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The native structure of beta-1,2-mannobiose phosphorylase from thermoanaerobacter sp.
Analyse The native structure of 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
- 7FIP
- Type
- protein
- Length
- 1,209 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
- ZN
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Beta-1,2-mannobiose phosphorylase (EC 2.4.1.339) | protein | 303 | 4% helix, 47% strand | B0K2C3 |
| B | Beta-1,2-mannobiose phosphorylase (EC 2.4.1.339) | protein | 302 | 3% helix, 49% strand | B0K2C3 |
| D | Beta-1,2-mannobiose phosphorylase (EC 2.4.1.339) | protein | 301 | 5% helix, 46% strand | B0K2C3 |
Ligands and binding sites
- ZN · Zinc ion · metal · 16 copies · chains A, B, D, C
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 | 913 | 0.81 | 0.83 | 92 | ZN |
| 2 | 571 | 0.77 | 0.84 | 54 | ZN |
| 3 | 274 | 0.69 | 0.84 | 34 | ZN |
| 4 | 385 | 0.68 | 0.80 | 32 | ZN |
| 5 | 320 | 0.66 | 0.81 | 43 | ZN |
Interfaces
5 interfaces between chains.
- B–D · 632 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 575 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 369 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 355 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 184 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 7FIP · The native structure of beta-1,2-mannobiose phosphorylase from Thermoanaerobacter sp. · 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 7FIP · PDBe 7FIP · UniProt B0K2C3
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