MolNFT v1 · #107547 · protein
Crystal structure of B-1,4-mannopyranosyl-chitobiose phosphorylase at 1.60 ångström in complex with beta-D-mannopyranose and inorganic phosphate
4UDJ · UHGB_MP: “Crystal structure of B-1,4-mannopyranosyl-chitobiose phosphorylase at 1.60 ångström in complex with…”. X-ray diffraction, 3 ligands (BMA, K, PO4), 20 pockets (best druggability 0.79). MolNFT v1 #107547 on GenesisL1: 3D…
- PDB
- 4UDJ
- Type
- protein
- Length
- 1,922 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, 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, C, D, F | UHGB_MP (EC 2.4.1.-) | protein | 320 | 5% helix, 49% strand | D9ZDQ9 |
| B, E | UHGB_MP (EC 2.4.1.-) | protein | 321 | 5% helix, 49% strand | D9ZDQ9 |
Ligands and binding sites
- BMA · beta-D-mannopyranose · sugar · 6 copies · chains A, C, B, D, F, E
- K · Potassium ion · metal · 8 copies · chains A, F, B, C, D, E
- PO4 · Phosphate ion · ion · 6 copies · chains A, B, C, D, E, F
- EDO · 1,2-ethanediol · additive · 11 copies · chains A, E, B, C, D, F
- PGE · Triethylene glycol · additive · 9 copies · chains A, B, C, D, 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 410 | 0.79 | 0.88 | 38 | PO4, BMA |
| 2 | 432 | 0.79 | 0.87 | 41 | PO4, BMA |
| 3 | 414 | 0.78 | 0.87 | 42 | K, PO4, BMA |
| 4 | 427 | 0.78 | 0.87 | 36 | PO4, BMA |
| 5 | 429 | 0.78 | 0.87 | 43 | PO4, BMA, K |
Interfaces
9 interfaces between chains.
- B–D · 1326 Ų buried · 17 hydrogen bonds · protein-protein
- A–E · 1320 Ų buried · 16 hydrogen bonds · protein-protein
- C–F · 1314 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 893 Ų buried · 11 hydrogen bonds · protein-protein
- D–E · 879 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 4UDJ · Crystal structure of b-1,4-mannopyranosyl-chitobiose phosphorylase at 1.60 Angstrom in… · 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 4UDJ · PDBe 4UDJ · UniProt D9ZDQ9
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