MolNFT v1 · #114430 · protein
Ent-copalyl diphosphate synthase from streptomyces platensis
5BP8: “Ent-copalyl diphosphate synthase from streptomyces platensis”. X-ray diffraction, 1 ligand (SO4), 5 pockets (best druggability 0.78). MolNFT v1 #114430 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5BP8
- Type
- protein
- Length
- 515 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ent-copalyl diphosphate synthase
- UniProt
- A0A023VSF1
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 57% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ent-copalyl diphosphate synthase | protein | 515 | 57% helix, 3% strand | A0A023VSF1 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 483 | 0.78 | 0.86 | 48 | SO4 |
| 2 | 164 | 0.76 | 0.93 | 24 | empty |
| 3 | 211 | 0.53 | 0.77 | 28 | empty |
| 4 | 60 | 0.35 | 0.78 | 17 | empty |
| 5 | 55 | 0.28 | 0.74 | 18 | empty |
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 5BP8 · ent-Copalyl diphosphate synthase from Streptomyces platensis · 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 A0A023VSF1
- Elsewhere: RCSB PDB 5BP8 · PDBe 5BP8 · UniProt A0A023VSF1
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