Research workbench
X-ray structure uridine phosphorylase from vibrio cholerae in complex with thymidine at 1.29 a resolution
Analyse X-ray structure uridine phosphorylase from vibrio cholerae in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LZW
- 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
- Q9K4U1
- Ligands
- THM, MG, NA, CL
- Pockets
- 15 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | Uridine phosphorylase (EC 2.4.2.3) | protein | 245 | 32% helix, 29% strand | Q9K4U1 |
| B | Uridine phosphorylase (EC 2.4.2.3) | protein | 252 | 34% helix, 29% strand | Q9K4U1 |
| C, D, E | Uridine phosphorylase (EC 2.4.2.3) | protein | 251 | 33% helix, 29% strand | Q9K4U1 |
Ligands and binding sites
- THM · Thymidine · ligand · 6 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 7 copies · chains A, C, B, F, D, E
- NA · Sodium ion · metal · 3 copies · chains A, B, C, D, E, F
- CL · Chloride ion · ion · 8 copies · chains A, B, C, D, E, F
- EOH · Ethanol · additive · 7 copies · chains A, B, F, C, D, E
- EDO · 1,2-ethanediol · additive · 2 copies · chains C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 502 | 0.73 | 0.81 | 68 | EOH |
| 2 | 505 | 0.73 | 0.81 | 77 | EOH, EDO |
| 3 | 215 | 0.72 | 0.88 | 42 | THM, CL |
| 4 | 294 | 0.71 | 0.84 | 32 | THM, CL |
| 5 | 346 | 0.71 | 0.83 | 41 | THM, CL |
Interfaces
12 interfaces between chains.
- E–F · 2051 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 2040 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 2004 Ų buried · 18 hydrogen bonds · protein-protein
- D–E · 1071 Ų buried · 5 hydrogen bonds · protein-protein
- A–F · 1064 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4LZW · X-ray structure uridine phosphorylase from Vibrio cholerae in complex with thymidine at… · 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 4LZW · PDBe 4LZW · UniProt Q9K4U1
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