Research workbench
Structural and catalytic analysis of two diverse uridine phosphorylases in the oomycete phytophthora capsici.
Analyse Structural and catalytic analysis of two diverse uridine phosphorylases in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6K8P
- Type
- protein
- Length
- 1,148 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uridine phosphorylase
- EC
- 2.4.2.3
- UniProt
- A0A410UCT3
- Ligands
- THM, R1P, TDR, PO4
- Pockets
- 13 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Uridine phosphorylase (EC 2.4.2.3) | protein | 294 | 33% helix, 25% strand | A0A410UCT3 |
| B, D | Uridine phosphorylase (EC 2.4.2.3) | protein | 280 | 32% helix, 26% strand | A0A410UCT3 |
Ligands and binding sites
- THM · Thymidine · ligand · 2 copies · chains A, B, C, D
- R1P · 1-O-phosphono-alpha-D-ribofuranose · ligand · 2 copies · chains A, B, C, D
- TDR · Thymine · ligand · 2 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 387 | 0.78 | 0.88 | 41 | empty |
| 2 | 961 | 0.78 | 0.80 | 82 | PO4, THM |
| 3 | 282 | 0.77 | 0.90 | 42 | empty |
| 4 | 350 | 0.72 | 0.84 | 40 | R1P, TDR |
| 5 | 331 | 0.71 | 0.84 | 40 | R1P, TDR |
Interfaces
6 interfaces between chains.
- A–B · 2737 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 2669 Ų buried · 32 hydrogen bonds · protein-protein
- A–D · 270 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 112 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 71 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6K8P · Structural and catalytic analysis of two diverse uridine phosphorylases in the oomycete… · 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 A0A410UCT3
- Elsewhere: RCSB PDB 6K8P · PDBe 6K8P · UniProt A0A410UCT3
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