Research workbench
Pyrimidine-specific ribonucleoside hydrolase from gardnerella vaginalis
Analyse Pyrimidine-specific ribonucleoside hydrolase from gardnerella vaginalis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BA0
- Type
- protein
- Length
- 1,232 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CYTIDINE/URIDINE-specific hydrolase
- EC
- 3.2.-.-
- UniProt
- F5LUB1
- Ligands
- CA, CL
- Pockets
- 12 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | CYTIDINE/URIDINE-specific hydrolase (EC 3.2.-.-) | protein | 312 | 38% helix, 17% strand | F5LUB1 |
| C, D | CYTIDINE/URIDINE-specific hydrolase (EC 3.2.-.-) | protein | 304 | 39% helix, 17% strand | F5LUB1 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 9 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 738 | 0.74 | 0.79 | 87 | CA |
| 2 | 382 | 0.67 | 0.80 | 57 | CA |
| 3 | 262 | 0.59 | 0.79 | 34 | empty |
| 4 | 188 | 0.48 | 0.76 | 35 | empty |
| 5 | 81 | 0.41 | 0.78 | 18 | empty |
Interfaces
5 interfaces between chains.
- A–D · 1006 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 993 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 925 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 909 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 26 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6BA0 · Pyrimidine-specific Ribonucleoside Hydrolase from Gardnerella vaginalis · 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 F5LUB1
- Elsewhere: RCSB PDB 6BA0 · PDBe 6BA0 · UniProt F5LUB1
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