Research workbench
Crystal structure of B. subtilis glucose-1-phosphate uridylyltransferase yngb
Analyse Crystal structure of B. subtilis glucose-1-phosphate uridylyltransferase yngb in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7B1R
- Type
- protein
- Length
- 582 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable UTP--glucose-1-phosphate uridylyltransferase yngb
- EC
- 2.7.7.9
- UniProt
- O31822
- Pockets
- 8 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable UTP--glucose-1-phosphate uridylyltransferase yngb (EC 2.7.7.9) | protein | 292 | 42% helix, 23% strand | O31822 |
| B | Probable UTP--glucose-1-phosphate uridylyltransferase yngb (EC 2.7.7.9) | protein | 290 | 40% helix, 22% strand | O31822 |
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 406 | 0.63 | 0.77 | 50 | empty |
| 2 | 357 | 0.61 | 0.77 | 53 | empty |
| 3 | 154 | 0.51 | 0.79 | 26 | empty |
| 4 | 100 | 0.49 | 0.81 | 23 | empty |
| 5 | 105 | 0.43 | 0.78 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1172 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 7B1R · Crystal structure of B. subtilis glucose-1-phosphate uridylyltransferase YngB · the same entry in another collection · chain A against A, TM-score 1.00
- O31822 · AlphaFold monomer V2.0 prediction for probable UTP-- glucose-1-phosphate… · a predicted model of the same protein · chain B against A, TM-score 0.97
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 O31822
- Elsewhere: RCSB PDB 7B1R · PDBe 7B1R · UniProt O31822
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