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The crystal structure of beta-1,2-mannobiose phosphorylase in complex with 1,4-mannobiose
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
- 7FIR
- 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
- Z2D, GUP, ZN
- Pockets
- 11 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-1,2-mannobiose phosphorylase (EC 2.4.1.339) | protein | 302 | 4% helix, 48% strand | B0K2C3 |
| C | Beta-1,2-mannobiose phosphorylase (EC 2.4.1.339) | protein | 304 | 4% helix, 46% strand | B0K2C3 |
| D | Beta-1,2-mannobiose phosphorylase (EC 2.4.1.339) | protein | 301 | 5% helix, 47% strand | B0K2C3 |
Ligands and binding sites
- Z2D · alpha-L-allopyranose · ligand · 4 copies · chains A, B, C, D
- GUP · alpha-L-gulopyranose · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 17 copies · chains A, B, D, C
- PGE · Triethylene glycol · additive · chains A
- 1PE · Pentaethylene glycol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 889 | 0.80 | 0.82 | 86 | Z2D, GUP, ZN |
| 2 | 582 | 0.78 | 0.84 | 58 | Z2D, GUP, ZN |
| 3 | 266 | 0.69 | 0.84 | 32 | Z2D, GUP, ZN |
| 4 | 246 | 0.69 | 0.84 | 34 | Z2D, GUP, ZN |
| 5 | 276 | 0.63 | 0.81 | 32 | ZN |
Interfaces
5 interfaces between chains.
- B–D · 659 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 566 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 368 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 338 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 182 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7FIR · The crystal structure of beta-1,2-mannobiose phosphorylase in complex with 1,4-mannobiose · 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 7FIR · PDBe 7FIR · UniProt B0K2C3
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