Research workbench
The three-dimensional structure of bovine platelet factor 4 at 3.0 ångströms resolution
Analyse The three-dimensional structure of bovine platelet factor 4 at 3.0 ångströms… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1PLF
- Type
- protein
- Length
- 256 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Platelet factor 4
- UniProt
- P02777
- Ligands
- TCN
- Pockets
- 2 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 20% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Platelet factor 4 | protein | 63 | 21% helix, 29% strand | P02777 |
| B, D | Platelet factor 4 | protein | 65 | 18% helix, 29% strand | P02777 |
Ligands and binding sites
- TCN · Tetracyanonickelate ion · ligand · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 588 | 0.80 | 0.86 | 78 | empty |
| 2 | 55 | 0.27 | 0.73 | 11 | empty |
Interfaces
6 interfaces between chains.
- A–C · 888 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 779 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 757 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 706 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 179 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 1PLF · The three-dimensional structure of bovine platelet factor 4 at 3.0 ångströms resolution · the same entry in another collection · chain A against A, TM-score 1.00
- P02777 · AlphaFold monomer V2.0 prediction for platelet factor 4 (P02777) · a predicted model of the same protein · chain A against A, TM-score 0.83
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 P02777
- Elsewhere: RCSB PDB 1PLF · PDBe 1PLF · UniProt P02777
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