Research workbench
Crystal structure of pnra from S. pneumoniae in complex with adenosine
Analyse Crystal structure of pnra from S. pneumoniae in complex with adenosine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Y9U
- 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
- ADN, NI
- Pockets
- 13 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lipoprotein | protein | 332 | 40% helix, 22% strand | A0A0H2UPF3 |
| B, C | Lipoprotein | protein | 331 | 41% helix, 22% strand | A0A0H2UPF3 |
| D | Lipoprotein | protein | 330 | 40% helix, 22% strand | A0A0H2UPF3 |
Ligands and binding sites
- ADN · Adenosine · ligand · 4 copies · chains A, B, C, D
- NI · Nickel (II) ion · metal · 6 copies · chains A, B, C, D
- ACT · Acetate ion · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 71 | 0.74 | 0.97 | 22 | ADN |
| 2 | 67 | 0.72 | 0.97 | 22 | ADN |
| 3 | 73 | 0.72 | 0.96 | 23 | ADN |
| 4 | 69 | 0.70 | 0.96 | 24 | ADN |
| 5 | 659 | 0.67 | 0.76 | 59 | empty |
Interfaces
4 interfaces between chains.
- A–B · 704 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 303 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 254 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 63 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6Y9U · Crystal structure of PnrA from S. pneumoniae in complex with adenosine · 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 A0A0H2UPF3
- Elsewhere: RCSB PDB 6Y9U · PDBe 6Y9U · UniProt A0A0H2UPF3
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