Research workbench
Crystal structure of DR2231, the mazg-like protein from deinococcus radiodurans, complex with manganese
Analyse Crystal structure of DR2231, the mazg-like protein from deinococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YF3
- Type
- protein
- Length
- 906 residues
- Chains
- 6
- 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
- MN, SO4
- Pockets
- 16 · best druggability 0.66
Structure
x-ray diffraction · 5 distinct chains · 61% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mazg-like nucleoside triphosphate pyrophosphohydrolase (EC 3.6.1.19) | protein | 150 | 59% helix, 1% strand | Q9RS96 |
| B | Mazg-like nucleoside triphosphate pyrophosphohydrolase (EC 3.6.1.19) | protein | 149 | 60% helix, 1% strand | Q9RS96 |
| C, E | Mazg-like nucleoside triphosphate pyrophosphohydrolase (EC 3.6.1.19) | protein | 153 | 59% helix, 1% strand | Q9RS96 |
| D | Mazg-like nucleoside triphosphate pyrophosphohydrolase (EC 3.6.1.19) | protein | 153 | 63% helix, 1% strand | Q9RS96 |
| F | Mazg-like nucleoside triphosphate pyrophosphohydrolase (EC 3.6.1.19) | protein | 148 | 61% helix, 1% strand | Q9RS96 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 11 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 14 copies · chains A, B, C, D, E, F
- GOL · Glycerol · additive · 30 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 645 | 0.66 | 0.76 | 67 | GOL |
| 2 | 337 | 0.57 | 0.76 | 36 | SO4, MN, GOL |
| 3 | 252 | 0.54 | 0.76 | 27 | GOL |
| 4 | 213 | 0.50 | 0.76 | 26 | GOL |
| 5 | 188 | 0.48 | 0.75 | 26 | GOL |
Interfaces
12 interfaces between chains.
- A–B · 2924 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 2855 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 2849 Ų buried · 15 hydrogen bonds · protein-protein
- C–E · 499 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 327 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 2YF3 · Crystal structure of DR2231, the MazG-like protein from Deinococcus radiodurans, complex… · 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 2YF3 · PDBe 2YF3 · UniProt Q9RS96
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