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Crystal structure of DSS1 exoribonuclease active site mutant D477N from candida glabrata
Analyse Crystal structure of DSS1 exoribonuclease active site mutant D477N from candida… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6F3H
- Type
- protein + RNA
- Length
- 1,564 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exoribonuclease II, mitochondrial; RNA (5'-R(P*AP*GP*AP*UP*AP*C)-3'); RNA…
- UniProt
- Q6FJE0
- Ligands
- MG
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Exoribonuclease II, mitochondrial | protein | 762 | 42% helix, 20% strand | Q6FJE0 |
| B | Exoribonuclease II, mitochondrial | protein | 790 | 43% helix, 19% strand | Q6FJE0 |
| C | RNA (5'-R(P*AP*GP*AP*UP*AP*C)-3') | rna | 6 | — | — |
| D | RNA (5'-R(P*CP*AP*CP*UP*GP*A)-3') | rna | 6 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1161 | 0.83 | 0.85 | 101 | empty |
| 2 | 1011 | 0.83 | 0.84 | 84 | empty |
| 3 | 649 | 0.72 | 0.79 | 57 | empty |
| 4 | 507 | 0.68 | 0.79 | 42 | empty |
| 5 | 212 | 0.63 | 0.83 | 35 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1010 Ų buried · 35 hydrogen bonds · protein-nucleic
- B–D · 974 Ų buried · 34 hydrogen bonds · protein-nucleic
- A–B · 143 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 25 modified (engineered).
Compared structures
- 6F3H · Crystal structure of Dss1 exoribonuclease active site mutant D477N from Candida glabrata · 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 Q6FJE0
- Elsewhere: RCSB PDB 6F3H · PDBe 6F3H · UniProt Q6FJE0
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