Research workbench
2.6 a crystal structure of uracil phosphoribosyltransferase from burkholderia pseudomallei
Analyse 2.6 a crystal structure of uracil phosphoribosyltransferase from burkholderia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DMP
- Type
- protein
- Length
- 855 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uracil phosphoribosyltransferase
- EC
- 2.4.2.9
- UniProt
- Q63VS8
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Uracil phosphoribosyltransferase (EC 2.4.2.9) | protein | 214 | 34% helix, 27% strand | Q63VS8 |
| C | Uracil phosphoribosyltransferase (EC 2.4.2.9) | protein | 213 | 36% helix, 29% strand | Q63VS8 |
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1021 | 0.78 | 0.80 | 101 | empty |
| 2 | 263 | 0.74 | 0.88 | 37 | empty |
| 3 | 68 | 0.70 | 0.96 | 19 | empty |
| 4 | 206 | 0.69 | 0.86 | 31 | empty |
| 5 | 299 | 0.65 | 0.81 | 34 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1004 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 987 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 395 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 288 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 273 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3DMP · 2.6 A crystal structure of uracil phosphoribosyltransferase from Burkholderia pseudomallei · the same entry in another collection · chain A against A, TM-score 1.00
- Q63VS8 · AlphaFold monomer V2.0 prediction for uracil phosphoribosyltransferase (Q63VS8) · a predicted model of the same protein · chain C against A, TM-score 0.94
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 Q63VS8
- Elsewhere: RCSB PDB 3DMP · PDBe 3DMP · UniProt Q63VS8
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