Research workbench
Crystal structure of B-1,4-mannopyranosyl-chitobiose phosphorylase at 1.76 ångström from unknown human gut bacteria (UHGB_MP) in complex with N-acetyl-D-glucosamine, beta-D-mannopyranose and inorganic phosphate
Analyse Crystal structure of B-1,4-mannopyranosyl-chitobiose phosphorylase at 1.76… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4UDK
- Type
- protein
- Length
- 1,920 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- UHGB_MP
- EC
- 2.4.1.-
- UniProt
- D9ZDQ9
- Ligands
- BMA, NDG, K, PO4
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, F | UHGB_MP (EC 2.4.1.-) | protein | 320 | 7% helix, 49% strand | D9ZDQ9 |
| C | UHGB_MP (EC 2.4.1.-) | protein | 319 | 5% helix, 48% strand | D9ZDQ9 |
| E | UHGB_MP (EC 2.4.1.-) | protein | 321 | 7% helix, 50% strand | D9ZDQ9 |
Ligands and binding sites
- BMA · beta-D-mannopyranose · sugar · 6 copies · chains A, C, B, D, F, E
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 6 copies · chains A, C, B, D, F, E
- K · Potassium ion · metal · 6 copies · chains A, B, C, D, E, F
- PO4 · Phosphate ion · ion · 6 copies · chains A, B, C, D, E, F
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, D, F, E
- PGE · Triethylene glycol · additive · 3 copies · chains A, E, D
- GOL · Glycerol · additive · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 352 | 0.78 | 0.88 | 38 | PO4, BMA, NDG |
| 2 | 328 | 0.77 | 0.88 | 35 | PO4, BMA, NDG, EDO |
| 3 | 338 | 0.77 | 0.87 | 39 | PO4, BMA, NDG |
| 4 | 351 | 0.77 | 0.87 | 43 | PO4, BMA, NDG |
| 5 | 330 | 0.76 | 0.87 | 38 | PO4, BMA, NDG |
Interfaces
9 interfaces between chains.
- A–E · 1297 Ų buried · 15 hydrogen bonds · protein-protein
- C–F · 1294 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 1291 Ų buried · 16 hydrogen bonds · protein-protein
- D–E · 886 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 881 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4UDK · Crystal structure of b-1,4-mannopyranosyl-chitobiose phosphorylase at 1.76 Angstrom from… · the same entry in another collection · 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 D9ZDQ9
- Elsewhere: RCSB PDB 4UDK · PDBe 4UDK · UniProt D9ZDQ9
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