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Structure of a ubia homolog from archaeoglobus fulgidus bound to dmapp and MG2+
Analyse Structure of a ubia homolog from archaeoglobus fulgidus bound to dmapp and MG2+ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4TQ4
- Type
- protein
- Length
- 1,155 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prenyltransferase
- UniProt
- O28625
- Ligands
- DMA, MG
- Pockets
- 14 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 75% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prenyltransferase | protein | 288 | 75% helix, 1% strand | O28625 |
| B | Prenyltransferase | protein | 289 | 75% helix, 1% strand | O28625 |
| C | Prenyltransferase | protein | 288 | 76% helix, 1% strand | O28625 |
| D | Prenyltransferase | protein | 290 | 75% helix, 1% strand | O28625 |
Ligands and binding sites
- DMA · Dimethylallyl diphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1168 | 0.88 | 0.89 | 98 | MG, DMA |
| 2 | 698 | 0.88 | 0.91 | 69 | MG, DMA |
| 3 | 1111 | 0.86 | 0.87 | 101 | MG, DMA |
| 4 | 935 | 0.86 | 0.87 | 85 | MG, DMA |
| 5 | 799 | 0.80 | 0.82 | 52 | empty |
Interfaces
3 interfaces between chains.
- A–D · 678 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 655 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 336 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4TQ4 · Structure of a UbiA homolog from Archaeoglobus fulgidus bound to DMAPP and Mg2+ · 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 O28625
- Elsewhere: RCSB PDB 4TQ4 · PDBe 4TQ4 · UniProt O28625
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