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X-ray structure uridine phosphorylase from vibrio cholerae in complex with 2.2'-anhydrouridine at 1.34 a
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
- 6RCA
- Type
- protein
- Length
- 1,508 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
- BJE, NA, MG, CL
- Pockets
- 13 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, F | Uridine phosphorylase (EC 2.4.2.3) | protein | 251 | 33% helix, 28% strand | Q9K4U1 |
| B, D | Uridine phosphorylase (EC 2.4.2.3) | protein | 252 | 34% helix, 29% strand | Q9K4U1 |
Ligands and binding sites
- BJE · 2,2'-Anhydro-(1-beta-D-ribofuranosyl)uracil · ligand · 6 copies · chains A, B, C, D, E, F
- NA · Sodium ion · metal · 3 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal
- CL · Chloride ion · ion · 2 copies · chains B, C, A, F
- GOL · Glycerol · additive · 8 copies · chains B, C, D, E, F, A
- EDO · 1,2-ethanediol · additive · chains A, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 917 | 0.79 | 0.81 | 108 | GOL |
| 2 | 347 | 0.71 | 0.83 | 50 | BJE |
| 3 | 346 | 0.70 | 0.83 | 39 | BJE |
| 4 | 367 | 0.70 | 0.82 | 41 | BJE |
| 5 | 390 | 0.69 | 0.81 | 47 | BJE |
Interfaces
12 interfaces between chains.
- E–F · 1991 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1969 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1969 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 1092 Ų buried · 6 hydrogen bonds · protein-protein
- D–E · 1088 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6RCA · X-ray structure uridine phosphorylase from Vibrio cholerae in complex with… · 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 6RCA · PDBe 6RCA · UniProt Q9K4U1
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