Research workbench
Crystal structure of a trimeric exonuclease phoexo I from pyrococcus horikoshii OT3 in complex with poly-dt and MG2+ ion
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
- 4YOY
- 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
- Ligands
- MG
- Pockets
- 3 · best druggability 0.41
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 | 36% helix, 34% 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 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 116 | 0.41 | 0.76 | 29 | empty |
| 2 | 66 | 0.40 | 0.80 | 17 | empty |
| 3 | 59 | 0.27 | 0.73 | 16 | empty |
Interfaces
6 interfaces between chains.
- A–E · 857 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 831 Ų buried · 9 hydrogen bonds · protein-protein
- C–E · 817 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 669 Ų buried · 18 hydrogen bonds · protein-nucleic
- C–D · 663 Ų buried · 18 hydrogen bonds · protein-nucleic
Compared structures
- 4YOY · 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 4YOY · PDBe 4YOY · UniProt A0A060P168
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