Research workbench
Crystal structure of pnra from S. pneumoniae in complex with cytidine
Analyse Crystal structure of pnra from S. pneumoniae in complex with cytidine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YA4
- Type
- protein
- Length
- 1,324 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lipoprotein
- UniProt
- A0A0H2UPF3
- Ligands
- CTN, NI
- Pockets
- 11 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, A | Lipoprotein | protein | 332 | 40% helix, 22% strand | A0A0H2UPF3 |
| B, D | Lipoprotein | protein | 330 | 40% helix, 22% strand | A0A0H2UPF3 |
Ligands and binding sites
- CTN · 4-amino-1-beta-D-ribofuranosyl-2(1H)-pyrimidinone · ligand · 4 copies · chains C, A, B, D
- NI · Nickel (II) ion · metal · 7 copies · chains C, A, B, D
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
- ACT · Acetate ion · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 70 | 0.70 | 0.95 | 20 | CTN |
| 2 | 70 | 0.68 | 0.94 | 23 | CTN |
| 3 | 638 | 0.68 | 0.77 | 58 | empty |
| 4 | 73 | 0.67 | 0.93 | 23 | CTN |
| 5 | 83 | 0.65 | 0.91 | 24 | CTN |
Interfaces
3 interfaces between chains.
- C–A · 773 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 256 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 188 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6YA4 · Crystal structure of PnrA from S. pneumoniae in complex with cytidine · the same entry in another collection · chain D against D, 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 A0A0H2UPF3
- Elsewhere: RCSB PDB 6YA4 · PDBe 6YA4 · UniProt A0A0H2UPF3
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