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Structure of a polyisoprenoid binding domain from saccharophagus degradans implicated in plant cell wall breakdown
Analyse Structure of a polyisoprenoid binding domain from saccharophagus degradans… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2X32
- Type
- protein
- Length
- 350 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cellulose-binding protein
- UniProt
- Q21LI5
- Ligands
- OTP
- Pockets
- 4 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cellulose-binding protein | protein | 174 | 20% helix, 49% strand | Q21LI5 |
| B | Cellulose-binding protein | protein | 176 | 22% helix, 51% strand | Q21LI5 |
Ligands and binding sites
- OTP · (2E,6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-octamethyldotriaconta-2,6,10,14,18,22,26,30-octaenyl trihydrogen diphosphate · ligand · 2 copies · chains A, B
- IMD · Imidazole · additive · 3 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 | 423 | 0.85 | 0.92 | 62 | OTP |
| 2 | 431 | 0.85 | 0.92 | 62 | OTP |
| 3 | 434 | 0.70 | 0.81 | 64 | IMD |
| 4 | 111 | 0.45 | 0.79 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 743 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 2X32 · Structure of a polyisoprenoid binding domain from Saccharophagus degradans implicated in… · 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 Q21LI5
- Elsewhere: RCSB PDB 2X32 · PDBe 2X32 · UniProt Q21LI5
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