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Crystal structure of a trimeric exonuclease phoexo I from pyrococcus horikoshii OT3 in complex with poly-dc
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
- 4YOW
- Type
- protein + DNA
- Length
- 693 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-5 exonuclease phoexo I; 5'-D(*CP*CP*CP*CP*CP*CP*C)-3'
- UniProt
- A0A060P168
- Pockets
- 5 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | 3-5 exonuclease phoexo I | protein | 227 | 37% helix, 33% strand | A0A060P168 |
| B, D, F | 5'-D(*CP*CP*CP*CP*CP*CP*C)-3' | dna | 4 | — | — |
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 60 | 0.61 | 0.92 | 21 | empty |
| 2 | 63 | 0.61 | 0.91 | 23 | empty |
| 3 | 131 | 0.40 | 0.75 | 29 | empty |
| 4 | 61 | 0.27 | 0.73 | 13 | empty |
| 5 | 54 | 0.25 | 0.73 | 11 | empty |
Interfaces
6 interfaces between chains.
- A–E · 865 Ų buried · 11 hydrogen bonds · protein-protein
- C–E · 853 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 852 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 657 Ų buried · 20 hydrogen bonds · protein-nucleic
- E–F · 648 Ų buried · 19 hydrogen bonds · protein-nucleic
Compared structures
- 4YOW · 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 4YOW · PDBe 4YOW · UniProt A0A060P168
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