MolNFT v1 · #34169 · protein
Phb depolymerase (S39A) complexed with R3HB trimer
2D81: “Phb depolymerase (S39A) complexed with R3HB trimer”. X-ray diffraction, 2 ligands (RB3, NAG), 1 pocket (best druggability 0.56). MolNFT v1 #34169 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2D81
- Type
- protein
- Length
- 318 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phb depolymerase
- EC
- 3.1.1.75
- Ligands
- RB3, NAG
- Pockets
- 1 · best druggability 0.56
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phb depolymerase (EC 3.1.1.75) | protein | 318 | 29% helix, 23% strand | — |
Ligands and binding sites
- RB3 · (1R)-3-{[(1R)-3-methoxy-1-methyl-3-oxopropyl]oxy}-1-methyl-3-oxopropyl (3R)-3-hydroxybutanoate · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 174 | 0.56 | 0.80 | 27 | RB3 |
Modifications
Observed in the structure: 4 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 2D81 · PHB depolymerase (S39A) complexed with R3HB trimer · 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
- Elsewhere: RCSB PDB 2D81 · PDBe 2D81
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