MolNFT v1 · #139583 · protein
Structure of a prenyltransferase soaked with ipp
5XK6 · Undecaprenyl diphosphate synthase: “Structure of a prenyltransferase soaked with ipp”. X-ray diffraction, 3 ligands (POP, MG, SO4), 11 pockets (best druggability 0.80). MolNFT v1 #139583 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5XK6
- Type
- protein
- Length
- 856 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Undecaprenyl diphosphate synthase
- UniProt
- M4T4U9
- Ligands
- POP, MG, SO4
- Pockets
- 11 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Undecaprenyl diphosphate synthase | protein | 218 | 48% helix, 14% strand | M4T4U9 |
| B, D | Undecaprenyl diphosphate synthase | protein | 210 | 48% helix, 15% strand | M4T4U9 |
Ligands and binding sites
- POP · Pyrophosphate 2- · ligand · 6 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 131 | 0.80 | 0.98 | 31 | MG, POP |
| 2 | 139 | 0.80 | 0.97 | 31 | MG, POP |
| 3 | 251 | 0.65 | 0.83 | 37 | MG, POP, SO4 |
| 4 | 253 | 0.62 | 0.81 | 33 | MG, POP, SO4 |
| 5 | 164 | 0.44 | 0.75 | 25 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1844 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 1816 Ų buried · 25 hydrogen bonds · protein-protein
- A–D · 260 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 223 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5XK6 · Structure of a prenyltransferase soaked with IPP · 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 M4T4U9
- Elsewhere: RCSB PDB 5XK6 · PDBe 5XK6 · UniProt M4T4U9
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