MolNFT v1 · #111366 · protein
Crystal structure of a trimeric exonuclease phoexo I from pyrococcus horikoshii OT3 at 1.52A resolution.
4YOR · 3-5 exonuclease phoexo I: “Crystal structure of a trimeric exonuclease phoexo I from pyrococcus horikoshii OT3 at 1.52A resolution.”. X-ray diffraction, 1 ligand (MG), 5 pockets (best druggability 0.57). MolNFT v1 #111366 on…
- PDB
- 4YOR
- Type
- protein
- Length
- 449 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-5 exonuclease phoexo I
- UniProt
- A0A060P168
- Ligands
- MG
- Pockets
- 5 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-5 exonuclease phoexo I | protein | 227 | 38% helix, 34% strand | A0A060P168 |
| B | 3-5 exonuclease phoexo I | protein | 222 | 38% helix, 35% strand | A0A060P168 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 340 | 0.57 | 0.76 | 38 | MG |
| 2 | 180 | 0.46 | 0.75 | 25 | empty |
| 3 | 113 | 0.38 | 0.74 | 23 | empty |
| 4 | 61 | 0.33 | 0.76 | 17 | empty |
| 5 | 58 | 0.25 | 0.72 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 305 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4YOR · Crystal structure of a trimeric exonuclease PhoExo I from Pyrococcus horikoshii OT3 at… · 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 4YOR · PDBe 4YOR · UniProt A0A060P168
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