Research workbench
Neryl diphosphate synthase from solanum lycopersicum
Analyse Neryl diphosphate synthase from solanum lycopersicum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VPC
- Type
- protein
- Length
- 472 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neryl-diphosphate synthase 1
- EC
- 2.5.1.28
- UniProt
- C1K5M2
- Ligands
- MLT
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Neryl-diphosphate synthase 1 (EC 2.5.1.28) | protein | 237 | 49% helix, 14% strand | C1K5M2 |
| B | Neryl-diphosphate synthase 1 (EC 2.5.1.28) | protein | 235 | 48% helix, 14% strand | C1K5M2 |
Ligands and binding sites
- MLT · D-malate · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 714 | 0.74 | 0.79 | 74 | EDO, MLT |
| 2 | 460 | 0.67 | 0.79 | 47 | EDO, MLT |
| 3 | 147 | 0.60 | 0.84 | 27 | EDO |
| 4 | 59 | 0.28 | 0.74 | 13 | EDO |
Interfaces
1 interface between chains.
- A–B · 2612 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7VPC · Neryl diphosphate synthase from Solanum lycopersicum · the same entry in another collection · chain B against B, TM-score 1.00
- C1K5M2 · AlphaFold monomer V2.0 prediction for dimethylallylcistransferase CPT1, chloroplastic… · a predicted model of the same protein · chain B against A, TM-score 0.93
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 C1K5M2
- Elsewhere: RCSB PDB 7VPC · PDBe 7VPC · UniProt C1K5M2
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