Research workbench
Atomic resolution X-ray structure of the uridine phosphorylase from vibrio cholerae on crystals grown under microgravity
Analyse Atomic resolution X-ray structure of the uridine phosphorylase from vibrio… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Z9Z
- Type
- protein
- Length
- 1,499 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, MG
- Pockets
- 14 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Uridine phosphorylase (EC 2.4.2.3) | protein | 251 | 33% helix, 28% strand | Q9K4U1 |
| B, F | Uridine phosphorylase (EC 2.4.2.3) | protein | 252 | 34% helix, 29% strand | Q9K4U1 |
| D | Uridine phosphorylase (EC 2.4.2.3) | protein | 246 | 32% helix, 30% strand | Q9K4U1 |
| E | Uridine phosphorylase (EC 2.4.2.3) | protein | 247 | 32% helix, 30% strand | Q9K4U1 |
Ligands and binding sites
- NA · Sodium ion · metal · 11 copies · chains A, C, B, D, E, F
- MG · Magnesium ion · metal · 2 copies · chains D, E
- EDO · 1,2-ethanediol · additive · 12 copies · chains A, B, C, D, E, F
- GOL · Glycerol · additive · 5 copies · chains A, B, C, D, E, F
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · 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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 409 | 0.76 | 0.86 | 46 | GOL |
| 2 | 273 | 0.75 | 0.88 | 39 | GOL |
| 3 | 451 | 0.75 | 0.84 | 51 | GOL, EDO |
| 4 | 281 | 0.75 | 0.88 | 40 | GOL |
| 5 | 505 | 0.75 | 0.83 | 84 | EDO, PEG |
Interfaces
12 interfaces between chains.
- A–B · 2046 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 1998 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1995 Ų buried · 18 hydrogen bonds · protein-protein
- A–F · 1085 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 1073 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6Z9Z · Atomic resolution X-ray structure of the Uridine phosphorylase from Vibrio cholerae on… · 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 6Z9Z · PDBe 6Z9Z · UniProt Q9K4U1
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