Research workbench
X-ray structure of the uridine phosphorylase from salmonella typhimurium in complex with thymidine at 2.40 a resolution
Analyse X-ray structure of the uridine phosphorylase from salmonella typhimurium in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OGK
- Type
- protein
- Length
- 1,495 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uridine phosphorylase
- EC
- 2.4.2.3
- UniProt
- P0A1F6
- Ligands
- THM, K
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Uridine phosphorylase (EC 2.4.2.3) | protein | 250 | 29% helix, 26% strand | P0A1F6 |
| F | Uridine phosphorylase (EC 2.4.2.3) | protein | 245 | 29% helix, 28% strand | P0A1F6 |
Ligands and binding sites
- THM · Thymidine · ligand · 5 copies · chains A, B, C, D, E, F
- K · Potassium ion · metal · chains E, F
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, C, E, F
- IPA · Isopropyl alcohol · additive · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains D
- PG4 · Tetraethylene glycol · additive · chains D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 498 | 0.74 | 0.83 | 53 | THM |
| 2 | 536 | 0.73 | 0.81 | 68 | THM, EDO |
| 3 | 344 | 0.72 | 0.85 | 44 | empty |
| 4 | 416 | 0.72 | 0.83 | 43 | THM |
| 5 | 503 | 0.70 | 0.80 | 44 | empty |
Interfaces
12 interfaces between chains.
- C–D · 2102 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 2094 Ų buried · 26 hydrogen bonds · protein-protein
- E–F · 2060 Ų buried · 23 hydrogen bonds · protein-protein
- A–F · 1090 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 1069 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4OGK · X-ray structure of the uridine phosphorylase from Salmonella typhimurium in complex with… · the same entry in another collection · chain E against E, 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 P0A1F6
- Elsewhere: RCSB PDB 4OGK · PDBe 4OGK · UniProt P0A1F6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.