MolNFT v1 · #123844 · protein
Wild type D4 in orthorhombic space group
5JX3 · Uracil-DNA glycosylase: “Wild type D4 in orthorhombic space group”. X-ray diffraction, 1 ligand (CL), 20 pockets (best druggability 0.85). MolNFT v1 #123844 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5JX3
- Type
- protein
- Length
- 1,741 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uracil-DNA glycosylase
- EC
- 3.2.2.27
- UniProt
- P04303
- Ligands
- CL
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E, F, G | Uracil-DNA glycosylase (EC 3.2.2.27) | protein | 218 | 39% helix, 17% strand | P04303 |
| C | Uracil-DNA glycosylase (EC 3.2.2.27) | protein | 217 | 37% helix, 18% strand | P04303 |
| D | Uracil-DNA glycosylase (EC 3.2.2.27) | protein | 219 | 38% helix, 17% strand | P04303 |
| H | Uracil-DNA glycosylase (EC 3.2.2.27) | protein | 215 | 39% helix, 17% strand | P04303 |
Ligands and binding sites
- CL · Chloride ion · ion · 4 copies · chains D, F, G, H
- GOL · Glycerol · additive · 15 copies · chains A, B, C, D, E, G, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 803 | 0.85 | 0.88 | 106 | empty |
| 2 | 693 | 0.76 | 0.81 | 50 | empty |
| 3 | 549 | 0.75 | 0.82 | 50 | GOL |
| 4 | 579 | 0.69 | 0.79 | 51 | empty |
| 5 | 116 | 0.64 | 0.88 | 33 | GOL |
Interfaces
15 interfaces between chains.
- A–B · 716 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 708 Ų buried · 3 hydrogen bonds · protein-protein
- E–F · 658 Ų buried · 8 hydrogen bonds · protein-protein
- G–H · 536 Ų buried · 5 hydrogen bonds · protein-protein
- A–G · 483 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5JX3 · Wild type D4 in orthorhombic space group · 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 P04303
- Elsewhere: RCSB PDB 5JX3 · PDBe 5JX3 · UniProt P04303
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