Research workbench
Crystal structure of kojibiose phosphorylase complexed with glucose
Analyse Crystal structure of kojibiose phosphorylase complexed with glucose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WIR
- Type
- protein
- Length
- 3,024 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kojibiose phosphorylase
- EC
- 2.4.1.230
- UniProt
- A4XGP2
- Ligands
- BGC, PO4
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Kojibiose phosphorylase (EC 2.4.1.230) | protein | 756 | 34% helix, 27% strand | A4XGP2 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 8 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 6 copies · chains A, B, D, C
- GOL · Glycerol · additive · 9 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1099 | 0.82 | 0.83 | 65 | GOL |
| 2 | 624 | 0.82 | 0.87 | 69 | empty |
| 3 | 902 | 0.78 | 0.80 | 75 | BGC, PO4 |
| 4 | 876 | 0.76 | 0.80 | 71 | BGC, PO4 |
| 5 | 1104 | 0.76 | 0.78 | 85 | BGC, PO4 |
Interfaces
4 interfaces between chains.
- B–D · 1267 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1246 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 725 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 467 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 3WIR · Crystal structure of kojibiose phosphorylase complexed with glucose · 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 A4XGP2
- Elsewhere: RCSB PDB 3WIR · PDBe 3WIR · UniProt A4XGP2
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