MolNFT v1 · #97198 · protein
X-ray structure uridine phosphorylase from vibrio cholerae in complex with 6-methyluracil at 1.17 a resolution
4K6O: “X-ray structure uridine phosphorylase from vibrio cholerae in complex with 6-methyluracil at 1.17 a resolution”. X-ray diffraction, 4 ligands (6MU, MG, NA), 14 pockets (best druggability 0.75). MolNFT v1 #97198 on GenesisL1: 3D…
- PDB
- 4K6O
- Type
- protein
- Length
- 1,502 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uridine phosphorylase
- EC
- 2.4.2.3
- UniProt
- Q9K4U1
- Ligands
- 6MU, MG, NA, CL
- Pockets
- 14 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, F | Uridine phosphorylase (EC 2.4.2.3) | protein | 252 | 33% helix, 29% strand | Q9K4U1 |
| B | Uridine phosphorylase (EC 2.4.2.3) | protein | 248 | 33% helix, 29% strand | Q9K4U1 |
| C | Uridine phosphorylase (EC 2.4.2.3) | protein | 247 | 32% helix, 30% strand | Q9K4U1 |
| E | Uridine phosphorylase (EC 2.4.2.3) | protein | 251 | 34% helix, 28% strand | Q9K4U1 |
Ligands and binding sites
- 6MU · 6-methylpyrimidine-2,4-diol · ligand · 6 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 16 copies · chains A, C, B, F, E, D
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D, E, F
- CL · Chloride ion · ion · 12 copies · chains A, B, F, C, D, E
- EOH · Ethanol · additive · 7 copies · chains A, B, C, D, E, F
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, F, B, D, E
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 4 copies · chains A, B, C, D, E, F
- GOL · Glycerol · additive · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 268 | 0.75 | 0.88 | 42 | CL, 6MU, TRS |
| 2 | 380 | 0.74 | 0.85 | 44 | CL, 6MU, TRS |
| 3 | 278 | 0.73 | 0.87 | 41 | CL, 6MU, TRS |
| 4 | 469 | 0.73 | 0.83 | 53 | GOL, CL, 6MU |
| 5 | 355 | 0.73 | 0.84 | 44 | TRS, CL, 6MU |
Interfaces
12 interfaces between chains.
- E–F · 2069 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 2041 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 2026 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 1077 Ų buried · 4 hydrogen bonds · protein-protein
- A–F · 1074 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4K6O · X-ray structure uridine phosphorylase from Vibrio cholerae in complex with 6-methyluracil… · 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 Q9K4U1
- Elsewhere: RCSB PDB 4K6O · PDBe 4K6O · UniProt Q9K4U1
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