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Crystal structure of ruminococcus albus beta-(1,4)- mannooligosaccharide phosphorylase (RAMP2) in complexes with phosphate
Analyse Crystal structure of ruminococcus albus beta-(1,4)- mannooligosaccharide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5AYD
- Type
- protein
- Length
- 2,010 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-1,4-mannooligosaccharide phosphorylase
- EC
- 2.4.1.319
- UniProt
- E6UBR9
- Ligands
- PO4
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Beta-1,4-mannooligosaccharide phosphorylase (EC 2.4.1.319) | protein | 335 | 6% helix, 49% strand | E6UBR9 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 463 | 0.74 | 0.83 | 45 | PO4 |
| 2 | 441 | 0.74 | 0.83 | 42 | PO4 |
| 3 | 438 | 0.74 | 0.83 | 38 | PO4 |
| 4 | 453 | 0.74 | 0.83 | 40 | PO4 |
| 5 | 441 | 0.74 | 0.84 | 42 | PO4 |
Interfaces
9 interfaces between chains.
- A–D · 1400 Ų buried · 18 hydrogen bonds · protein-protein
- C–F · 1393 Ų buried · 20 hydrogen bonds · protein-protein
- B–E · 1388 Ų buried · 16 hydrogen bonds · protein-protein
- D–E · 976 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 973 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5AYD · Crystal structure of Ruminococcus albus beta-(1,4)-mannooligosaccharide phosphorylase… · the same entry in another collection · chain C against C, TM-score 1.00
- E6UBR9 · AlphaFold monomer V2.0 prediction for beta-1,4-mannooligosaccharide phosphorylase (E6UBR9) · a predicted model of the same protein · 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 E6UBR9
- Elsewhere: RCSB PDB 5AYD · PDBe 5AYD · UniProt E6UBR9
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