MolNFT v1 · #6260 · protein
Crystal structure of undecaprenyl diphosphate synthase from micrococcus luteus B-P 26
1F75 · Undecaprenyl pyrophosphate synthetase: “Crystal structure of undecaprenyl diphosphate synthase from micrococcus luteus B-P 26”. X-ray diffraction, 1 ligand (SO4), 2 pockets (best druggability 0.62). MolNFT v1 #6260 on GenesisL1: 3D…
- PDB
- 1F75
- Type
- protein
- Length
- 429 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Undecaprenyl pyrophosphate synthetase
- EC
- 2.5.1.31
- UniProt
- O82827
- Ligands
- SO4
- Pockets
- 2 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Undecaprenyl pyrophosphate synthetase (EC 2.5.1.31) | protein | 217 | 47% helix, 14% strand | O82827 |
| B | Undecaprenyl pyrophosphate synthetase (EC 2.5.1.31) | protein | 212 | 48% helix, 14% strand | O82827 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 295 | 0.62 | 0.79 | 30 | empty |
| 2 | 76 | 0.38 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1824 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 1F75 · Crystal structure of undecaprenyl diphosphate synthase from micrococcus luteus B-P 26 · the same entry in another collection · chain A against A, TM-score 1.00
- O82827 · AlphaFold monomer V2.0 prediction for DITRANS,POLYCIS-undecaprenyl- diphosphate synthase… · a predicted model of the same protein · chain A against A, TM-score 0.97
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 O82827
- Elsewhere: RCSB PDB 1F75 · PDBe 1F75 · UniProt O82827
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