MolNFT v1 · #139584 · protein
Crystal structure of isosesquilavandulyl diphosphate synthase from streptomyces sp. strain cnh-189 in complex with dmapp
5XK7 · Undecaprenyl diphosphate synthase: “Crystal structure of isosesquilavandulyl diphosphate synthase from streptomyces sp. strain cnh-189 in complex…”. X-ray diffraction, 4 ligands (POP, DMA, MG), 8 pockets (best druggability 0.81).…
- PDB
- 5XK7
- 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
- POP, DMA, MG, SO4
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Undecaprenyl diphosphate synthase | protein | 217 | 48% helix, 14% strand | M4T4U9 |
| B | Undecaprenyl diphosphate synthase | protein | 210 | 49% helix, 15% strand | M4T4U9 |
| C | Undecaprenyl diphosphate synthase | protein | 217 | 48% helix, 14% strand | M4T4U9 |
| D | Undecaprenyl diphosphate synthase | protein | 209 | 50% helix, 15% strand | M4T4U9 |
Ligands and binding sites
- POP · Pyrophosphate 2- · ligand · 5 copies · chains A, B, C, D
- DMA · Dimethylallyl diphosphate · ligand · 3 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 2 copies · chains A, B, C, D
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 134 | 0.81 | 0.98 | 32 | MG, POP, DMA |
| 2 | 139 | 0.80 | 0.97 | 32 | MG, POP, DMA |
| 3 | 313 | 0.66 | 0.81 | 51 | MG, POP, DMA |
| 4 | 258 | 0.62 | 0.81 | 34 | MG, POP |
| 5 | 400 | 0.55 | 0.73 | 53 | MES |
Interfaces
4 interfaces between chains.
- A–B · 1853 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 1842 Ų buried · 26 hydrogen bonds · protein-protein
- A–D · 271 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 257 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5XK7 · Crystal structure of Isosesquilavandulyl Diphosphate Synthase from Streptomyces sp.… · 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 5XK7 · PDBe 5XK7 · UniProt M4T4U9
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