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Structural and functional insights of DR2231 protein, the mazg-like nucleoside triphosphate pyrophosphohydrolase from deinococcus radiodurans, complexed with mg and dump
Analyse Structural and functional insights of DR2231 protein, the mazg-like nucleoside… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YFD
- Type
- protein
- Length
- 535 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mazg-like nucleoside triphosphate pyrophosphohydrolase
- EC
- 3.6.1.19
- UniProt
- Q9RS96
- Ligands
- UMP, MG, CL
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 66% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mazg-like nucleoside triphosphate pyrophosphohydrolase (EC 3.6.1.19) | protein | 138 | 62% helix, 1% strand | Q9RS96 |
| B | Mazg-like nucleoside triphosphate pyrophosphohydrolase (EC 3.6.1.19) | protein | 130 | 70% helix, 0% strand | Q9RS96 |
| C | Mazg-like nucleoside triphosphate pyrophosphohydrolase (EC 3.6.1.19) | protein | 137 | 63% helix, 1% strand | Q9RS96 |
| D | Mazg-like nucleoside triphosphate pyrophosphohydrolase (EC 3.6.1.19) | protein | 130 | 70% helix, 0% strand | Q9RS96 |
Ligands and binding sites
- UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 2 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 2 copies · chains A, D
- ACT · Acetate ion · additive · 2 copies · chains A, B, C, D
- GOL · Glycerol · additive · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 970 | 0.81 | 0.83 | 102 | UMP, GOL |
| 2 | 70 | 0.40 | 0.80 | 17 | empty |
| 3 | 80 | 0.40 | 0.79 | 20 | empty |
| 4 | 80 | 0.40 | 0.78 | 18 | empty |
| 5 | 91 | 0.38 | 0.76 | 19 | empty |
Interfaces
6 interfaces between chains.
- C–D · 3016 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 2963 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 229 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 130 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 124 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 2YFD · STRUCTURAL AND FUNCTIONAL INSIGHTS OF DR2231 PROTEIN, THE MAZG-LIKE NUCLEOSIDE… · 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 Q9RS96
- Elsewhere: RCSB PDB 2YFD · PDBe 2YFD · UniProt Q9RS96
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