Research workbench
Chlorovirus pbcv-1 bi-functional DCMP/DCTP deaminase bi-dcd
Analyse Chlorovirus pbcv-1 bi-functional DCMP/DCTP deaminase bi-dcd in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7FH4
- Type
- protein
- Length
- 280 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CMP/DCMP-type deaminase domain-containing protein
- UniProt
- O41078
- Ligands
- DCM, DCP, ZN, MG
- Pockets
- 5 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | CMP/DCMP-type deaminase domain-containing protein | protein | 140 | 41% helix, 18% strand | O41078 |
Ligands and binding sites
- DCM · 2'-deoxycytidine-5'-monophosphate · ligand · 2 copies · chains A, B
- DCP · 2'-deoxycytidine-5'-triphosphate · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 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
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 122 | 0.62 | 0.86 | 24 | DCM |
| 2 | 250 | 0.62 | 0.80 | 31 | empty |
| 3 | 108 | 0.61 | 0.87 | 22 | DCM |
| 4 | 78 | 0.36 | 0.77 | 19 | DCP, MG |
| 5 | 69 | 0.32 | 0.75 | 18 | DCP, MG |
Interfaces
1 interface between chains.
- A–B · 1739 Ų buried · 39 hydrogen bonds · protein-protein
Compared structures
- 7FH4 · Chlorovirus PBCV-1 bi-functional dCMP/dCTP deaminase bi-DCD · 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 O41078
- Elsewhere: RCSB PDB 7FH4 · PDBe 7FH4 · UniProt O41078
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