Research workbench
X-ray structure of the complex vchuph with phosphate ion at 1.92A resolution.
Analyse X-ray structure of the complex vchuph with phosphate ion at 1.92A resolution. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4H1T
- Type
- protein
- Length
- 1,504 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
- NA, K, SO4, PO4, CL
- Pockets
- 17 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E | Uridine phosphorylase (EC 2.4.2.3) | protein | 251 | 34% helix, 29% strand | Q9K4U1 |
| D, F | Uridine phosphorylase (EC 2.4.2.3) | protein | 250 | 34% helix, 29% strand | Q9K4U1 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A, B, E, F
- K · Potassium ion · metal · chains C, D
- SO4 · Sulfate ion · ion · 7 copies · chains B, D, F, C, E, A
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, D, E, F
- CL · Chloride ion · ion · 2 copies · chains C, F
- EDO · 1,2-ethanediol · additive · 43 copies · chains A, C, E, B, F, D
- PEG · Di(hydroxyethyl)ether · additive · 28 copies · chains A, B, C, D, F, E
- EOH · Ethanol · additive · 6 copies · chains A, B, C, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 384 | 0.73 | 0.84 | 50 | SO4, EDO |
| 2 | 515 | 0.73 | 0.81 | 73 | EDO, PEG |
| 3 | 368 | 0.71 | 0.83 | 41 | EDO |
| 4 | 545 | 0.71 | 0.80 | 47 | PEG |
| 5 | 307 | 0.68 | 0.83 | 33 | EDO, EOH |
Interfaces
12 interfaces between chains.
- C–D · 1994 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1974 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 1951 Ų buried · 17 hydrogen bonds · protein-protein
- A–F · 1085 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 1084 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4H1T · X-RAY Structure of the Complex VchUPh with Phosphate ion at 1.92A Resolution. · 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 4H1T · PDBe 4H1T · UniProt Q9K4U1
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