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Crystal structure of DR2231, the mazg-like protein from deinococcus radiodurans, apo structure
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
- 2YF4
- Type
- protein
- Length
- 887 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
- SO4
- Pockets
- 19 · best druggability 0.61
Structure
x-ray diffraction · 4 distinct chains · 61% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | 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 | 146 | 62% helix, 1% strand | Q9RS96 |
| C, E | Mazg-like nucleoside triphosphate pyrophosphohydrolase (EC 3.6.1.19) | protein | 149 | 60% helix, 1% strand | Q9RS96 |
| F | Mazg-like nucleoside triphosphate pyrophosphohydrolase (EC 3.6.1.19) | protein | 143 | 62% helix, 1% strand | Q9RS96 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 19 copies · chains A, B, D, C, E, F
- GOL · Glycerol · additive · 22 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 589 | 0.61 | 0.73 | 58 | GOL, SO4 |
| 2 | 235 | 0.51 | 0.75 | 27 | empty |
| 3 | 202 | 0.49 | 0.75 | 27 | empty |
| 4 | 202 | 0.47 | 0.75 | 30 | GOL, SO4 |
| 5 | 153 | 0.46 | 0.76 | 20 | empty |
Interfaces
12 interfaces between chains.
- A–B · 2977 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 2871 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 2852 Ų buried · 15 hydrogen bonds · protein-protein
- C–E · 472 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 350 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 2YF4 · Crystal structure of DR2231, the MazG-like protein from Deinococcus radiodurans, Apo… · 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 2YF4 · PDBe 2YF4 · UniProt Q9RS96
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