MolNFT v1 · #98311 · protein
Crystallographic structure of hhv-1 uracil-DNA glycosylase complexed with the bacillus phage pza inhibitor protein P56
4L5N: “Crystallographic structure of hhv-1 uracil-DNA glycosylase complexed with the bacillus phage pza inhibitor…”. X-ray diffraction, 3 pockets (best druggability 0.81). MolNFT v1 #98311 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4L5N
- Type
- protein
- Length
- 650 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uracil-DNA glycosylase; Early protein GP1B
- EC
- 3.2.2.27
- UniProt
- P10186, P06948
- Pockets
- 3 · best druggability 0.81
Structure
x-ray diffraction · 6 distinct chains · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uracil-DNA glycosylase (EC 3.2.2.27) | protein | 229 | 42% helix, 11% strand | P10186 |
| B | Uracil-DNA glycosylase (EC 3.2.2.27) | protein | 227 | 40% helix, 11% strand | P10186 |
| C | Early protein GP1B | protein | 50 | 20% helix, 52% strand | P06948 |
| D | Early protein GP1B | protein | 49 | 18% helix, 53% strand | P06948 |
| E | Early protein GP1B | protein | 47 | 19% helix, 55% strand | P06948 |
| F | Early protein GP1B | protein | 48 | 19% helix, 54% strand | P06948 |
Ligands and binding sites
- ACT · Acetate ion · additive · 15 copies · chains A, C, D, F, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1014 | 0.81 | 0.82 | 124 | ACT |
| 2 | 97 | 0.46 | 0.80 | 28 | ACT |
| 3 | 76 | 0.30 | 0.73 | 15 | empty |
Interfaces
9 interfaces between chains.
- A–C · 757 Ų buried · 11 hydrogen bonds · protein-protein
- B–E · 733 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 701 Ų buried · 22 hydrogen bonds · protein-protein
- E–F · 683 Ų buried · 19 hydrogen bonds · protein-protein
- A–F · 652 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 4L5N · Crystallographic Structure of HHV-1 Uracil-DNA Glycosylase complexed with the Bacillus… · 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 P10186
- Every structure of UniProt P06948
- Elsewhere: RCSB PDB 4L5N · PDBe 4L5N · UniProt P10186 · UniProt P06948
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.