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The crystal structure of beta-1,2-mannobiose phosphorylase in complex with mannose 1-phosphate (M1P)
Analyse The crystal structure of beta-1,2-mannobiose phosphorylase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7FIS
- Type
- protein
- Length
- 1,208 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-1,2-mannobiose phosphorylase
- EC
- 2.4.1.339
- UniProt
- B0K2C3
- Ligands
- M1P, ZN
- Pockets
- 12 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, B, A, D | Beta-1,2-mannobiose phosphorylase (EC 2.4.1.339) | protein | 302 | 4% helix, 47% strand | B0K2C3 |
Ligands and binding sites
- M1P · 1-O-phosphono-alpha-D-mannopyranose · ligand · 5 copies · chains C, B, A, D
- ZN · Zinc ion · metal · 17 copies · chains C, D, B, A
- PG4 · Tetraethylene glycol · additive · 2 copies · chains C, B
- 1PE · Pentaethylene glycol · additive · chains D
- GOL · Glycerol · additive · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 850 | 0.80 | 0.83 | 81 | M1P, ZN |
| 2 | 1158 | 0.80 | 0.81 | 96 | ZN, M1P |
| 3 | 475 | 0.70 | 0.80 | 47 | M1P, ZN, GOL |
| 4 | 345 | 0.70 | 0.83 | 33 | M1P, ZN |
| 5 | 176 | 0.53 | 0.79 | 18 | empty |
Interfaces
5 interfaces between chains.
- B–D · 657 Ų buried · 7 hydrogen bonds · protein-protein
- C–A · 557 Ų buried · 7 hydrogen bonds · protein-protein
- B–A · 359 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 335 Ų buried · 4 hydrogen bonds · protein-protein
- C–B · 183 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7FIS · The crystal structure of beta-1,2-mannobiose phosphorylase in complex with mannose… · the same entry in another collection · chain D against D, TM-score 1.00
- B0K2C3 · AlphaFold monomer V2.0 prediction for beta-1,2-mannobiose phosphorylase (B0K2C3) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 B0K2C3
- Elsewhere: RCSB PDB 7FIS · PDBe 7FIS · UniProt B0K2C3
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