MolNFT v1 · #114872 · protein
Crystal structure of streptococcus mutans deoxycytidylate deaminase complexed with dttp
5C2O · Putative deoxycytidylate deaminase: “Crystal structure of streptococcus mutans deoxycytidylate deaminase complexed with dttp”. X-ray diffraction, 3 ligands (TTP, ZN, MG), 3 pockets (best druggability 0.63). MolNFT v1 #114872 on…
- PDB
- 5C2O
- Type
- protein
- Length
- 288 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative deoxycytidylate deaminase
- UniProt
- Q8DSE5
- Ligands
- TTP, ZN, MG
- Pockets
- 3 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Putative deoxycytidylate deaminase | protein | 144 | 33% helix, 26% strand | Q8DSE5 |
Ligands and binding sites
- TTP · Thymidine-5'-triphosphate · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
- MG · Magnesium ion · metal · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 444 | 0.63 | 0.77 | 46 | empty |
| 2 | 109 | 0.39 | 0.75 | 24 | empty |
| 3 | 53 | 0.29 | 0.76 | 15 | TTP |
Interfaces
1 interface between chains.
- A–B · 1649 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 5C2O · Crystal structure of Streptococcus mutans Deoxycytidylate Deaminase complexed with dTTP · 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 Q8DSE5
- Elsewhere: RCSB PDB 5C2O · PDBe 5C2O · UniProt Q8DSE5
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