Research workbench
Purine-preferring ribonucleoside hydrolase from gardnerella vaginalis
Analyse Purine-preferring 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
- 6BA1
- Type
- protein
- Length
- 5,688 residues
- Chains
- 18
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inosine-uridine preferring nucleoside hydrolase
- EC
- 3.2.2.1
- UniProt
- F5LUS2
- Ligands
- CA
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R | Inosine-uridine preferring nucleoside hydrolase (EC 3.2.2.1) | protein | 316 | 44% helix, 16% strand | F5LUS2 |
Ligands and binding sites
- CA · Calcium ion · metal · 18 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 962 | 0.77 | 0.79 | 105 | CA |
| 2 | 925 | 0.75 | 0.78 | 90 | empty |
| 3 | 834 | 0.73 | 0.78 | 64 | CA |
| 4 | 786 | 0.72 | 0.78 | 65 | empty |
| 5 | 317 | 0.67 | 0.82 | 38 | empty |
Interfaces
33 interfaces between chains.
- F–H · 1130 Ų buried · 10 hydrogen bonds · protein-protein
- J–P · 1121 Ų buried · 10 hydrogen bonds · protein-protein
- K–N · 1120 Ų buried · 9 hydrogen bonds · protein-protein
- M–R · 1108 Ų buried · 10 hydrogen bonds · protein-protein
- O–Q · 1107 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6BA1 · Purine-Preferring 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 F5LUS2
- Elsewhere: RCSB PDB 6BA1 · PDBe 6BA1 · UniProt F5LUS2
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