Research workbench
Simvastatin synthase (lovd) from aspergillus terreus, unliganded, selenomethionyl derivative
Analyse Simvastatin synthase (lovd) from aspergillus terreus, unliganded… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HLB
- Type
- protein
- Length
- 1,599 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transesterase
- UniProt
- Q9Y7D1
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Transesterase | protein | 404 | 36% helix, 16% strand | Q9Y7D1 |
| C | Transesterase | protein | 398 | 36% helix, 17% strand | Q9Y7D1 |
| D | Transesterase | protein | 393 | 36% helix, 17% strand | Q9Y7D1 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 13 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 665 | 0.84 | 0.88 | 77 | SO4 |
| 2 | 581 | 0.82 | 0.88 | 82 | SO4 |
| 3 | 1085 | 0.81 | 0.82 | 94 | SO4 |
| 4 | 378 | 0.71 | 0.83 | 50 | empty |
| 5 | 438 | 0.70 | 0.81 | 51 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1531 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1393 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 796 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 367 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3HLB · Simvastatin Synthase (LovD) from Aspergillus terreus, unliganded, selenomethionyl… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9Y7D1 · AlphaFold monomer V2.0 prediction for monacolin J acid methylbutanoyltransferase (Q9Y7D1) · a predicted model of the same protein · chain D against A, TM-score 0.96
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 Q9Y7D1
- Elsewhere: RCSB PDB 3HLB · PDBe 3HLB · UniProt Q9Y7D1
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