36% helix, 19% strand | A5WF35 |
| F | Vrr-nuc | protein | 122 | 36% helix, 20% strand | A5WF35 |
| C | Vrr-nuc | protein | 123 | 37% helix, 20% strand | A5WF35 |
Ligands and binding sites
- MG · Magnesium ion · metal · 6 copies · chains A, B, D, E, F, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 310 | 0.54 | 0.75 | 30 | empty |
| 2 | 165 | 0.41 | 0.73 | 25 | empty |
| 3 | 103 | 0.34 | 0.73 | 24 | empty |
| 4 | 61 | 0.27 | 0.73 | 13 | empty |
| 5 | 50 | 0.24 | 0.73 | 17 | empty |
Interfaces
8 interfaces between chains.
- A–E · 1885 Ų buried · 34 hydrogen bonds · protein-protein
- D–C · 1844 Ų buried · 31 hydrogen bonds · protein-protein
- B–F · 1814 Ų buried · 32 hydrogen bonds · protein-protein
- E–C · 290 Ų buried · 4 hydrogen bonds · protein-protein
- D–F · 154 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 18 modified (engineered).
Compared structures
- 4QBL · VRR_NUC domain protein · 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 A5WF35
- Elsewhere: RCSB PDB 4QBL · PDBe 4QBL · UniProt A5WF35
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