MolNFT v1 · #154266 · protein
Structural and catalytic analysis of two diverse uridine phosphorylases in the oomycete phytophthora capsici.
6K5K: “Structural and catalytic analysis of two diverse uridine phosphorylases in the oomycete phytophthora capsici.”. X-ray diffraction, 2 ligands (DUR, PO4), 11 pockets (best druggability 0.81). MolNFT v1 #154266 on GenesisL1: 3D…
- PDB
- 6K5K
- Type
- protein
- Length
- 1,151 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
- DUR, PO4
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Uridine phosphorylase (EC 2.4.2.3) | protein | 287 | 33% helix, 26% strand | A0A410UCT3 |
| B | Uridine phosphorylase (EC 2.4.2.3) | protein | 288 | 31% helix, 26% strand | A0A410UCT3 |
| C | Uridine phosphorylase (EC 2.4.2.3) | protein | 289 | 32% helix, 26% strand | A0A410UCT3 |
Ligands and binding sites
- DUR · 2'-deoxyuridine · ligand · 4 copies · chains A, C, B, D
- PO4 · Phosphate ion · ion · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 357 | 0.81 | 0.91 | 40 | empty |
| 2 | 355 | 0.81 | 0.91 | 36 | empty |
| 3 | 385 | 0.69 | 0.81 | 43 | PO4, DUR |
| 4 | 308 | 0.69 | 0.83 | 44 | empty |
| 5 | 231 | 0.65 | 0.83 | 31 | empty |
Interfaces
5 interfaces between chains.
- A–C · 2589 Ų buried · 27 hydrogen bonds · protein-protein
- B–D · 2528 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 582 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 69 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 66 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6K5K · 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 6K5K · PDBe 6K5K · UniProt A0A410UCT3
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