Research workbench
Cytidine and deoxycytidylate deaminase zinc-binding region from nitrosomonas europaea.
Analyse Cytidine and deoxycytidylate deaminase zinc-binding region from nitrosomonas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2G84
- Type
- protein
- Length
- 371 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytidine and deoxycytidylate deaminase zinc-binding region
- UniProt
- Q82Y41
- Ligands
- ZN, NA
- Pockets
- 3 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytidine and deoxycytidylate deaminase zinc-binding region | protein | 189 | 40% helix, 19% strand | Q82Y41 |
| B | Cytidine and deoxycytidylate deaminase zinc-binding region | protein | 182 | 40% helix, 20% strand | Q82Y41 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · chains B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
- BME · Beta-mercaptoethanol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 152 | 0.57 | 0.82 | 30 | EDO |
| 2 | 187 | 0.57 | 0.80 | 33 | EDO |
| 3 | 94 | 0.41 | 0.78 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 1900 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 1 disulfide (additive adduct, disulfide).
Compared structures
- 2G84 · Cytidine and deoxycytidylate deaminase zinc-binding region 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 Q82Y41
- Elsewhere: RCSB PDB 2G84 · PDBe 2G84 · UniProt Q82Y41
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