Research workbench
Crystal structure of a trimeric exonuclease phoexo I from pyrococcus horikoshii OT3 in complex with poly-dt
Analyse Crystal structure of a trimeric exonuclease phoexo I from pyrococcus horikoshii… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YOX
- Type
- protein + DNA
- Length
- 688 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-5 exonuclease phoexo I; 5'-D(*TP*TP*TP*TP*TP*TP*T)-3'
- UniProt
- A0A060P168
- Pockets
- 4 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | 3-5 exonuclease phoexo I | protein | 226 | 35% helix, 35% strand | A0A060P168 |
| B, D, F | 5'-D(*TP*TP*TP*TP*TP*TP*T)-3' | dna | 4 | — | — |
| E | 3-5 exonuclease phoexo I | protein | 224 | 36% helix, 34% strand | A0A060P168 |
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 54 | 0.64 | 0.95 | 18 | empty |
| 2 | 167 | 0.52 | 0.79 | 34 | empty |
| 3 | 63 | 0.27 | 0.73 | 13 | empty |
| 4 | 51 | 0.25 | 0.73 | 15 | empty |
Interfaces
6 interfaces between chains.
- A–E · 847 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 840 Ų buried · 10 hydrogen bonds · protein-protein
- C–E · 823 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 666 Ų buried · 12 hydrogen bonds · protein-nucleic
- A–B · 662 Ų buried · 15 hydrogen bonds · protein-nucleic
Compared structures
- 4YOX · Crystal structure of a trimeric exonuclease PhoExo I from Pyrococcus horikoshii OT3 in… · 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 A0A060P168
- Elsewhere: RCSB PDB 4YOX · PDBe 4YOX · UniProt A0A060P168
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