MolNFT v1 · #139580 · protein
Crystal structure of apo form isosesquilavandulyl diphosphate synthase from streptomyces sp. strain cnh-189
5XK3 · Undecaprenyl diphosphate synthase: “Crystal structure of apo form isosesquilavandulyl diphosphate synthase from streptomyces sp. strain cnh-189”. X-ray diffraction, 1 ligand (SO4), 11 pockets (best druggability 0.76). MolNFT v1…
- PDB
- 5XK3
- Type
- protein
- Length
- 853 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Undecaprenyl diphosphate synthase
- UniProt
- M4T4U9
- Ligands
- SO4
- Pockets
- 11 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Undecaprenyl diphosphate synthase | protein | 217 | 48% helix, 14% strand | M4T4U9 |
| B, D | Undecaprenyl diphosphate synthase | protein | 210 | 50% helix, 15% strand | M4T4U9 |
| C | Undecaprenyl diphosphate synthase | protein | 216 | 49% helix, 14% strand | M4T4U9 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 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 | 101 | 0.76 | 0.97 | 30 | SO4 |
| 2 | 90 | 0.76 | 0.97 | 29 | SO4 |
| 3 | 307 | 0.68 | 0.83 | 50 | SO4 |
| 4 | 242 | 0.67 | 0.84 | 32 | SO4 |
| 5 | 189 | 0.44 | 0.74 | 33 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1866 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 1839 Ų buried · 27 hydrogen bonds · protein-protein
- A–D · 261 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 230 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5XK3 · Crystal structure of apo form Isosesquilavandulyl Diphosphate Synthase from Streptomyces… · 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 5XK3 · PDBe 5XK3 · UniProt M4T4U9
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