Research workbench
Designed phosphodeoxyribosyltransferase
Analyse Designed phosphodeoxyribosyltransferase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HX9
- Type
- protein
- Length
- 1,245 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoside deoxyribosyltransferase
- EC
- 2.4.2.6
- UniProt
- Q9R5V5
- Ligands
- SO4
- Pockets
- 17 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, F, C, G, H | Nucleoside deoxyribosyltransferase (EC 2.4.2.6) | protein | 156 | 40% helix, 15% strand | Q9R5V5 |
| B | Nucleoside deoxyribosyltransferase (EC 2.4.2.6) | protein | 154 | 43% helix, 16% strand | Q9R5V5 |
| D | Nucleoside deoxyribosyltransferase (EC 2.4.2.6) | protein | 155 | 43% helix, 15% strand | Q9R5V5 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 14 copies · chains A, B, E, F, C, D, G, H
- PG4 · Tetraethylene glycol · additive · 6 copies · chains A, B, E, F, C, D, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 343 | 0.84 | 0.93 | 46 | PG4 |
| 2 | 335 | 0.84 | 0.93 | 44 | empty |
| 3 | 643 | 0.83 | 0.88 | 79 | SO4 |
| 4 | 297 | 0.83 | 0.93 | 48 | PG4 |
| 5 | 627 | 0.81 | 0.86 | 68 | SO4 |
Interfaces
15 interfaces between chains.
- G–H · 1636 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 1537 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 1525 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 1400 Ų buried · 6 hydrogen bonds · protein-protein
- E–C · 659 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
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 Q9R5V5
- Elsewhere: RCSB PDB 4HX9 · PDBe 4HX9 · UniProt Q9R5V5
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