Research workbench
The structure of conserved bacterial protein SP0830 from streptococcus pneumoniae. (casp target)
Analyse The structure of conserved bacterial protein SP0830 from streptococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2HIY
- Type
- protein
- Length
- 724 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein
- UniProt
- Q97RI5
- Ligands
- MG, CL
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypothetical protein | protein | 180 | 41% helix, 25% strand | Q97RI5 |
| B | Hypothetical protein | protein | 180 | 40% helix, 25% strand | Q97RI5 |
| C | Hypothetical protein | protein | 181 | 39% helix, 27% strand | Q97RI5 |
| D | Hypothetical protein | protein | 183 | 40% helix, 25% strand | Q97RI5 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, B, C
- GOL · Glycerol · additive · 2 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1009 | 0.70 | 0.74 | 93 | GOL |
| 2 | 499 | 0.64 | 0.77 | 46 | CL |
| 3 | 643 | 0.62 | 0.74 | 70 | empty |
| 4 | 61 | 0.29 | 0.74 | 16 | empty |
| 5 | 50 | 0.28 | 0.75 | 14 | empty |
Interfaces
4 interfaces between chains.
- B–D · 535 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 535 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 198 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 154 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 2HIY · The structure of conserved bacterial protein SP0830 from Streptococcus pneumoniae. · 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 Q97RI5
- Elsewhere: RCSB PDB 2HIY · PDBe 2HIY · UniProt Q97RI5
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