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Crystal structure of cellvibrio gilvus cellobiose phosphorylase complexed with sulfate and isofagomine
Analyse Crystal structure of cellvibrio gilvus cellobiose phosphorylase complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QFY
- Type
- protein
- Length
- 1,644 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cellobiose phosphorylase
- EC
- 2.4.1.20
- UniProt
- O66264
- Ligands
- IFM, BGC, SO4
- Pockets
- 14 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cellobiose phosphorylase (EC 2.4.1.20) | protein | 822 | 30% helix, 27% strand | O66264 |
Ligands and binding sites
- IFM · 5-hydroxymethyl-3,4-dihydroxypiperidine · ligand · 2 copies · chains A, B
- BGC · beta-D-glucopyranose · sugar · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1060 | 0.81 | 0.83 | 116 | BGC, SO4, IFM |
| 2 | 146 | 0.79 | 0.96 | 29 | empty |
| 3 | 241 | 0.70 | 0.86 | 38 | empty |
| 4 | 224 | 0.70 | 0.86 | 37 | empty |
| 5 | 289 | 0.68 | 0.83 | 37 | empty |
Interfaces
1 interface between chains.
- A–B · 3417 Ų buried · 63 hydrogen bonds · protein-protein
Compared structures
- 3QFY · Crystal Structure of Cellvibrio gilvus Cellobiose Phosphorylase Complexed with Sulfate… · 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 O66264
- Elsewhere: RCSB PDB 3QFY · PDBe 3QFY · UniProt O66264
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