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The crystal structure of mannose-bound beta-1,2-mannobiose phosphorylase from thermoanaerobacter sp.
Analyse The crystal structure of mannose-bound beta-1,2-mannobiose phosphorylase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7FIQ
- 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
- MAN, ZN
- Pockets
- 10 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 48% 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, 48% strand | B0K2C3 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains C, B, A, D
- ZN · Zinc ion · metal · 17 copies · chains C, D, B, A
- PGE · Triethylene glycol · additive · 2 copies · chains C, D
- GOL · Glycerol · additive · chains C
- 1PE · Pentaethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 891 | 0.81 | 0.83 | 87 | MAN, ZN |
| 2 | 860 | 0.80 | 0.83 | 84 | ZN, MAN |
| 3 | 349 | 0.69 | 0.82 | 37 | MAN, ZN |
| 4 | 238 | 0.69 | 0.85 | 31 | MAN, ZN |
| 5 | 183 | 0.54 | 0.79 | 19 | empty |
Interfaces
5 interfaces between chains.
- B–D · 683 Ų buried · 5 hydrogen bonds · protein-protein
- C–A · 587 Ų buried · 7 hydrogen bonds · protein-protein
- B–A · 399 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 354 Ų buried · 5 hydrogen bonds · protein-protein
- C–B · 180 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 7FIQ · The crystal structure of mannose-bound beta-1,2-mannobiose phosphorylase from… · 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 7FIQ · PDBe 7FIQ · UniProt B0K2C3
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