MolNFT v1 · #140618 · protein
Crystal structure of a synthase from streptomyces sp. CL190
5YGJ · Cyclolavandulyl diphosphate synthase: “Crystal structure of a synthase from streptomyces sp. CL190”. X-ray diffraction, 8 pockets (best druggability 0.59). MolNFT v1 #140618 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5YGJ
- Type
- protein
- Length
- 823 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclolavandulyl diphosphate synthase
- UniProt
- X5IYJ5
- Pockets
- 8 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclolavandulyl diphosphate synthase | protein | 204 | 47% helix, 16% strand | X5IYJ5 |
| B, C | Cyclolavandulyl diphosphate synthase | protein | 207 | 50% helix, 15% strand | X5IYJ5 |
| D | Cyclolavandulyl diphosphate synthase | protein | 205 | 49% helix, 14% strand | X5IYJ5 |
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 | 374 | 0.59 | 0.76 | 41 | empty |
| 2 | 128 | 0.55 | 0.82 | 22 | empty |
| 3 | 236 | 0.55 | 0.77 | 32 | empty |
| 4 | 161 | 0.55 | 0.80 | 24 | empty |
| 5 | 152 | 0.54 | 0.80 | 28 | empty |
Interfaces
3 interfaces between chains.
- B–D · 1434 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 1409 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 154 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5YGJ · Crystal structure of a synthase from Streptomyces sp. CL190 · 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 X5IYJ5
- Elsewhere: RCSB PDB 5YGJ · PDBe 5YGJ · UniProt X5IYJ5
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