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The structure of a putative platelet activating factor from streptococcus pneumonia.
Analyse The structure of a putative platelet activating factor from streptococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2HSJ
- Type
- protein
- Length
- 849 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative platelet activating factor
- UniProt
- Q97PY9
- Ligands
- MG
- Pockets
- 4 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 53% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative platelet activating factor | protein | 211 | 53% helix, 13% strand | Q97PY9 |
| B, C | Putative platelet activating factor | protein | 212 | 54% helix, 13% strand | Q97PY9 |
| D | Putative platelet activating factor | protein | 214 | 53% helix, 13% strand | Q97PY9 |
Ligands and binding sites
- MG · Magnesium ion · metal · 7 copies · chains A, B, D, C
- GOL · Glycerol · additive · 9 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 992 | 0.85 | 0.86 | 88 | GOL |
| 2 | 1159 | 0.84 | 0.85 | 97 | GOL |
| 3 | 568 | 0.70 | 0.79 | 47 | empty |
| 4 | 50 | 0.33 | 0.78 | 17 | GOL |
Interfaces
4 interfaces between chains.
- B–C · 1100 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 1080 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 619 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 18 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 2HSJ · The structure of a putative platelet activating factor from Streptococcus pneumonia. · 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 Q97PY9
- Elsewhere: RCSB PDB 2HSJ · PDBe 2HSJ · UniProt Q97PY9
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