Research workbench
Double-stranded DNA-specific cytidine deaminase type VI secretion system effector and cognate immunity complex from burkholderia cenocepacia
Analyse Double-stranded DNA-specific cytidine deaminase type VI secretion system… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6U08
- Type
- protein
- Length
- 1,017 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Double-stranded DNA-specific cytidine deaminase; Dddi
- UniProt
- A0A1V2VU04, A0A1V6L5G6
- Ligands
- ZN
- Pockets
- 10 · best druggability 0.76
Structure
x-ray diffraction · 5 distinct chains · 18% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Double-stranded DNA-specific cytidine deaminase | protein | 133 | 16% helix, 29% strand | A0A1V2VU04 |
| B | Dddi | protein | 120 | 20% helix, 43% strand | A0A1V6L5G6 |
| D | Dddi | protein | 121 | 20% helix, 42% strand | A0A1V6L5G6 |
| E, G | Double-stranded DNA-specific cytidine deaminase | protein | 132 | 16% helix, 28% strand | A0A1V2VU04 |
| F, H | Dddi | protein | 123 | 20% helix, 41% strand | A0A1V6L5G6 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, C, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 105 | 0.76 | 0.96 | 29 | empty |
| 2 | 145 | 0.74 | 0.93 | 31 | ZN |
| 3 | 146 | 0.72 | 0.91 | 35 | empty |
| 4 | 261 | 0.68 | 0.84 | 43 | empty |
| 5 | 126 | 0.45 | 0.78 | 18 | empty |
Interfaces
8 interfaces between chains.
- C–D · 1211 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1192 Ų buried · 20 hydrogen bonds · protein-protein
- G–H · 1157 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 1146 Ų buried · 18 hydrogen bonds · protein-protein
- C–E · 197 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 6U08 · Double-stranded DNA-specific cytidine deaminase type VI secretion system effector and… · 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 A0A1V2VU04
- Every structure of UniProt A0A1V6L5G6
- Elsewhere: RCSB PDB 6U08 · PDBe 6U08 · UniProt A0A1V2VU04 · UniProt A0A1V6L5G6
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