MolNFT v1 · #107546 · protein
Crystal structure of B-1,4-mannopyranosyl-chitobiose phosphorylase at 1.85 ångström from unknown human gut bacteria (UHGB_MP)
4UDI: “Crystal structure of B-1,4-mannopyranosyl-chitobiose phosphorylase at 1.85 ångström from unknown human gut…”. X-ray diffraction, 2 ligands (K, PO4), 20 pockets (best druggability 0.79). MolNFT v1 #107546 on GenesisL1: 3D structure…
- PDB
- 4UDI
- Type
- protein
- Length
- 1,923 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
- K, PO4
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | UHGB_MP (EC 2.4.1.-) | protein | 321 | 5% helix, 49% strand | D9ZDQ9 |
| D, E, F | UHGB_MP (EC 2.4.1.-) | protein | 320 | 5% helix, 49% strand | D9ZDQ9 |
Ligands and binding sites
- 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
- GOL · Glycerol · additive · 27 copies · chains A, C, B, D, F, E
- EDO · 1,2-ethanediol · additive · 21 copies · chains A, C, E, B, D, F
- PGE · Triethylene glycol · additive · 3 copies · chains A, 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 | 448 | 0.79 | 0.87 | 44 | PO4, GOL |
| 2 | 442 | 0.79 | 0.87 | 40 | PO4, GOL, EDO |
| 3 | 485 | 0.78 | 0.85 | 52 | PO4, GOL |
| 4 | 447 | 0.78 | 0.86 | 36 | PO4, GOL |
| 5 | 473 | 0.78 | 0.85 | 49 | PO4, GOL |
Interfaces
9 interfaces between chains.
- A–E · 1375 Ų buried · 19 hydrogen bonds · protein-protein
- C–F · 1366 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 1361 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 874 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 866 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4UDI · Crystal structure of b-1,4-mannopyranosyl-chitobiose phosphorylase at 1.85 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 4UDI · PDBe 4UDI · UniProt D9ZDQ9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.